commit 8c20e7076a30b83e5f18f315bb0ed339b69c6c99 Author: Scott Williams Date: Tue Feb 25 20:59:21 2025 -0500 Initial commit diff --git a/README.md b/README.md new file mode 100644 index 000000000..94bb1516c --- /dev/null +++ b/README.md @@ -0,0 +1,5 @@ +Cancer.Gov +========== + + +Public data archives from [cancer.gov](https://www.cancer.gov). diff --git a/auth.nih.gov/CertAuthV3/forms/mfa/Help.html b/auth.nih.gov/CertAuthV3/forms/mfa/Help.html new file mode 100644 index 000000000..5b5d437c5 --- /dev/null +++ b/auth.nih.gov/CertAuthV3/forms/mfa/Help.html @@ -0,0 +1,93 @@ + + + + Login Help - NIH Login + + + + + + + + + + +
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+

Login Help


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+ Trouble with your PIV card? +

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PIV FAQs - Find answers to frequently asked PIV-related questions.
Smart Card Help Documentation - Help materials covering a range of topics, includinng PIV certificates, email encryption, PIN resets, badge replacement, and more.
NIH Smart Card Validation - Confirm your PIV card is working properly (note:must be behind the firewall to access).
Search Knowledge Base Articles for more help(note: must be behind the firewall to access).
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+ Need to reset your password? +

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For NIH, HRSA, or NIH External Accounts
Password Self Service (PSS) - This link can be used if you need to register or if you are already registered. For additional assistance, call the NIH IT Service Desk at 301-496-4357(6-HELP) or 866-319-4357(toll-free)
Other Account Types
eRA Commons - eRA Password Reset [info]
HHS OPDIVs - HHS AMS Login Help
OpenID - Use the password reset options from your OpenID provider (e.g.,Google or Microsoft)
InCommon - Contact the support team for your affiliated organization.
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+
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+
+

+ Trouble with Authenticator App? +

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+
+
If you are not using a PIV card to sign in with your NIH credentials, you may register for the Authenticator App.
Need to Register? - Please follow these instructions to register for the Authenticator App.
New Phone? - Please follow these instructions to reset your Authenticator App.
No internet on your phone? - Please refer to these instructions to view and/or change your default method to One-time Password (OTP) (OTP does not require internet).
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+
+
+
+

+ Can't sign in and don't know why? +

+
+
+
If you are sure you entered the correct credentials but you're still unable to sign in: Check your phone. Did you get a push notification from the Authenticator App? If so, click the notification and select "Approve".
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+ + + diff --git a/auth.nih.gov/CertAuthV3/forms/passwordlinks.html b/auth.nih.gov/CertAuthV3/forms/passwordlinks.html new file mode 100644 index 000000000..75254a2d2 --- /dev/null +++ b/auth.nih.gov/CertAuthV3/forms/passwordlinks.html @@ -0,0 +1,87 @@ + + + Login Help - NIH Login + + + + + + + +
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+ + +

Login Help

+
+
+

Password Reset Guidance

+

NIH, HRSA, and NIH External Accounts

+ +

+ + Password Self Service (PSS) + - This link can be used if you need to register or if you are already registered.

For additional assistance, call the NIH IT Service Desk at 301-496-4357 (6-HELP) or 866-319-4357 (toll-free)

+ + + + +

Other Account Types

eRA Commons - eRA Password Reset + [info] +

+

HHS OPDIVs - HHS AMS Login Help

+

OpenID - Use the password reset options from your OpenID provider (e.g., Google or Microsoft). +

+

InCommon - Contact the support team for your affiliated organization.

+

Login.Gov - Login.Gov Help

+
+
+

Smart Card Guidance

+

PIV FAQs - Find answers to frequently asked PIV-related questions.

+ +

Smart Card Help Documentation - Help materials covering a range of topics, including PIV certificates, email encryption, PIN resets, badge replacement, and more.

+ +

NIH Smart Card Validation - Confirm your PIV card is working properly (note: must be behind the firewall to access).

+ +

Search Knowledge Base articles for more help (note: must be behind the firewall to access).

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+
+ + + +
+
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+ +
+ + + + \ No newline at end of file diff --git a/auth.nih.gov/certauthv3/forms/help/NIHLoginPolicies.html b/auth.nih.gov/certauthv3/forms/help/NIHLoginPolicies.html new file mode 100644 index 000000000..d94381bb0 --- /dev/null +++ b/auth.nih.gov/certauthv3/forms/help/NIHLoginPolicies.html @@ -0,0 +1,193 @@ + + + + Web Policies and Notices + + + + + + + + + + + +
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NIH Login Service Privacy Policy


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The NIH Login Service (NIH Login) facilitates access by National Institutes of Health (NIH) staff and registered external collaborators to NIH operated websites, applications, and services that require a log in. Protecting your privacy is very important to us. NIH never collects information for commercial marketing or any purpose unrelated to the NIH’s mission and goals. Therefore, NIH Login will never sell your information to anyone, and we will only use it to provide secure access to the NIH websites and systems you log in to. Remember that once you leave the NIH Login screen, you will be subject to the privacy policies for the site(s) you are visiting. + +
+ + +
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+ Types of Information Collected +

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+ +
NIH Login automatically collects and retains a limited set of information about you when you use the service. We collect different information for badged NIH staff and non-NIH external collaborators: +
    +          
  • NIH Staff: first name, last name, email address, and HHS identification number (HHSID); and
    • +
  • Non-NIH External Collaborators: first name, last name, email address, and persistent identifier from the external identity provider (the owner of the account you used to log in).
    • + +
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The NIH Login Service only allows you to provide the information indicated above. You cannot provide information we do not automatically request from the identity provider (the owner of the account you used to log in). +
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+ How NIH Login Collects Information +

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+ +
After you log in, NIH Login asks the identity provider (the owner of the account you used to log in) to send the information listed in the Types of Information Collected section.
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+

+ How NIH Login Uses Cookies +

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+ +
When you visit any website, its server may generate a piece of text known as a "cookie" to place on your computer. The cookie allows the server to "remember" specific information about your visit while you are connected. The cookie makes it easier for you to use the dynamic features of webpages.
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There are two types of cookies, single session (temporary), and multi-session (persistent). Session cookies last only as long as your web browser is open. Once you close your browser, the session cookie disappears. Persistent cookies are stored on your computer for longer periods.
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The Office of Management and Budget M-10-22, Guidance for Online Use of Web Measurement and Customization Technologies allows Federal agencies to use both session and persistent cookies. The NIH Login Service uses session cookies to facilitate your secure access to NIH applications and websites. These session cookies contain only information about your browser’s visit to the site; they do not contain any personal information about you. NIH Login does not use persistent cookies.
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+ How to Disable Cookies +

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+ + +
If you do not wish to allow the NIH Login Service to place session cookies on your computer, you can disable in your web browser. You can find instructions to disable cookies in the most popular browsers at https://www.usa.gov/optout-instructions.
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Notes:
  • If you choose to disable cookies, you will experience issues accessing information and resources at sites and applications that rely on the NIH Login service.
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  • Configuring your browser to disable cookies will disable cookies for all websites, not just NIH sites that rely on NIH Login services.
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+ + +
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+ Your Right to Correct Your Personal Information at NIH +

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Your right to request corrections to errors in your personal information used by the NIH Login Service is specified in the published NIH System of Records Notice (SORN) 09-25-0216.
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+ + NIH Staff + +
+
For NIH staff, the NIH Login Service uses information from the NIH Enterprise Directory (NED). You may update your personal information in NED via the NED self-service portal. You may also contact the NIH IT Service Desk if you need help.
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+ + Non-NIH Individuals + +
+
NIH does not have a process in place for non-NIH individuals to correct your personal information used by NIH Login because the information is sent directly to the NIH Login Service by the identity provider (the owner of the account you used to log in) when you log in. To correct your personal information, you will need to contact the owner of the account you used to log in. For example, if you work at a research institution and use your institution’s credentials to log in via NIH Login, you must contact your research institution’s information technology (IT) department.
+ +
+

+ How NIH Login Protects Your Personal Information +

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+ +
NIH Login has implemented administrative, technical, and physical controls to protect your personal information that we collect.
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+ Administrative +
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NIH Login assigns specific roles on a case-by-case basis to qualified, vetted, and authorized NIH staff. Through those role assignments, authorized NIH staff get the system permissions they need to perform various job functions. NIH Login regularly reviews role assignments, and revokes role assignments when they are no longer required or appropriate.
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+ + Technical + +
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NIH Login segregates IT hardware and software from the internet to prevent unauthorized or malicious access. NIH Login maintains and monitors access control lists and event logs to detect unauthorized, suspicious, or malicious activity. Only authorized NIH IT technical staff have access to these logs and access lists, and they must use multi-factor authentication to access the information. In addition, NIH Login uses an array of tools to monitor and audit file and system integrity.
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+ + Physical + +
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NIH Login limits physical access to NIH Login servers that are all located in a secured facility or cloud environment. Security personnel are stationed at the main entrance of the complex, 24 hours a day, seven days a week. Anyone entering the facility must be pre-authorized and must display a valid government identification (ID) showing a current identification photo. All entrance doors to the data centers are controlled by card-activated locks that restrict access 24 hours a day, seven days a week.
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+ Data Safeguarding and Privacy +

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The session cookies used by NIH Login are considered web measurement and customization technologies. These technologies comply with existing Federal and NIH policies with respect to privacy and data safeguarding standards.
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NIH conducts and publishes a Privacy Impact Assessment (PIA) for each use of an IT system or third-party website application (TPWA) because each application or site may have different functionality or practices. PIAs are stored with the NIH Privacy Office and TPWAs are posted for public view on DHHS’ Third Party Websites and Applications web site.
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Because NIH Login relies on groups of records that are designed to be retrieved by an individual’s name or other personal identifier linked to the individual, NIH Login is covered by the Privacy Act of 1974, as amended (5 U.S.C. Section 552a). NIH System of Records Notices are published in the Federal Register and posted on the HHS System of Records Notices Website.
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+ Data Retention and Access Limits +

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NIH Login retains records for NIH users until business use ceases, or for six (6) years after their password is altered or user account is terminated, but longer retention is authorized if required for business use. Records are destroyed six years after cutoff, unless continuation is requested by the NIH, in accordance with the National Archives and Records Administration (NARA) approved disposition schedule #s DAA-GRS-2013-0006-0003 and DAA-GRS-2013-0006-0004. NIH Login retains a limited set of information for non-NIH individuals only for the short duration of time when they are using the service.
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NIH Login employs the principles of least privilege and need to know, allowing only authorized accesses for NIH staff where access is required to perform primary job responsibilities in accordance with organizational missions and business functions. Information collected by the NIH Login Service is available only to NIH Login System Administrators, and other designated NIH staff who require this information to perform their duties.
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For further information about NIH privacy policy, please contact the NIH Senior Official for Privacy at privacy@mail.nih.gov ; call 301-496-4606 or visit the NIH Privacy Program web page.
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Link to NIH Privacy Policy
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+ + + + + + diff --git a/bioinformatics.ccr.cancer.gov/index.html b/bioinformatics.ccr.cancer.gov/index.html new file mode 100644 index 000000000..feab11c7a --- /dev/null +++ b/bioinformatics.ccr.cancer.gov/index.html @@ -0,0 +1,135 @@ + + + + + + + + + Bioinformatics + + + + + + + + + +
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Bioinformatics Training & Education Program
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The goal of BTEP is to increase the awareness and understanding of bioinformatics techniques and processes among CCR scientists.

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+ Bioinformatics Training and Education Program +
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CCR Collaborative Bioinformatics Resource
 +

CCBR is a resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals.

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+ CCR Collaborative Bioinformatics Resource +
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Genome Analysis Unit
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GAU provides bioinformatics assistance to CCR investigators by engaging in long-term collaborative projects, and by developing custom tools and pipelines to address specific novel challenges.

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+ Genome Analysis Unit +
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NCI Bioinformatics Community
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NCI BC is an environment that aims to promote interdisciplinary collaboration on tool, algorithm, workflow, and pipeline development benefiting the larger bioinformatics community.

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+ NCI Bioinformatics Community +
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+ + + diff --git a/chernobyltissuebank.cancer.gov/index.html b/chernobyltissuebank.cancer.gov/index.html new file mode 100644 index 000000000..d09910df9 --- /dev/null +++ b/chernobyltissuebank.cancer.gov/index.html @@ -0,0 +1,473 @@ + + + + + + + + + + + Chernobyl Tissue Bank + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ Chernobyl Tissue Bank +

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+ The Chernobyl (Chornobyl in Ukrainian) Tissue Bank (CTB) is + a repository of samples donated by patients with thyroid tumors who live in the areas + affected by the accident at the Chernobyl Nuclear Power Plant. The purpose of the CTB is to + collect, document, and store these materials, and to facilitate access to these unique + resources by bona fide researchers. +
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The CTB website is hosted by the U.S. National Cancer Institute (NCI), Division of Cancer + Epidemiology and Genetics. +
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About
+
An introduction to the CTB project
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Research and Data + Access +
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Information to research into the Chernobyl accident
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Search the + Biorepository +
+
Find your biological samples for your study
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+ Chernobyl Tissue Bank +

+
+ The Chernobyl (Chornobyl in Ukrainian) Tissue Bank (CTB) is + a repository of samples donated by patients with thyroid tumors who live in the areas + affected by the accident at the Chernobyl Nuclear Power Plant. The purpose of the CTB is to + collect, document, and store these materials, and to facilitate access to these unique + resources by bona fide researchers. +
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+ The CTB website is hosted by the U.S. National Cancer Institute (NCI), Division of Cancer + Epidemiology and Genetics. +
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+ +
About
+
An introduction to the CTB project
+ +
+
+ +
Research & Data + Access +
+
Information to research into the Chernobyl accident
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+ +
Search the + Biorepository +
+
Find your biological samples for your study
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About the CTB

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+ The Chernobyl (Chornobyl in Ukrainian) Tissue Bank (CTB) is a repository of biological material + and data from patients with thyroid tumors who were exposed as children or adolescents to + radioactive fallout from the April 26, 1986, accident at the Chernobyl nuclear power plant in + Ukraine. The CTB also houses a digital collection of data derived by researchers using our + samples. +
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+

History, Funding, and Organization

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Since CTB was found in October 1998, the project has been supported by a number of + sponsors including the European Commission, the World Health Organization, the U.S. National + Cancer Institute (NCI), and the Sasakawa Health Foundation of Japan (SHF). At the time of its + founding, the CTB established a Coordinating Center at Imperial College, London, UK. In 2023, + the Coordinating Center moved to the Division of Cancer Epidemiology and Genetics at the NCI, + part of the National Institutes of Health, which now funds and coordinates the CTB in + collaboration with the V.P. Komisarenko Institute of Endocrinology (IEM) and Metabolism of the + National Academy of Medical Sciences of Ukraine in Kiev, with the full support of the Government + of Ukraine. Initially, Belarus and Russia were included in the project, but those collaborations + are currently suspended for political reasons. +
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+
+

Purpose of the CTB

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+ The objective of the CTB is to provide a research resource for studies of the health + consequences of the Chernobyl accident. It aims to: +
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  • Ensure that specimens of thyroid cancer removed on or after October 1, 1998, are + consistently described and sampled; that the materials (extracted tumor and normal + DNA/RNA, blood samples, and in some cases fixed tissue sections) along with the + demographic, clinical and pathological information, are available for appropriate + research studies; and that all specimens and data are collected and shared with + appropriate informed consent. +
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  • Review tumor specimens and provide a consensus diagnosis by an international committee + of expert pathologists for all cases. Diagnostic information is available to research + groups carrying out molecular biological, therapeutic, epidemiological, and other + studies. +
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  • Maximize the amount of information obtained from small pieces of tumor and promote + collaborative, rather than competitive, research on a limited biological resource. +
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  • Ensure that knowledge pertaining to the consequences of this accident may benefit the + patients affected and be of value in responding to future nuclear accidents as well as + in understanding and treating thyroid tumors more generally. +
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+

CTB Location

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+ The tissue bank is located at the V.P. Komisarenko Institute of Endocrinology and Metabolism + (IEM) in Kiev, Ukraine. The staff of the CTB obtains informed consent from patients and prepares + and stores their donated materials. (Historically, a separate tissue bank was also maintained in + Russia.) The CTB maintains a database of samples and data that are shared via an integrated + database managed by the coordinating center. The CTB staff work closely with the coordinating + center staff who make key information available to researchers wishing to access the material. +
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+ +
+

Description of Available Samples and Sample Access

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+ The CTB currently includes material and information from patients with thyroid carcinomas and + cellular follicular adenomas from the contaminated oblasts of Ukraine (Kiev, Kiev city, + Cherkasse, Chernigov, Rovno, Zhitomyr and Sumy) who were born after April 26, 1967, (i.e., + younger than 19 years of age at the time of the Chernobyl accident), were treated with surgery + on or after October 1,1998, at the Institute of Endocrinology and Metabolism in Kiev, Ukraine, + and who consent to donate to the project. The CTB also includes patients who were born after the + accident, and thus were not exposed to radioactive iodine, as a comparison. +
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The CTB collects a variety of biospecimen from patients undergoing operations for + thyroid + cancer or adenoma. Tissue collection follows an approved standard operating procedure (SOP) and + is snap frozen whenever possible; the presence or absence of tumor is verified by frozen + section. A representative paraffin block is also obtained for each case. Where appropriate, the + CTB also collects fresh and paraffin-embedded tissue from loco-regional metastases. +
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Histological slides from all tumors are reviewed by the CTB Pathology Panel, an + international + group of expert thyroid pathologists, and a consensus diagnosis agreed before any materials are + released to researchers. +
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Available samples include frozen aliquots of DNA and RNA extracted from normal and + neoplastic + thyroid tissue and DNA extracted from blood. A frozen section is taken from each portion of + tissue before extraction to verify its nature. Quality control is performed on nucleic acid + extracted from all tissues and blood samples. In addition, paraffin sections and tissue + microarrays are available. Researchers who request access to + samples are provided with extracted + nucleic acid from thyroid tissue, rather than a small piece of tissue. This maximizes the amount + of data that can potentially be obtained from a single specimen and enables multiple molecular + biological studies to be carried out for each case. Aliquots of serum are also available. +
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The CTB website is equipped with a robust search function that allows researchers + wishing to + access biomaterials to select cases from which they would wish to receive samples. The search + function returns information on specimen type, patient characteristics, tumor characteristics, + and, for certain tumor specimens, the driver mutation(s) identified to date. +
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+

Maintaining an Archive of Findings

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All data generated with samples from the CTB are collected and maintained in an + online + archive that can be accessed for future studies. Researchers who obtain material from the CTB + agree + to provide the results of their investigation on a case-by-case basis. This information will not + be + available until after publication of their findings. +
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+
+

Contact CTB

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+
+
For queries regarding the Chernobyl Tissue Bank:
+
+ Please contact us via email
+
+
+
For questions on the operation of the CTB website:
+
+ Please contact the CTB Web Support Team via email. +
+
+
+
For more information, please visit:
+
Division of Cancer Epidemiology and Genetics (DCEG), + NCI
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Password Reset

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Forgot your password? Enter your email address below to reset it.

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+ Please contact us if you have + trouble resetting your password. +
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Privacy Policy

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+ Protecting your privacy is very important to us. Our Web site links to other National Institutes of + Health (NIH) sites, + federal agency sites, and private organizations. Once you leave the primary CTB site, you are + subject to the privacy + policy for the site(s) you are visiting. In addition to name and email address, we collect some data + about your visit to + our Web site to help us better understand how the public uses the site and how to make it more + helpful. We collect + information from visitors who read, browse, and/or download information from our Web site. We never + collect information + for commercial marketing or any purpose unrelated to the CTB mission and goals. +

+ +
Types of Information Collected
+

+ When you browse through any Web site, certain information about your visit can be collected. We + automatically collect and + store the following type of information about your visit: +

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  • Domain from which you access the Internet
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  • IP address (an IP address is a number that is automatically assigned to a computer when surfing + the Web) +
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  • Operating system and information about the browser used when visiting the site
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  • Date and time of your visit
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  • Pages you visited
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  • Address of the Web site that connected you to the CTB site (such as google.com or bing.com)
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  • Email address associated to your Google Account
    • +
  • Name (as available in your Google Account profile)
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+ CTB will retain data collected using the following technologies long enough to achieve the specified + objective for which they were collected. The data generated from these activities falls under the + National + Archives and Records Administration (NARA) General Records Schedule (GRS) 20-item IC 'Electronic + Records,' and + will be handled per the + requirements of that schedule (link is external). +

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Research and CTB Data Access

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+ Researchers interested in using material, information, or data for research purposes must submit + a proposal via the online application system, accessed through the search function. Researchers + can refine their search by sample type and/or data required and obtain an instant report on the + availability of samples and data that match the search criteria. Interested researchers can + submit a request for data and materials using an application form and enter key information + on the research question, study design, laboratory and analytic methods, as well as researcher + qualifications. +
+
The CTB will communicate with researchers who submit a request, if the questions + in their proposal have been addressed by previous projects or questions or is likely to produce + results that complement other studies.
List of + projects which have used or are using CTB materials +
+
The CTB does not provide funding for research projects.
+ +
+
+

Evaluation of Applications

+
Applications are evaluated for scientific merit and appropriate use of CTB + resources by a Review Panel comprised of scientists from the centers contributing samples + (currently V.P. Komisarenko Institute of Endocrinology and Metabolism), the coordinating center, + managed by the NCI, and other independent, multi-disciplinary senior researchers in the fields + of thyroid cancer and radiobiological research. +
+
Projects may be submitted at any time and the review procedures are, in most + cases, completed by email. After evaluating applications according to the criteria below, each + application will be: 1) approved for access, 2) returned with comments and reconsidered after + the Principal Investigator responses to reviewers, or 3) rejected. +
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+
+

Criteria for Evaluation

+
+ Researchers applying for CTB samples and data must provide evidence that the following criteria + are satisfied: +
    +
  • The research question is of considerable scientific and/or medical interest. +
    • +
  • + The study design is appropriate to address the question. +
    • +
  • + The requested sample size is sufficient to provide a good chance of answering the + question. +
    • +
  • + The researcher and research team have appropriate qualifications and experience to + conduct the study, including fluency with the accepted standards and quality control + relevant to necessary laboratory analytical procedures as well as appropriate + permissions from human subjects’ research and/or research ethics committees. +
    • +
  • + The researchers demonstrate familiarity with the relevant literature. +
    • +
  • + The proposed work cannot be undertaken without the data and/or materials of the type + available through the CTB. +
    • +
  • + If case information other than the standard data set (date of birth, date of operation, + sex, oblast of residence, calculated dose, and international Pathology Panel review + diagnosis) are required, the costs of obtaining these data and ethical and consent + should be adequately addressed. +
    • +
  • + The researchers can cover the costs of shipping the material. +
    • +
  • + The amounts of material requested are appropriate for the specified study, and not + excessive, given the limited availability of material. +
    • +
  • + The research can be undertaken within the time consistent with the researchers funding + and the availability of the necessary data and materials. +
    • +
  • + The researchers agree to share immediately with the CTB coordinating center any data + that may be clinically relevant uncovered during the course of the study. +
    • +
  • The researchers agree to provide within three months of the completion of their project + a brief report on their work, including the results of their investigations on each + sample studied, using the CTB sample code number. This report will not be disseminated + beyond the CTB without the agreement of the Principal Investigator. The aim of the CTB + is to maximize the value of the research data derived from the unique tissue collection + and researchers are therefore required to submit their research data back to the CTB. +
    • +
  • The researchers will inform the CTB coordinating center if any material has not been + used in the performance of their study and will return this material, if requested, to + the CTB coordinating center. +
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+ The researchers agree not to use the material for any purpose other than those explicitly + proposed in their approved project, or to pass any material supplied by the CTB to third parties + without the explicit permission of the CTB coordinating center. +
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+
+

Procedures for Approved Projects

+ +
+ Once approved, researchers will sign a Material and Data Transfer Agreement with the CTB + Coordinating Center, then biospecimens and data will be sent to the researcher. Samples are + provided free of charge, but shipping costs will be covered by the researchers. Where possible, + material for a given project will be provided in one batch, however, in some cases, materials + may be sent in stages. +
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+ Each sample will be accompanied by a minimum data set comprising the following information: +
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  • + Age at accident - complying with HIPAA regulations +
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  • + Age at surgical treatment - complying with HIPAA regulations +
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  • + Sex +
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  • + Oblast of residence +
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  • + International Pathology Review Panel diagnosis +
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  • + Estimated thyroid radiation dose (if requested) +
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+ Access to additional research data, if requested, may be made available. Additional clinical + information may require collaboration with IEM and NCI. +
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+ Researchers are strongly encouraged to publish their data and are asked to ensure that the CTB + is acknowledged in any publications arising from their study. +
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+ Principal Investigators who receive materials are required to: +
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  1. + Agree to conform to the conditions set out in the Material and Data Transfer Agreement +
    2. +
  2. + Notify the CTB coordinating center of any proposed modification of the number and size + of samples required (modification dependent on approval and the availability of the + material). +
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/chornobyltissuebank.cancer.gov/research/research_projects/index.html b/chornobyltissuebank.cancer.gov/research/research_projects/index.html new file mode 100644 index 000000000..01ce165b5 --- /dev/null +++ b/chornobyltissuebank.cancer.gov/research/research_projects/index.html @@ -0,0 +1,2308 @@ + + + + + + + + + + + + Chernobyl Tissue Bank | Research Projects Using CTB Materials + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Research Projects Using CTB Materials

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Please select one of the sections below to view a breakdown of the research projects:

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    +
  • [001/2001] Expression profiling of tyrosine kinase genes in malignant + tumors of the thyroid gland. +
    Heinz-Ulrich Weier, LBNL, + University of California, Berkeley Email +
    +

    + +

    +
    +
    +

    + Abnormal + expression of tyrosine kinase (tk) + genes is a common phenomenon in papillary thyroid carcinomas + (PTCs), + where it is believed to alter + cell growth and response to external signals such as growth + factors, + hormones etc. While the + pathogenesis of radiation-induced PTC remains unclear, there is + evidence + that tk genes such as the + receptor tyrosine kinases ret and NTRK-1 are abnormally + expressed, + and + that the overexpression of + some tk genes due to gene amplification or changes in gene + regulation in + the absence of structural + alterations may lead to oncogenic transformation of cells. Using + a + DNA + microarray based technique, + we have identified several tk genes with abnormal expression in + human + tumor cell lines. We now + propose to apply the technique to measure the relative + expression + levels + of more than 50 tk genes in + the PTC's that arose after the Chernobyl nuclear accident and to + compare + these expression profiles + with the gene expression pattern found in sporadic PTC cases and + tumors + that arose following low + level therapeutic irradiation of the thyroid. Results from this + study + may allow the identification + of molecular markers that can be used to facilitate tumor + diagnosis + and + staging, and, eventually, + provide targets for therapeutic intervention.

    +
    +
    +
    • +
  • [002/2001] Chernobyl, an Integrated Pan-European Study, morphology, + oncogenes, + DNA repair and outcome in radiation carcinogenesis. +
    + GA Thomas, South West Wales Cancer Institute, University of Wales, Swansea, + UK. Email +
    +

    + +

    +
    +
    +

    + The objective of this study is to + investigate the link between exposure of children to radiation, + the + subsequent development of + tumors and how their morphology, molecular and cell biology + influence + clinical outcome. The project + is an integrated approach involving 5 leading European centers. + Samples + of the same tumors will be + studied by the 5 different centers to determibe tumor morphology + and + type; the degree of variation + within the tumor, including the variation of the proportion of + cells + in + cycle using antibodies to + novel DNA replication associated peptides; the gene involved in + the + carcinogenic process, using DNA + chip technology; specific studies of the pathways associated + with + one + oncogene (ret) known to be + linked to the tumor type involved; and studies of novel gene + rearrangements using FISH technology. + By using the same tumor/normal pairs in these studies, + integrating + the + results from the different + centers and studies and correlating these with detailed + morphological + analysis and patient details + including evidence on tumor aggressiveness and recurrence, we + will + increase our understanding of + the link between radiation exposure and cancer development, and + provide + evidence which will inform + decisions on radiation protection and on clinical management of + patients + with radiation associated + cancers.

    +
    +
    +
    • +
  • [004/2001] RET proto-oncogene rearrangements and tyrosine kinase gene + expression + in radiation induced papillary thyroid carcinomas developed after the + Chernobyl + accident. +
    + Horst Zitzelsberger, GSF, Munich, Germany + Email +
    +

    + +

    +
    +
    +

    + The papillary thyroid + carcinoma oncogene (RET/PTC) is a rearranged version of the + tyrosine + kinase RET. It is know that the + incidence of RET/PTC activation is increased in + radiation-induced + papillary thyroid carcinomas + compared to papillary thyroid carcinomas without a radiation + history. + The prognostic value of + RET/PTC rearrangements and its importance as a + radiation-specific + marker + is still unclear. It is + proposed to screen 70 childhood cases from Belarus and Ukraine + with + interphase FISH in conjunction + with RT-PCR to confirm the presence and type of the chimeric + transcripts. Cases with indications for + atypical RET/PTC rearrangements will be further investigated + using + 5'RACE for the presence of novel + types of alteration. For this part of the proposal RNA samples + as + well + as a limited number of + paraffin-embedded sections would be needed. The RNA samples will + be + further investigated for + expression profiles of other tyrosine kinase genes to identify + other + gene rearrangements which may + occur as a sole abnormality or in addition to RET/PTC + rearrangements.

    +
    +
    +
    • +
  • [005/2001] Mitochondrial DNA deletions and mutations in post Chernobyl + thyroid + tumors and in the respective normal thyroid parenchyma. +
    + Manuel Sobrinho-Simoes, IPATIMUP, Porto, Portugal + Email +
    +

    + +

    +
    +
    +

    + Mittochondrial DNA (mtDNA) is a likely hotspot for mutation in + cancer as + it is preferentially modified by many carcinogens. We have + previously + shown that there is a specific association between sequence + variants + of + Complex I genes and ATPase6, one of the two mitochondrial genes + of + Complex V, and the occurrence of malignancy and of oxyphil + features + in + thyroid tumors. We have also found a significant association + between + mitochondrial sequence variants and the occurrence (and degree) + of + the + so-called mitochondrial common deletion. In an attempt to + elucidate + the + role of post-Chernobyl irradiation in mtDNA alterations and to + find + out + whether or not such alterations are involved in the + etiopathogenesis + of + thyroid tumors we will search for the mtDNA common deletion and + for + somatic mutations and sequence variants in the D-loop region, in + the + 13 + coding genes and in the 22 tRNAs genes of cases from which there + are + RNA + and DNA samples extracted from blood (set without radiation), + normal + thyroid (set irradiation) and tumors (set irradiation and + tumorigenesis). In a first step, we will study exhaustively 20 + cases. + The results obtained in this first part will be used together + with + the + data we and others have previously obtained to decide the most + appropriate targets for the second part of the study. If + possible we + would like to correlate the results of our study on mtDNA + deletions + and + mutations with those on ret oncogene. In case there are also + clinico-pathyological data available, we would like to + collaborate + with + the pathologists who have studied the cases in order to clarify + the + putative clinical significance of the mtDNA alterations.

    +
    +
    +
    • +
  • [007/2001] Expression of the RET proto-oncogene in post-Chernobyl thyroid + tumors + and unirradiated controls: analysis of RET/PTC rearrangements, RET wild type + and + RET-TK domain, with quantitative assessment of mRNA and protein expression. +
    + Aldo Pinchera, University of Pisa, Italy + Email +
    +

    + +

    +
    +
    +

    + Genetic alterations of the ret proto-oncogene play a critical + role + in + the pathogenesis of papillary thyroid carcinomas both naturally + occurring and radiation induced. We have recently found that + classical + RET/PTC rearrangements are present also in benign thyroid + nodular + disease. Furthermore, in several cases the independent + expression of + tyrosine kinase (TK) and extracellular (EC) domains of RET was + found. + This finding may be interpreted as RET wild type gene + expression. In + other cases, especially radiation exposed, the TK domain in the + absence + of EC was found and was interpreted as unknown RET/PTC + rearrangements + (PTCX). Aim of this project is to clarify the modality of + expression + of + RET protooncogene in nodular thyroid diseases. In cases with EC + and + TK + expression, we will search for RET wild type by an extralong PCR + encompassing the TK and EC domains, followed by sequencing of + the + PCR + product. In cases of TK positive expression only (but not + classical + PTC1, PTC2 and PTC3) we will identify the 5' domain rearranged + with + the + TK domain. As for other unknown RET/PTC rearrangements will use + the + 5'race approach.

    +

    + All samples positive for TK expression will be submitted to + quantitative PCR (ABI Prism 7700 sequence detector, Perkin + Elmer) + for TK + mRNA. The TK mRNA expression will be correlated with the + histological + characteristics of the analysed tissues, and the + immunohistochemical + pattern of RET protein expression, using an antibody to + recognize + the TK + domain.

    +
    +
    +
    • +
  • [001/2002] Analysis of RET/PTC transforming ability in Thyroid cells using + Oligonucleotide DNA Micro Array. + +
    + Giuliana Salvatore, University of Naples, Italy + Email +
    +

    + +

    +
    +
    + The expression of RET/PTC oncogenes in thyroid PC Cl 3 cells induces + a + complex phenotype with a block of the differentiation program, + hormone-independent proliferation and increased apoptotic rate. + Oligonucleotide GeneChips were used to analyse gene expression + profiles + of PC Cl 3 cells expressing either RET/PTC1 or RET/PTC3 oncogenes in + comparison to parental cells. About 2,000 genes showing at least + two-fold increase and 2,000 genes showing at least two-fold decrease + were identified in RET/PTC-expressing thyrocytes. Virtually all the + genes up-regulated by more than 5-folds (about 100) were confirmed + by + RT-PCR and some of them by immunoblot. Genes upregulated by RET/PTC + could be functionally divided in genes involved in proliferation + (such + as D-type cyclins), apoptosis, proteolysis, inflammation, and + metabolism. We plan to extend these studies on the identified genes + up + and on the downregulated by analyzing their expression in human + thyroid + tumors of different histotypes. We propose to study their expression + by + semiquantitative reverse transcriptase PCR and for selected genes by + real time quantitative PCR. Immunohistochemical analysis will be use + to + verify protein expression. +
    +
    + The findings of these studies can reveal clues to the molecular + pathways + involved in papillary thyroid carcinoma and may provide biomarkers + for + clinical use. +
    +
    +
    • +
  • [002/2002] A Comprehensive Molecular Profile of ChildhoodRadiation Induced + Papillary Thyroid Tumors Compared to Adult Sporadic Papillary Tumors. + +
    + Lesleyann Hawthorn, Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York, USA + Email +
    +

    + +

    +
    +
    + Papillary thyroid carcinoma (PTC) accounts for 80% of all thyroid + malignancies. It has a variable disease course and to date no + pathways + or specific genes have been implicated as causative in this tumor. + RET + activation, through translocations involving several genes, have + been + noted in a high incidence of PTCs. However, the activation of this + oncogene is found at all stages from benign through + well-differentiated + to undifferentiated carcinoma. This suggests that it represents an + early + event and that this defect is not in itself sufficient for + carcinogenesis. It may also suggest that the classification of PTC + covers more than one tumor subtype. The relationship between + radiation + exposure and PTC is well established. We plan to perform a genome + wide + scan using microarray analysis for alterations in tumors from + children + exposed to radiation and compare them to sporadic adult tumors to + identify which genes are commonly altered and which genes are + display + differential alteration expression patterns. We plan to extend this + study using high-resolution BAC-CGH to define a molecular pattern + for + these tumors and evaluate this approach for diagnostic applications. + The + study of molecular alterations which cause thyroid carcinoma is of + importance since the identification of causative factors could lead + to + new approaches for treatment. +
    +
    +
    • +
  • [001/2003] A comprehensive analysis to find out molecular biomarker(s) of + radiation exposure and grade of malignancy in human post-Chernobyl PTC +
    + Hiroyuki Namba, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan + Email +
    +

    + +

    +
    +
    + Development of papillary thyroid cancer (PTC), similarly to that of + most + of other human malignancies, is likely to comprise a multistep and + multihit process. It is quite probable that mutational events + initiating, promoting and/or driving the tumor progression are quite + similar in the sporadic and radiation-induced PTC. Along with this, + one + may expect there may be unidentified to date molecular distinctive + features peculiar to thyroid cancers of different etiology. Thus, a + comparative study of various molecular characteristics in the two + groups + of PTC may provide additional information for the determination of + the + molecular signature of radiation-induced thyroid cancerogenesis. +

    + In the proposed project we intend to study the following molecular + characteristics of the DNA extractedfrom normal and tumor tissue of + radiation-induced PTCs: i) relative content of mtDNA and number of + large-scale deletions in mtDNA; ii) prevalence of gene mutations of + MAPK + signal molecules, including the Ras,BRAF, Raf-1 and MEK genes; and + iii) + distribution of the codon 72 allelic variants of theTP53. +

    + After the data are obtained, we will perform a comprehensive + univariate + and multivariate statistical analysis against already available + results + of examination of sporadic PTC in order to identify molecular + parameter(s) specific to radiation-induced PTC. + +
    +
    +
    • +
  • [002/2003] Molecular Change and Thyroid Cancer Risk after Chernobyl +
    + Scott Davis, Fred Hutchinson Cancer Centre, Seattle, USA + Email +
    +

    + +

    +
    +
    + This study investigates the occurrence and molecular characteristics + of + thyroid cancer in residents of the Bryansk Oblast of the Russian + Federation, who were 0-50 years of age at the time of exposure to + radiation from the Chernobyl Power Station accident (ATA) on April + 26, + 1986. The study has three primary purposes: 1) to characterize cases + of + thyroid cancer according to specific molecular markers of genetic + change, and investigate whether the presence of such markers is + associated with individual thyroid radiation dose from the Chernobyl + accident; 2) to investigate whether age-at-exposure dependent + radiation + dose response for thyroid cancer differs between cancers that are + positive versus negative for the molecular markers investigated; and + 3) + to investigate whether the presence of these same molecular markers + is + associated with clinical outcomes. Included will be thyroid cancer + cases + diagnosed between April 1, 2001 and March 31, 2006 and confirmed by + a + panel of expert thyroid pathologists. An equal number of controls + will + be individually matched to cases by sex, age, type of settlement and + raion of residence on April 26, 1986. Data collected will include + in-person interviews for all participants, and for cases only, + paraffin + embedded tissue or fresh frozen tissue, clinical history and outcome + information. + +
    +
    +
    • +
  • [001/2004] Analysis of Genetic and Epigenetic Abnormalities in + Radiation-induced + Thyroid Cancers +
    + Michael M Xing, John Hopkins University School of Medicine, Baltimore USA + Email +
    +

    + +

    +
    +
    + Thyroid cancers are the most common endocrine malignancies and the + vast + majority of them are papillary thyroid cancers (PTC). Several + genetic + abnormalities, including Ras mutations and RET/PTC rearrangements + have + been well characterized in these cancers. Recently, we and several + other + groups have reported the BRAF mutation in PTC with a high + prevalence. We + have also characterized aberrant DNA methylation in several genes in + thyroid cancers, including novel tumor suppressor genes and some + thyroid-specific genes. Except for the RET/PCT rearrangements, these + genetic and epigenetic abnormalities have been studied mainly in + sporadic thyroid cancers, and their role is unknown in the special + group + of thyroid cancers induced by radiation, the most common and + well-established environmental risk factor for thyroid cancer. + Chernobyl + nuclear accident has been associated with a significant increase in + the + incidence of PTC, which represent an ideal thyroid tumor model for + the + study of radiation-induced thyroid tumorigenesis. In the present + project, we propose to use such special thyroid cancer samples to + study + novel genetic and epigenetic abnormalities, their relationship, and + their effects on the expression of key thyroid genes. + Well-established + experimental protocols and techniques, including RT-PCR, + methylation-specific PCR, real-time quantitative PCR, and a recently + established colorimetric mutation detection method will be used. The + study is expected to result in important insights into + radiation-induced + thyroid tumorigenesis and provide novel clinical implications for + this + special group of thyroid cancers. + +
    +
    +
    • +
  • [002/2004] Investigation of molecular genetic abnormalities associated with + progression of human thyroid follicular neoplasms +
    + D Wynford-Thomas, University of Wales College of Medicine, Cardiff UK + Email +
    +

    + +

    +
    +
    + Thyroid follicular carcinomas frequently exhibit RAS mutation, and + closely resemble benign follicular adenomas with respect to + morphology + and differentiation. Cell culture studies suggest that at least one + requirement for progression from an adenoma to a carcinoma is + failure of + an intrinsic mechanism that normally limits the proliferative + lifespan + of RAS-induced cell clones. One current candidate for over-riding + the + mechanism is the tumor suppressor gene p16 INK4a. +

    + There is great clinical interest in this area, as currently there is + no + marker to distinguish between thyroid follicular adenoma and + carcinoma + when evaluating fine needle aspirates and biopsies of thyroid + glands. + This means that many people have unnecessary operations on the basis + of + presumed malignancy. We now therefore wish to carry out a + comprehensive + comparison between thyroid carcinoma and adenoma cells to identify + differences that may confer an extended proliferative lifespan on + carcinoma cells. +
    +
    +
    • +
  • [003/2004] Molecular Definition of Gene Expression in Chernobyl Thyroid + Cancers +
    + Carine Maenhaut, ULB, Brussels + Email +
    +

    + +

    +
    +
    +

    + Chernobyl thyroid cancers represent a unique resource in + oncology + and radiation biology. They appear in a cohort of patients + irradiated at the same time and in which there is no doubt that + the + cancer originated from radiation exposure. The precise timing of + the + course allows to follow precisely the kinetics of appearance of + the + cancers. On the other hand study of the gene expression pattern + of + cancers by microarrays allows a precise molecular definition of + each + cancer. Using this methodology we were able to show that the + clustering of gene patterns of Chernobyl cancers of the first + wave + and European and US sporadic cases could not separate them. This + work should now be extended to a larger series of cases. +

      +
    1. + to try to distinguish subtypes of Chernobyl and sporadic + papillary carcinomas and their signature. +
      2. +
    2. + to relate patterns of gene expression with clinical + variables + such as the duration of the incubation period and with the + genetic diagnosis. +
      3. +
    3. + to validate data at the RNA level by PCR and at the protein + level by Western and to define potential diagnostic markers + and + therapeutic targets. +
      4. +
    +

    +
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    +
    • +
  • [001/2005] Genomic Analysis of Gene Copy Number in Thyroid Cancer. +
    + PE Neiman, FHCRC, Seattle, USA + Email +
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    + +

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    + High copy-number gene amplification is known to take place at a + few + genomic loci in numerous human cancers, but widespread low-level + copy-number changes in genomic DNA have not been described. cDNA + microarray-based comparative genome hybridization yields + high-resolution copy-number profiles that enable the detection + of + low-level amplification events at individual gene loci. We have + shown in a small pilot study that pediatric thyroid carcinoma in + residents of a region contaminated by 131I from the Chernobyl + accident (the Bryansk Oblast) exhibits gene amplification at a + higher frequency than that seen in pediatric thyroid carcinoma + in US + children with no history of radiation exposure. This result + suggests + that exposure to ionizing radiation from the environment may be + associated with an increased rate of gene amplification in a + human + cancer. The consistent amplification of many genes among cases + of + post-Chernobyl thyroid carcinoma from Bryansk suggests the + existence + of a target pool of radiation-sensitive genomic loci that + respond to + exposure by initiating local amplification events. The pattern + of + gene amplification may represent a radiation signature that + could be + used to map amplicons likely to harbor participating oncogenes. +

    + Based upon these differences observed in the pilot study in + apparent + gene amplification between post-Chernobyl and spontaneous + pediatric + papillary thyroid carcinoma (PTC), we hypothesize that radiation + exposure leaves a measurable genomic signature in the form of + stable + changes in gene amplification. Some chromosomal regions + identified + by this method are likely to harbor participating oncogenes, but + it + is unreasonable to expect that so many genes be directly + involved in + oncogenesis. We hypothesize the presence of genomic hot spots in + human DNA that are susceptible to radiation-induced + amplification. + These genomic targets are unlikely to be saturated by the doses + of + radiation delivered to these patients. The number of targets hit + in + each case should therefore be directly proportional to radiation + dose. +

    +
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    • +
  • [002/2005] The influence of genetic variation in DNA repair pathways on + cancer + risk following exposure to ionising radiation. +
    + S Forbes-Robertson, Swansea Medical School, Swansea UK + Email +
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    + +

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    + Genetic damage following radiation exposure is subject to + correction + by the caretaker systems of DNA repair. Our interest is in the + role + that these systems may play in the molecular pathogenesis of + cancer. + We propose a pilot project to assess the influence of genetic + variation on cancer risk following exposure to ionising + radiation. + This will be achieved by investigation of variation in the genes + involved in the DNA repair pathways, in DNA derived from blood + samples or normal tissue samples from patients with thyroid + tumors + of radiation-associated and non-radiation-associated etiology. + There + are two main justifications for such a study, first to identify + SNPs + which indicate possession of an at risk genotype, and secondly, + to + identify the genes in which genetic variation is a significant + modulator of cancer risk. This has particular and wider + relevance to + the involvement of DNA repair-associated factors in the + pathology of + other cancers as well, such as breast cancer. +

    + Genotyping of genes involved in double-strand break repair will + be + performed using a mass spectrometry-based SNPing platform which + has + been developed by our group at the University of Wales, Swansea. + Data will be provided to the Chernobyl Tissue Bank for + correlation + with pathology and expression of oncogenes such as ret and BRAF. +

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    • +
  • [001/2007] Array CGH analysis of RET/PTC-positive and RET/PTC-negative + post-Chernobyl thyroid tumors. +
    + H Zitzelsberger, Helmholtz Zentrum München, Neuherberg, Germany + Email +
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    + +

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    + It is proposed to study chromosomal imbalances in post-Chernobyl + papillary thyroid carcinomas (PTC) by means of array CGH using + 1Mb + BAC arrays. As derived from interphase FISH experiments RET/PTC + rearrangements are heterogeneously distributed within tumor + tissues + leading to the assumption that additional gene alterations may + play + an important role in these tumors. To address this question + post-Chernobyl PTC, with and without RET/PTC rearrangements, + will be + analysed by array CGH. Altered candidate genes will be derived + from + recurrent regions of amplifications and deletions and will be + confirmed by interphase FISH on paraffin sections and further + studies by PCR-based approaches to investigate expression of + these + genes. In a first pilot study it is intended to compare 10 + RET/PTC-positive (RET/PTC3) and 10 RET/PTC-negative cases with + similar histological features, a comparable age range of + patients at + time of exposure and a similar latency after exposure is a first + study. The pilot study will use cases from the age-matched + series + with known RET/PTC status. If successful this study will be + extended + to a larger series of cases linked to the GENRISK-T project. +

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    • +
  • [002/2007] Expression profiling of childhood thyroid cancer: a comparison of + those exposed to radioiodine and those exposed to low level radiocaesium. +
    + Carine Maenhaut, University of Brussels School of Medicine, Brussels, Belgium + Email +
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    + +

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    + The aim of this study is to investigate whether different + transcriptomic profiles can be related to exposure to + radioiodine in + fallout from the Chernobyl accident and to lower level + radiocaesium + exposure present in the contaminated environment. We will use + Affymetrix microarray technology to define transcriptomic + profiles + in two cohorts of children, matched on age, oblast and + pathological + type of tumor. The research will be carried out in two separate + laboratories and cross-validated. This project is one of a + series of + projects that will study the transcriptomic and genetic profile + of + two well-defined cohorts to investigate the relative effects of + radioiodine and radiocaesium exposure on the development of + thyroid + cancer. +

    +
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    • +
  • [003/2007] Gene expression in normal and cancerous tissue in relation to + I-131 + exposure. +
    + M Abend, Bundeswehr Institute of Radiobiology, Munich, Germany + Email +
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    + +

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    + Gene expression has received less attention than the role of + germline polymorphisms or somatic mutations in studies of + radiation + and thyroid cancer. The increase in papillary thyroid cancers + (PTC) + in exposed children following the Chernobyl nuclear accident + presents an opportunity to pursue the role of gene expression + further. Recently, we reported on expression of seven genes, + each of + which was able to distinguish post-Chernobyl PTCs from sporadic + PTCs + (Port et al 2007). Our approach involved (i) a whole genome + microarray used for screening purposes; and (ii) quantitative + examination of the 92 target genes with a high throughput + RTQ-PCR + technique (LDA). The study had some limitations such as the + origin + of sporadic PTCs (Eastern Germany), their different age at + diagnosis + and a small number of cases (n=11). Subsequently another group + has + reported on expression of thirteen genes involved in homologous + recombination suggesting a distinct radiation pattern of + post-Chernobyl PTCs (Detours et al 2007). Using the already + established 2-stage design, the purpose of the present + application + is to overcome limitations in the previous study and extend the + findings (Port et al 1007) by evaluating a dose-dependent gene + expression pattern in 74 post-Chernobyl PTCs with individual + I-131 + dose estimates. +

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  • [004/2007] Genetic predisposition to radiation-induced carcinogenesis and to + specific genetic alterations in post-Chernobyl thyroid cancer. +
    + Y Nikiforov, University of Pittsburgh School of Medicine, Pittsburgh, USA + Email +
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    + +

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    + Radiation exposure is a well established risk factor for thyroid + cancer. Ionising radiation is known to cause extensive DNA + damage + including double strand breaks, which may lead to the generation + of + somatic mutations in thyroid cells and cancer initiation. + However, + environmental triggers cannot fully explain the inter-patient + heterogeneity in the individual response to exposure to + radiation, + which points to the existence of genetic variations that define + the + individual susceptibility to radiation-related cancer. We + propose to + analyse several candidate DNA repair genes and perform a + genome-wide + analysis of single nucleotide polymorphisms (SNPs) in Ukrainian + patients who developed thyroid cancer after Chernobyl and in + control + cancer-free individuals to identify mutations and SNPs that are + involved in genetic predisposition and to identify the genes + that + are affected. We will then perform functional analysis to find + whether these genetic variations alter gene function. We will + also + study the link between specific SNPs and known or new mutations + found in these tumors. The overall goal of this study is to + identify + genes involved in genetic predisposition to radiation-associated + thyroid carcinogenesis and a pattern of SNPs that can detect it. +

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    • +
  • [001/2008] Genrisk-T - defining the risk of low dose radiation for thyroid + cancer - the role of germline SNPs. +
    + GA Thomas, Imperial College London, Hammersmith Hospital, London + Email +
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    + +

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    + Cancer of the non-medullary (follicular epithelium) component of + the + thyroid is induced by external irradiation and by radionuclides + deposited within the thyroid tissue. Estimates of the + radiological + risk of developing thyroid cancer are derived from + epidemiological + studies performed in. Populations receiving high doses where, + according to Ron et al, the threshold in 100 mSv. Extrapolation + of + this risk to exposures at much lower doses is compromised by the + lack of an accurate model of the dose response curve for thyroid + cancer at low doses. Moreover, such population based estimates + fail + to take into account the contribution of individual genetic + variability to the risk estimate. Individuals with an increased + genetic predisposition to develop thyroid cancer are not + identified, + and it is precisely these individuals who will be at greatest + risk + at low doses. The GENRISK-T consortium is composed of thyroid + cancer + experts with experience in the fields of radiation biology, + animal + models of radiation-induced cancer, tumor banking, cancer + biology, + molecular genetics, histopathology, cyto genetics and risk + modelling. We will use this interdisciplinary knowledge to + define + the genetic component influencing the risk of radiation-induced + thyroid cancer. This will be achieved through a combination of + studies using animal models and in human radiation-induced + thyroid + tumors. This new understanding of the genetic risk modifiers + will be + used to develop an animal model of thyroid cancer that is + responsive + to low dose radiation in the cGy range, thereby providing an + experimental solution to resolving the uncertainties of the low + dose-response curve. This EC collaborative project (PI Professor + M + Atkinson, Helmholtz Zentrum, Munich) combines the use of animal + models and human studies. This particular application is to + support + the investigation of human germline SNPs that may predispose to + radioiodine induced thyroid cancer in those exposed as children + and + adolescents. +

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    • +
  • [002/2008] Expression profiling of childhood follicular tumors: a comparison + of + those exposed and not exposed to radiation. Defining the genetic component + of + thyroid cancer risk at low doses. +
    + B Jarzab, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Gliwice, Poland + Email +
    +

    + +

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    + The aim of the study is to investigate transcriptomic profiles + of + follicular thyroid tumors (malignant and benign) that arose + after + expose to radioiodine fallout from Chernobyl power station and + to + low level radiocesium exposure present in the contaminated + environment. Affimetrix microarray technology will be employed + to + define transcriptomic profiles in two cohorts of children + matched on + age, oblast and pathological type of tumor. This project is the + continuation of a series of projects that are carry on to + investigate the transcriptomic and genetic profile of radiation + induced thyroid cancer. +

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  • [003/2008] Array CGH analysis of follicular post-Chernobyl thyroid tumors. +
    + H Zitzelsberger, Helmholtz Zentrum Muenchen, Neuherberg Germany + Email +
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    + +

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    + Follicular thyroid cancers are less frequent than papillary + thyroid + carcinomas (PTC), however, they are associated with a poorer + survival outcome than PTC. Although several genetic changes have + been identified so far, the molecular genetic mechanisms of + tumor + development in follicular thyroid neoplasms are still unclear. +

    + To investigate novel gene alterations and potential radiation + signatures in follicular thyroid adenomas (FA) and follicular + thyroid carcinomas (FTC) it is proposed to investigate + genome-wide + copy number changes of 100 thyroid tissue samples by array CGH + using + 1 Mb BAC arrays. For this purpose we want to compare genomic + profiles of tumors (FA and FTC) developed pre- and post-fallout + of + the Chernobyl accident. The proposed study aims to identify gene + alterations in follicular thyroid neoplasms from altered genomic + regions and to determine aberrations patterns that correlate + with + the radiation history of patients as well as with any of the + clinical phenotypes of the tumors. +

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    • +
  • [001/2009] Defining the genetic component of thyroid cancer risk at low + doses + request for RNA aliquots for QPCR validation and for the exon arrays. + (This project is an expansion of project 002/2008) +
    + B Jarzab, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Gliwice, Poland + Email +
    +

    + +

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    +

    + The aim of the study is to seek for differences in + transcriptomic + profiles of childhood papillary thyroid cancers that arose after + radiation exposure from Chernobyl power station fallout and + sporadic + cancers. As the first step Affimetrix microarray technology was + employed to define transcriptomic profiles in two cohorts of + children matched on age, oblast and pathological type of tumor. + The + second step of the study is to validate microarray results with + Q-PCR analysis. We also plan to extent the analysis to exon + microarray study which allow to detect transcript isoforms, + chromosomal deletions and amplifications. +

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    • +
  • [002/2009] Identification of somatically acquired rearrangements in + post-Chernobyl paediatric thyroid cancers using genome-wide massively + parallel + paired-end sequencing +
    + JA Fagin, Memorial Sloan-Kettering Cancer Center, New York, USA + Email +
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    + +

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    + Post-Chernobyl pediatric thyroid cancers are associated with a + high + frequency of recombination events leading to the generation of + fusion oncogenes, resulting in aberrant expression and + activation of + RET, and less frequently of NTRK and BRAF. Altogether, ~60% of + PTC + arising in this patient population harbor one of these + abnormalities. The discovery of novel somatic rearrangements + using + conventional methods has low sensitivity and/or resolution. We + propose to use genome-wide parallel paired-end sequencing to + identify somatic rearrangements in childhood thyroid cancers + induced + by radiation, as compared to age-matched thyroid cancers without + radiation exposure. Altogether we will select 6 samples of each + population: 2 with a known rearrangement in RET, NTRK or BRAF + (as + positive controls), and 4 without. We will construct 3kb insert + Illumina libraries from each tumor DNA sample, and ~35bp of + sequence + from both ends of each fragment will be obtained. Each end will + be + mapped back to the reference genome. Fragments for which the + ends do + not map back within 3kb of each other and/or are in + inappropriate + orientation will be further studied as they may represent + rearrangements present in the thyroid cancer genome. We will + acquire + ~1 fold genome coverage (~3Gb) from each sample. This will + approximate to 30-fold physical coverage, allowing detection of + essentially all rearrangements present in the dominant clone of + the + cancer. Rearrangements will be processed using a suite of + informatics tools to predict which may generate an in-frame + fusion + gene. RNA from each of the samples will then be tested by + exon-exon + PCR to determine whether the fusion is expressed, and based on + its + predicted function, whether it may correspond to a driver + mutation. + The number of rearrangements in each cancer and their + architecture + will then be compared between the two classes. Sequences at the + rearrangement junctions will also be compared particularly to + examine the complexity of the rearrangement, sequence contexts + of + breaks, presence of repeats and overlapping microhomology of the + rearrangement. Each of these indices may provide clues to the + way + large radiation doses induce DNA double strand breaks and how + they + are repaired. +

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  • [003/2009] miRNA profiles in childhood thyroid cancer +
    + GA Thomas, Imperial College London, Hammersmith Hospital, London + Email +
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    + +

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    + MicroRNAs (miRNAs) are 21-23 nucleotide long non-coding RNA + molecules that have been shown to regulate the stability or + translational efficiency of target messenger RNAs. Dysregulation + of + miRNAs has been implicated in a variety of cancers, and in the + thyroid germline SNPs in miRNA binding sites and in the coding + sequence for miRNAs themselves, have been implicated in + Papillary + Thyroid carcinogenesis. The Human Cancer Studies Group is part + of an + EC sponsored consortium (Genrisk-T) that has intensively studied + papillary carcinomas from a series of 100 patients, and is + currently + extending this approach to follicular tumors. Half of this group + were exposed to radiation and half were born after 1/1/87 and + not + exposed to radioiodine in fallout. The cohort is carefully age + and + sex matched. The Genrisk-T project has provided data on RNA + expression using Affymetrix technology, bac array CGH data on + copy + number variation in the tumors and SNP array data from normal + tissue + from these patients. We now seek to add miRNA data from this + cohort + and to correlate data on SNPs and copy number variation in the + tumor, with changes in miRNA level, and miRNA expression levels + with + changes in RNA expression levels. The combination of this data + will + give us a thorough understanding of the regulation of a number + of + different growth control pathways involved in carcinogenesis of + the + thyroid follicular cell and their relationship to radiation + exposure. +

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  • [002/2007-1] Validation of statistical and bioinformatics technologies to + allow + integration of Next generation RNA Sequencing and microarray data. +
    + L van Zyl, ArrayXpress, Inc. Raleigh, North Carolina, USA + Email +
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    + +

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    + We are a small biotech company developing statistical and + bioinformatics methodology that would allow for the direct + integration and co-analyses of RNA-seq and microarray data. As + quantitative RNA-seq data is becoming the method of choice for + gene + expression analyses, we are developing the statistical and + bioinformatics technology which that allow all previous + published + microarray data to be incorporated with new gene expression + platform + data, to ultimately provide more comprehensive data-sets for + downstream applications/analyses. +

    + We have been working with Dr C Maenhauts group to develop the + methodology to integrate her published Affymetrix gene + expression + data with our own Illumina RNA-seq data from papillary thyroid + cancers. We propose now to subject surplus material from the + samples + that Dr Maenhaut received from the CTB (project 002/2007) to + RNA-seq + in order to not only obtain additional expression data over and + above that obtained by microarray but also to further validate + our + methodologies. +

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  • [001/2011] EpiRadiBio +
    K Unger, Helmholtz Centre, Munich, Germany + Email +
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    + +

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    The EU funded project EpiRadBio project seeks to model the cancer + of the lung, breast and the thyroid after exposure to radiation + in the low-dose range (cumulative dose < 100 mGy). The + formalin-fixed paraffin-embedded (FFPE) papillary thyroid cancer + tissue sections we apply for will be used in a work package of + EpiRadBio that focuses on the cancer risk of papillary thyroid + cancer. In another, recently finished EU funded project on young + onset childhood thyroid carcinomas that also used CTB material + we found that a gain of the chromosome band 7q11 was associated + with exposure to low-dose ionising radiation (He et al., PNAS, + in press). The FFPE tumor sections from patients, which are part + of the UkrAm cohort and which come with estimates on radiation + dose the patients have received will be used for validation and + further characterisation of this marker. The FFPE sections will + be used for in situ hybridisation (FISH) using 7q11 specific + probes. DNA and total RNA will also be extracted from the FFPE + sections. The DNA will be used for high-resolution array CGH and + the total RNA for qRT-PCR mRNA expression analysis of candidate + genes from the gained region. The copy number data and qRT-PCR + data will be integrated with the dose estimates in order to + identify a potential relationship between the + radiation-associated biomarker and radiation dose. The resulting + data will be provided to the modellers of the project who will + use this information to build and refine their models on + radiation risk of papillary thyroid cancer after exposure to + low-dose ionising radiation.

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  • [002/2011] Molecular specificities of radiation-induced thyroid tumors. +
    + C Ory, Commissariat Energie Atomique, Departement Sciences du vivant, Institut de radiobiologie cellulaire et moleculaire, Laboratoire de Cancerologie Experimentale (CEA), France + UK. Email +
    +

    + +

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    + The constituted network to realise this program involved two teams + well known in diagnosis and treatment of thyroid tumors and one team + which were already implicated in the search of radiation-induced + signatures in the thyroid and in the identification of the molecular + mechanisms of radiation-induced tumorigenesis. To date, we focused + our approach at the transcriptomic level. We wish now to analyse + miRNA and mRNA deregulations in a series of post-Chernobyl thyroid + tumors by microarray analysis: 1) to identify a radiation-induced + miRNA and mRNA signatures. We will assess the robustness of these + signatures for a potential use as a diagnostic tool alone or in + combination. 2) to obtain an integrated miRNA/mRNA overview of + radiation-induced tumorigenesis by taking advantage of the + deregulated pathway identified by the transcriptomic approach. To + date, no such integrated analysis has been performed as most of the + studies focused on either transcriptome analysis or miRNA analysis + separately. Ultimately, we will cross the obtained data with others + results from analysis of post-radiotherapy tumors (Ory et al. 2011; + Ugolin et al. PLosONE under revision). +
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    • +
  • [003/2011] EpiRadBio - Validation of radiation-associated gain of chromosome + band 7q11. +
    + K Unger, Helmholtz Centre, Munich, Germany + Email +
    +

    + +

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    + The project using the applied biomaterial is an extension of the + EU-funded GENRISK-T project and aims to validate a gain on + chromosome band 7q11 that was found to be associated with papillary + thyroid carcinomas from young patients (< 19 years) that were + exposed to radiation from the Chernobyl fallout at very young age + (median: 2 years). The validation set containing exposed and + unexposed cases will be matched for age, morphology and residence - + these criteria were already used for case selection of the GENRISK-T + set. A high-definition array CGH platform will be used to validate + the gain and to type for additional radiation-markers that are + smaller in size and were therefore not detectable by 1Mb BAC array + CGH that was used in GENRISK-T. Further, we will use RNA samples and + paraffin sections for characterisation of expression candidate genes + and proteins by qRT-PCR and immunohistochemistry. Fresh-frozen + tissue from selected samples expressing the candidate gene CLIP2 + from the gained region on 7q11 and those that do not express the + gene will be analysed using a whole proteomics approach (liquid + chromatography-tandem mass spectrometry, LC-MS/MS). The results will + be used to identify the dysregulation networks in which CLIP2 is + specifically involved. The projects aims to validate the radiation + marker on chromosome band 7q11, to identify the networks that are + dysregulated in tumors harbouring the marker and to find new markers + that are associated with exposure to radiation. +
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  • [004/2011] A Sequence-based Approach to Identify Genetic Determinants of + Tumorigenesis in Radiation-Induced Pediatric Papillary Thyroid Carcinomas. +
    + L Hawthorn, Georgia Health Sciences University, USA + Email +
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    + +

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    + Cancer is a genetic disease, a concept which has been + consistently + observed for all tumors. Our approach is to survey the entire + genome + of these tumors to look for mutations and other perturbations + that + are involved in radiation-induced papillary thyroid carcinoma + (RI-PTC) and create a genomic profile of this tumor. A new + technology, termed Next-generation sequencing allows sequencing + of + the entire human genome in 8 days. We will begin by sequencing + the + DNA of 50 individual RI-PTC tumors from Chernobyl pediatric + patients + to look for mutations in genes. We will correlate this data with + RNA + sequencing from the same patient samples. This data will provide + information about events that are taking place at the level of + gene + expression, providing information about over and under expressed + genes and the expression of aberrant genes, and gene fusion + products. This data will be compared to RIP-PTC in age matched + patients who were not exposed to radiation to develop a + radiation-specific profile. We have bioinformatic specialists in + the + group who will integrate these various kinds of data. This study + will provide a comprehensive profile of RIP-PTC.

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  • [001/2012] EpiRadBio integrative analysis of molecular data. + +
    + W van Wieringen, VU University Medical Centre, Amsterdam, The Netherlands + Email +
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    + +

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    Within the scope of the EpiRadBio-project, Mark van de Wiel, + Carel Peeters and Wessel van Wieringen from the department of + Epidemiology & Biostatistics of the VU University Medical Center + are responsible for integrative analysis of the molecular data + from (radiation) exposed and non-exposed thyroid cancer samples. + Integrative analysis combines heterogeneous biological data, be + it experimental (e.g., copy number, gene expression, microRNA + expression) or from the biological literature (e.g., gene + annotation, pathway information). Integration of data from + multiple sources is imperative for a mechanistic understanding + of cancer. By putting together partial views of a complex + process like tumorgenesis, we may obtain a more accurate and + complete picture of the molecular mechanisms underlying it. No + off-the-shelf methodology for the statistical analysis of the + data is available. We therefore aim to develop statistical + models from the experimental data of these biological processes. + Such models will enhance our ability to identify biomarkers and + therapeutic targets more unambiguously and to interpret genotype + information. This should enhance the understanding of what + distinguishes the exposed from the non-exposed thyroid cancers. + In addition, the biological insight these models provide is + likely to result in more targeted follow-up experiments and + efficient use of available resources.

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    • +
  • [002/2012] Validation of the gene signature differentiating exposed from + non-exposed PTCs, obtained in the Genrisk-T project (no.: 036495) with an + independent QPCR method. +
    + B Jarzab, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Gliwice, Poland + Email +
    +

    + +

    +
    +
    +

    The aim of the study is to investigate transcriptomic profiles of + papillary thyroid carcinomas that arose after expose to + radioiodine fallout from Chernobyl power station and to low + level radiocesium exposure present in the contaminated + environment. This project is the continuation of a series of + projects that are carry on to investigate the transcriptomic and + genetic profile of radiation induced thyroid cancer. + As a first step of the study Affimetrix microarray technology + was employed to define transcriptomic profiles in two cohorts of + children matched on age, oblast and pathological type of tumor. + At present we want to validate the results with qPCR.

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  • [001/2013] A detailed study of the somatic genomics of radiation induced + thyroid cancer. +
    + GA Thomas, Imperial College, London + Email +
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    + +

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    + It has long been accepted that cancers arise by the sequential + accumulation of errors in the DNA of a clone of cells within a + given tissue. This in part explains their long latency. However, + recent studies using whole genome sequencing have suggested a + different mechanism for some cancers, particularly those that + arise in children. This mechanism is called chromothripsis and + involves shattering of chromosomes and then restitching them + together. This results in multiple small changes in the DNA that + occur simultaneously rather than sequentially. The aim of this + study is to use whole genome sequencing to identify novel + mutations in radiation induced thyroid cancer, to identify + changes in the mitochondrial genome and to investigate the + frequency of chromothripsis in childhood thyroid cancer, + especially with respect to radiation exposure.

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    • +
  • [001/2014] Assessing the impact of radiation exposure on the development of + medullary thyroid carcinoma. +
    + Elizabeth Grubbs, Department Surgical Oncology, MD Anderson Cancer Center, Houston, USA + Email +
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    + +

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    Convincing epidemiologic data has established a strong causative + association between ionizing radiation and the development of + papillary thyroid cancer (PTC). This finding was due, in large + part, to studying those affected by the Chernobyl accident. More + recently other solid tumors, such as lung and breast, have been + associated with radiation. Medullary thyroid cancer (MTC), a + rarer but more lethal thyroid cancer than PTC, has not been + associated with radiation exposure to date. However, there + appears to be a higher number of MTC cases than would be + expected in the Chernobyl population. We would like to determine + if there is a link between radiation and MTC by studying this + population to look for mutations that are associated with + radiation exposure. Additionally, because MTC is a hereditary + condition in 25% of cases, we would also like to assess whether + there could be a hereditary cause to MTC in this small + geographic region. Such data will give us an insight into the + mechanisms in which tumors are formed in MTC and potentially + help us target ways to stop these tumors.

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    • +
  • [002/2014] Anaplastic lymphoma kinase (ALK) rearrangements in + radiation-induced papillary thyroid carcinomas: a study on post Chernobyl + tissue samples +
    + S Eder, Bundeswehr Institute of Radiobiology, Munich Germany + Email +
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    + +

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    Previous analysis of data derived from the Chernobyl accident has + shown strong correlation between absorbed doses of IR and the + induction of papillary thyroid cancer (PTC). Specific genetic + alterations, such as rearrangements of the RET oncogene, are + linked to previous exposure to radioiodine. Recently, + rearrangements of the anaplastic lymphoma kinase (ALK) gene have + been found to be selectively expressed in papillary thyroid + cancer (PTC) amongst atomic bomb survivors (ABS), but not in PTC + patients lacking radiation exposure. In PTC, ALK rearrangements + have been shown to be associated with tumor aggressiveness and, + importantly, represent a possible pharmacologicaltarget for the + compound Crizotinib. Interestingly, radiation-induced PTCs that + show ALK rearrangements lack additional genetic alterations that + are frequently found in sporadic thyroid cancer, such as RET, + NTRK1, BRAF, or RAS; these findings underline the oncogenic + potential of ALK rearrangements in radiation-induced PTC. We + plan to investigate a possible correlation between radiation + exposure and ALK rearrangements in PTC biospecimens from + patients exposed to radioiodine in the context of the Chernobyl + accident as well as in a control cohort of sporadic PTCs, + performing fluorescence in situ hybridization (FISH) analyses. + Furthermore, we intend to assess the mutation status of commonly + altered oncogenes in PTC, such as BRAF or RAS, using + pyrosequencing.

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  • [003/2014] Comprehensive Genomic Characterization of Radiation-Related + Thyroid Cancer in Ukraine +
    + S Channock, Division of Cancer Epidemiology and Genetics, National Cancer Institute, USA + Email +
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    New advances in genomic characterization technologies afford new + opportunities to comprehensively investigate the genetic basis + of the established association between childhood exposure to + iodine-131 (I-131) from the Chernobyl Nuclear Power Plant + accident and risk of thyroid cancer. The opportunity to analyze + a large set of thyroid cancers and normal tissue/blood from the + Chernobyl Tissue Bank (CTB) could further our understanding of + the molecular mechanisms of radiation carcinogenesis in humans + based on careful evaluation of epidemiological risk factors and + genomic alterations. Previously, we had reported a preliminary + study of dose-related alterations in gene expression and + chromosomal translocations in approximately 70 cases drawn from + the Ukrainian-American (UkrAm) cohort component of the CTB + biorepository. Recently, we have completed a pilot study in + which we have conducted a comprehensive genomic characterization + of 12 UkrAm cases, including paired fresh frozen and + formalin-fixed paraffin-embedded tissue samples using the + infrastructure and analytical pipeline of the Cancer Genome + Atlas (TCGA) of the U.S.A. National Cancer Institute (NCI). This + includes whole genome sequence analysis of RNA, DNA and + micro-RNAs as well SNP and methylation microarrays of the tumor + tissue. SNP microarray and DNA analysis was performed on + peripheral blood for comparison of germline to somatic + alterations. The success of the feasibility study establishes a + strong scientific basis for extending this approach to a + substantially larger study of thyroid cancer cases drawn from + the CTB. Here, we propose conducting a comprehensive genomic + characterization study of 500 papillary thyroid cancers (PTC) + from the Ukraine using biological samples, information on + radiation exposure, and demographic characteristics. The main + objective of the study is to provide comprehensive, integrated + characterization of the genomic, transcriptomic, and epigenomic + landscapes of radiation-related PTC for comparison across a + spectrum of I-131 exposure as well as a comparison with + approximately 500 sporadic PTCs available from The Cancer Genome + Atlas recently published in Cell. The proposed study has the + potential to provide unique insights into the mechanisms of + radiation carcinogenesis and to generate a rich data resource + accessible to other investigators.

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  • [001/2018] Liquid biopsy in assessment of radio-induced thyroid cancer in + children and young adults +
    + Kirk Jensen, Department of Pediatrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA + Email +
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    In this study we plan to analyze samples from patients with + papillary thyroid cancer. We will examine primary tumors and + serum samples in 40 pediatric patients (aged ≤ 18 years in + 1986), and in 40 young adults (18-25 years in 1986). To + determine a possible correlation between the presence of + mutations/fusion in liquid biopsy and the extent of metastatic + spread we plan to examine samples from patients presenting with + lymph node metastases only and from patients with distant + metastases.

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    + We will first identify driver mutations in the primary tumor by + performing Ion Torrent Oncomine Pan-Cancer assay analysis using + DNA/RNA extracted from tumor. Next, we will employ the same + approach for analysis of DNA/RNA extracted from the serum sample + of the same patient. We expect to show that in patients with + metastatic thyroid cancers, results of NGS analysis in serum + will recapitulate results of NGS analysis in primary tumors. We + also plan to perform quantitative assessment of genomic + abnormalities using the digital PCR technique. To do so, we will + examine the presence of specific driver mutation(s) in primary + tumor by dPCR, and determine the mutant/wild copy numbers in + DNA/RNA samples extracted from the whole tumor. We also plan to + complete the assessment of primary tumors through the detection + of oncogenic proteins by immunohistochemistry, and by evaluation + of mutant/wild copy numbers after performing laser captured + microdissection. Serum from the same patient will be then + examined by dPCR.

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Once you’ve contacted CBIIT Application Support, we will either resolve the issue or create a ticket on your behalf so we can ensure resolution.

Contact Application Support

Email: NCIAppSupport@nih.gov

Application Support Telephone: (240) 276-5541 or toll free: (888) 478-4423
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IT Support for NCI Employees

If you’re an NCI staff member and need help or want to learn more about available IT services, visit NCI at Your Service. Services included but are not limited to:

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CBIIT Application Support

CBIIT Application Support is available at NCIAppSupport@mail.nih.gov and by telephone, 9:00 a.m. to 5:00 p.m. ET, Monday to Friday except federal holidays: (240) 781-5115 or (888) 478-4423 (toll-free).

Learn more about Application Support.

CBIIT Staff Directory

Check out the CBIIT staff directory for contact information, roles, and responsibilities of CBIIT federal employees.

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Media Requests

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The Center for Biomedical Informatics and Information Technology (CBIIT) mission is supported by the:

Office of Business Operations (OBO)

Director: Marcos Munozramos, M.S.

The OBO provides essential services and support to CBIIT by managing its business portfolio, financial and contract management, and staffing to improve the efficiency of CBIIT’s service to NCI. The OBO also:

  • coordinates timely and accurate information for NCI IT data calls from the U.S. Department of Health and Human Services (HHS), NIH, and the Office of Management and Budget.
  • administers the strategic and capital planning process, conforming to federal requirements.

Meet the OBO Team

 

Informatics and Data Science Program (IDS)

Acting CBIIT Director and Associate Director: Jill Barnholtz-Sloan, Ph.D.

The IDS Program delivers:

  • standardized vocabularies and data standards.
  • informatics infrastructure for NCI-sponsored precision medicine trials and clinical trials reporting.
  • centralized management and coordination of scientific software and training across NCI.
  • computational biology services for intramural research labs.
  • data science infrastructure for data storage, access and use, which leverages cloud computing, high-performance computing, and scientific collaboration tools.

These activities further the use of informatics and data science within the cancer research community.

Learn More About IDS
 

Office of the Chief Information Officer (OCIO)

NCI Chief Information Officer and OCIO Associate Director: Jeff Shilling

The OCIO oversees the implementation of IT at NCI, considering risks; costs; efficiencies, benefits, and other opportunities; according to governing federal mandates.

Meet the OCIO Team

 

Digital Services and Solutions Branch (DSSB)

Branch Chief: Sue Pan

DSSB:

  • provides professional services, business intelligence, and data analytics that support NCI’s adoption of emerging digital technologies and modernization of both business process and IT service management.
  • provides technical advisory and consultation for IT architecture and engineering design.
  • provides governance and management of cloud computing platforms, as well as enterprise Software‐as‐a‐Service (SaaS) platforms and tools, to develop security‐accredited digital systems and software solutions.
  • provides governance and management of processes for IT engineering and IT service management with a focus on human‐centered design.

NCI Cybersecurity Branch (NCB)

Branch Chief: Craig Hayn

NCB:

  • secures NCI’s systems, networks, and user endpoints against viruses, malware, misconfiguration, insider threats, and cyber attackers.
  • ensures all NCI’s IT systems are assessed, authorized, and monitored using the National Institute of Standards and Technology Risk Management Framework.
  • provides cybersecurity incident management, response, and coordination with NIH’s Threat Management and Incident Response team.
  • ensures NCI‐specific security policies, standards, and guidance are developed, maintained, and communicated to NCI staff and stakeholders.

IT Services and Support Branch (ITSSB)

Branch Chief: Jim Racheff

ITSSB:

  • provides IT support for all NCI staff, which includes computing needs (e.g., laptops, desktops, network, software, and data storage).
  • manages NCI’s IT infrastructure, including network resources, operational security architecture, scientific and business data repositories, telecommunications, and collaboration tools.
  • provides data protection, disaster recovery, IT training, and problem tracking services.
  • recommends state‐of‐the‐art scientific computing solutions and technologies and manages scientific computing support models based on NCI staff needs.

Office of Data Sharing (ODS)

Director: Jaime M. Guidry Auvil, Ph.D.

The mission of ODS is to create a comprehensive vision and strategy to enhance broad and equitable data sharing for NCI and the cancer research community at large. Data sharing is critical to foster collaboration, facilitate innovation, accelerate scientific discovery, and enhance rigor and reproducibility. ODS engages with many stakeholders within and across the cancer research community to guide interpretation and implementation of complex processes, programmatic initiatives, and policies needed to ensure impactful data sharing.

Learn More About ODS

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Our work at IDS lays the foundation for many of NCI’s biomedical informatics and data science initiatives, giving cancer researchers (like you) the resources you need to use data more efficiently and effectively.

Our program consists of three branches: the Clinical & Translational Research Informatics Branch, the Data Ecosystems Branch, and the Computational Genomics & Bioinformatics Branch.

NCI’s Cancer Research Data Commons (CRDC) just reached a significant milestone! Read about the CRDC in a four-part series commemorating the first 10 years of this important initiative.

Find Out What We Do

Clinical & Translational Research Informatics Branch (CTRIB)

Branch Chief: Umit Topaloglu, Ph.D.

At CTRIB, we’re working on new ways to use informatics across NCI, NIH, and the cancer research community. Our goal is to speed the translation of data-driven research into clinical practice. In particular, we’re focusing on:

Promoting Precision Medicine. We’re developing tools and pipelines that someday will help clinicians diagnose cancer early in the course of disease (when it’s highly treatable). We’re also helping develop new ways of predicting the best treatment for the best outcome for each person with cancer.

Capturing and Managing Data. We’re working on streamlining how researchers capture and report data from NCI-sponsored precision medicine trials and clinical trials. We’re also helping to advance the use of Real-World Data (RWD) from Electronic Health Records (EHRs). We’re identifying and addressing gaps in EHR data pipelines, establishing criteria for informatic tools to support quality RWD, and advancing reliable research methods.

Making Data Useful. We’re working to make certain the data you generate are useful to others in the cancer research field. We do this by developing and maintaining semantic resources and vocabularies.

Data Ecosystems Branch (DEB)

Branch Chief: Tanja Davidsen, Ph.D.

Our work at DEB centers on building, strengthening, and maintaining the infrastructure and tools that make up a sophisticated data ecosystem. We’re especially working on:

Fostering Collaboration. We work closely with other government agencies, industry, and academia to stay abreast of the latest in technology. This ensures we’re tapping the latest resources and most novel ideas for cancer research, especially in the areas of informatics, high-performance computing, and artificial intelligence (AI).

Setting Standards. We also work closely with international coordinating bodies to make certain that we keep pace with the latest data standards. We promote FAIR (i.e., Findable, Accessible, Interoperable, and Reusable) data principles, and ensure that data adhere to NIH’s Data Management and Sharing policy.

Sharing Resources. We’re centralizing resources, such as software and training, to help others (at NCI and the broader cancer research field) access and use data. This includes looking at new ways of working with data—both in the cloud and locally, using technologies such as federated learning and edge computing.

Computational Genomics & Bioinformatics Branch (CGBB)

Branch Chief: Daoud Meerzaman, Ph.D.

At CGBB, we help solve research problems. Our staff offer skills and expertise to others (at NCI, NIH, and in the broader research community) to develop new bioinformatic and computational-genomics tools. We’re focused on:

Advancing Research. We’re using the latest tools and technologies—such as proteogenomic approaches for sequencing and interpreting genomic, transcriptomics, and proteomic data—to advance cancer research.

Developing Tomorrow’s Technology. Our team also is working to develop and implement new approaches, such as AI, machine learning, and algorithms, to find better ways of using data (e.g., genomic, proteomic, and imaging) to predict, diagnose, and treat cancer.

Education and Training. We’re fostering the next generation of researchers and fellows through a robust training program. We also coordinate webinars and seminars, featuring renowned experts in the biomedical and technology fields, who share their insight and skills in bioinformatics and computational-genomics tools.

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Read the Latest From Us

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CRDC in Publications: How Are People Using the Available Resources?
The NCI Cancer Research Data Commons (CRDC) is a great resource for accessing cancer research data. So, how have your colleagues been using it recently? Read this article to find out!
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United States Core Data for Interoperability (USCDI+) Seeks Feedback on Adverse Event Data Elements
If you’re working with adverse event cancer and immune-related data, USCDI+ program staff need to hear from you! See how you can give your feedback on the new USCDI+Cancer draft data set.
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Dr. Jill Barnholtz-Sloan Talks Informatics, Data Science, and Epidemiology in NCI Podcast
She speaks to how these areas are interconnected, shares her personal career journey, and uses her experience to advise you on how to be a successful cancer researcher.
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Office of Data Sharing (ODS)

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Office of Data Sharing (ODS)

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At ODS, our work centers on the policies, programs, and processes involved in sharing data—both within NCI and across the larger cancer research community.

Find Out What We Do

We work with everyone who has a stake in cancer research, from researchers and data scientists to administrators and patients. While navigating an ever-shifting landscape of technology and tools, we devise concrete strategies—ensuring you comply with current polices, but also helping you add value to your research data. 

Why is data sharing important? When you share data, you’re able to:  

  • extend the usefulness of data beyond a single study, making scientific discovery faster and more efficient,
  • increase the rigor and reproducibility of cancer research, and
  • foster collaboration that leads to further innovation and tangible results.

Scientific Policy and Program Branches (SPBBs)

Branch A Chief: Subhashini Jagu, Ph.D.
Branch B Chief: Emily Boja, Ph.D.

Our office includes two branches, and our chief responsibilities are:

Leading NCI’s Efforts in Data Sharing. We’re leading NCI’s strategic vision and making certain that the approaches for managing, sharing, and accessing data adhere to the latest policies.

Helping You Comply With Policies. We’re seeking new ways to help you comply with current policies, establishing and coordinating processes so data from NCI-supported studies are easy to access, share, and use.

Supporting NCI Initiatives. We’re leading and guiding data-related NCI initiatives to help others share data with the wider research community.

Fostering Collaboration. We’re working with others at NCI to ensure that data-related initiatives and data management processes meet the required federal policies.

Serving as Advocates for Data Sharing. We’re making certain you’re up to date on the latest policies, tools, and resources you need to make your data available to the fuller cancer research community.  

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Meet Our People

Meet the team of professionals behind our efforts.

Director

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Jaime M. Guidry Auvil, Ph.D.
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Meet the Rest of the Team

 

Read the Latest From Us

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CCDI Workshop Addresses the Needs of Its Rare Cancer Initiative
Learn about the Childhood Cancer Data Initiative’s national strategy for studying children, adolescents, and young adults with very rare cancers. The Pediatric, Adolescent, and Young Adult Rare Cancer Initiative supplies researchers (like you) the data requirements for collecting data from study participants.
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Updates to NIH’s Genomic Data Sharing Policy
If you’re working with NIH genomic data, you’ll need to be aware of some new security requirements for data management and access that take effect on January 25, 2025. Learn more about how this could impact your work.
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Input Needed for Pediatric Data Standards
NCI’s Childhood Cancer Data Initiative seeks your feedback for the Pediatric Cancer Core Common Data Elements, a newly created resource which facilitates data integration and analysis.
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Read More News

 

Collaborate/Work With Us

Want to learn about our efforts to enhance data sharing? Subscribe to our listserv for updates and email us for more information. 

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Abigail Joyce

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Writer-Editor

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    Current Role

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    As the social media/internal lead at CBIIT, my main areas of focus are reviewing content and strategy for all social media channels; brainstorming, implementing, and developing internal campaigns; and reviewing content and strategy for those internal campaigns.

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    Background

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    Education

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    • B.S., Political Science, Indiana University
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    Previous Work

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    • Contractor, NCI’s Office of Communications and Public Liaison (OCPL)
    • Fundraiser, Food Marketing Institute
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Alex Nordan

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Program Analyst

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    I am focused on software asset management, mobile device account management, and central receiving warehouse management.

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    Background

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    Education

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    • B.S., Environmental Science Policy, University of Maryland
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Staff Directory

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To find a federal staff member, select a branch/office or search by name. 

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+ + Kanakadurga “Durga” Addepalli, Ph.D. + +

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+ Health Scientist (Bioinformatics) +
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+ Data Ecosystems Branch +
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+ Informatics and Data Science Program +
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+ Branch Chief, Supervisory Health Scientist Administrator +
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+ + Lawrence “Larry” Brem, M.S. + +

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+ Computer Scientist (Configuration Manager, Code 4 Supervisor) +
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+ Digital Services and Solutions Branch +
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+ + Brian Capaldo, Ph.D. + +

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+ Bioinformatics Specialist +
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+ + Esmeralda “Emi” Casas-Silva, Ph.D. + +

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+ Health Science Administrator +
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Allison Dennis, Ph.D.

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Supervisory Health Science Administrator

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Blaise Czekalski, M.S.

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IT Specialist (Systems Analysis)

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    As one of the information security officer alternates, I’m dedicated to protecting NCI’s information assets through coordination, implementation, and communication of IT security policies and procedures. I focus on the management of vulnerability remediation, IT security training compliance, encryption certificate service, and IT security contract review. I also work within the Federal Information Security Management Act (FISMA) mandates and National Institute of Standards and Technology (NIST) guidelines to ensure security assessment and authorization of NCI’s information systems.

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    Education

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    • M.S., Engineering, Auburn University
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    Previous Work

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    • Engineer and Systems Administrator, National Aeronautics and Space Administration
    • Engineer and Systems Administrator, U.S. Navy
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Brandon J. Wright, Ph.D.

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Health Science Administrator

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  • Office of Data Sharing
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Brenda R. Duggan, R.N.

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Biomedical Informatics Specialist

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    I currently serve as the NCI Metadata Repository content program manager, overseeing a team of expert metadata curators who provide centralized curation, training in caDSR and metadata, and cancer research standards implementation.

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    Projects

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    + + Scientist, sitting in a lab, looking at bar chart displayed on a computer screen. + +
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    + Cancer Data Standards Registry and Repository +
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    + Provides access to oncology research, common data elements, and forms. + +
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    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
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    + Cancer Research Data Commons +
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    + Connects you to the data ecosystem, NCI's primary platform for cancer research. + +
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    Background

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    Education

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    • B.S., Nursing, Boise State University
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    Recent Awards

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    • 2023 NIH Director’s Award
    • 2009 NIH Director’s Award, for leadership in the development of the National Community Cancer Center Program (NCCCP)
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Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

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Brent Reynolds

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Program Specialist

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    As CBIIT’s Acquisitions and Purchasing Program Specialist, I acquire supplies and/or services using simplified acquisition procedures governed by CBIIT policies and procedures, NCI, NIH, and HHS protocols, and The Federal Acquisition Regulation. I complete acquisition plans for all purchases over $250,000 and act as the liaison with the Office of Acquisitions.

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    Background

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    Education

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    • B.S., Multi-disciplinary Studies, Liberty University
    • A.A., General Studies, Liberty University
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    Previous Work

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    • U.S. Army
      • Master Trainer, Ft. Meade, MD
      • HealthCare Recruiter, 1st Medical Recruiting Battalion
      • Station Commander, Westminster, MD
      • Retired with rank of Sergeant First Class
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Brian Capaldo, Ph.D.

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Bioinformatics Specialist

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Carl W. McCabe, Ph.D.

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Supervisory Biomedical Information Specialist, Scientific IT Advisor

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    I am involved in HPC and scientific computing special initiatives.

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    Background

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    Education

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    • Ph.D., Anthropology, University of California, Davis
    • B.S., Anthropology, University of Nebraska-Lincoln
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    Previous Work

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    • IT and Informatics Coordinator, NCI’s Division of Cancer Epidemiology and Genetics
    • Presidential Management Fellow, NIH Office of the Director’s Office of Extramural Research
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Christopher Knill

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Information Technology Specialist

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    As an information technology (IT) specialist within the IT Services and Support Branch, I collaborate with various departments to establish interdisciplinary teams. These teams provide comprehensive solutions aligned with stakeholders' needs. I also maintain a close partnership with the Desktop Platform Management team to guarantee the delivery of customer-centric, compliant, and reliable desktop platform solutions. I have a certificate of Executive Leadership and Management from the University of Notre Dame, and a certificate in Organizational Development from Mount Saint Mary’s University.

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    Education

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    • M.B.A., Mount Saint Mary’s University
    • B.S., Business, Mount Saint Mary’s University
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    Previous Work

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    • Program Director, Computer and Statistical Services Contract, DMS, a BRMi Company
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    Recent Awards

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    • NCI Special Recognition Award, in support of NCI-wide remote operations during the COVID-19 pandemic
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Christopher Siwy, Ph.D., CISSP

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Computer Scientist

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    As the scientific applications program official within CBIIT’s Digital Services and Solutions Branch, I manage the Communications Hub and Research Management System and oversee a portfolio of analysis tools that support many of NCI’s intramural efforts.

    Prior to joining CBIIT, I was a data scientist in the Integrated Infrastructure and Emerging Technologies Unit within the Office of Data Science Strategy in the National Institutes of Health (NIH) Office of the Director. There, I served as a program official for the NIH Cloud Platform Interoperability program and coordinated engagements of NIH Partner Systems for the RAS Initiative. My professional experience also includes leading custom electronic health record software solutions at the NIH Clinical Center, where I played a crucial role in developing a web platform for managing asymptomatic COVID-19 testing and vaccine administration for the NIH workforce.

    While earning my doctorate, my research focused on molecular dynamics simulations targeting the human blood-brain barrier for Alzheimer’s disease research. During my undergraduate studies, I participated in a biodiversity field study in Ecuador and the Galapagos Islands. In addition to my academic and research achievements, I am a Certified Information Systems Security Professional.

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    Publications

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    View Christopher’s PubMed Summary
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    Featured Publications

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    Differential Diagnosis of Bone Marrow Failure Syndromes Guided by Machine Learning. Blood, 2023.

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    Unveiling the Silent Threat Among Us: Leveraging Health Information Technology in the Search for Asymptomatic COVID 19 Healthcare Workers. Journal of the American Medical Informatics Association, 2021.

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    Is the Conformational Ensemble of Alzheimer’s Aβ10-40 Peptide Force Field Dependent? PLoS Computational Biology. 2017.

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    Background

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    Education

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    • Ph.D., Bioinformatics and Computational Biology, George Mason University
    • M.S., Computer Science, Johns Hopkins University
    • B.S., Management Science and Information Systems, The Pennsylvania State University
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    Previous Work

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    • Data Scientist, Office of Data Science Strategy, Office of the Director, NIH
    • Application Software Developer, Department of Clinical Research Informatics, Clinical Center, NIH
    • Forensic Software Engineer, ManTech International Corporation
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    Recent Awards

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    • 2022 Office of the Director Award, for extraordinary initiative in the implementation and administration of the NIH COVID-19 Vaccine Clinics (primary and booster) at Multiple Geographical Locations
    • 2021 Clinical Center Award, for superior efforts to plan and implement a site in the NIH Clinical Center to screen for SARS‑CoV‑2 infection in asymptomatic staff
    • 2021 Clinical Center Award, for dedication and collaboration in establishing sites for COVID‑19 asymptomatic testing in Shady Grove and Frederick to support the health and safety of NIH staff
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Follow Us on LinkedIn

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Chunhua Yan, Ph.D.

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Biomedical Informatics Program Manager

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Cliff Wong

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Computer Scientist

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Craig Hayn

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Supervisory IT Specialist (Information Security), Branch Chief

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    As the Chief Information Security Officer (CISO), I maintain information security and privacy as well as implement cybersecurity measures that help protect NCI’s vast information system resources, networks, applications, and data. I lead a team of deputy security officers and direct contractor support staff who help carry out NCI’s complex and diverse security mission, which ranges from cyber governance, risk management and compliance/auditing, to security operations. My team and I strive to fulfill customer needs and ensure that solutions are practical, re-usable, and compliant with federal policies and mandates.

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    Background

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    Education

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    • B.S., Information Systems Management, University of Maryland Global Campus
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    Previous Work

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    • Information Security Manager, Attain, LLC
    • Cyber Security Lead Associate, Booz Allen Hamilton
    • Network Systems Administrator, SAIC
    • IT Support and Records Management, EG&G and Rockwell International
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    Recent Awards

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    • 2020 NCI Director’s Award, as a member of the NCI IT Onsite and Remote Computer Deployment Brigade
    • 2017 NCI CIO Award for Successful Sponsorship of the FedRAMP Druva inSync Remote Backup Service, Authority to Operate
    • 2017 NCI CBIIT Award for Cross-Collaboration Award
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    Federal Staff

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    My Team

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    Rachel Leffler

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    + IT Specialist +
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    + NCI Cybersecurity Branch +
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Follow Us on LinkedIn

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Cu Nguyen

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Staff Scientist

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Danny Rebolledo

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Program Analyst

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    As a program analyst in the Office of Business Operations, I lead the Acquisition Support Team. This includes supporting acquisition approach recommendations, HHS market research, and Statement of Work development support.

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  • + Background +
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    Background

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    Education

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    • B.P.S., Business and Management, Excelsior College
    • Project Management Professional, Project Management Institute
    • Pre-Command/Command Sergeant Major Course, USA Command & General Staff College
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    Previous Work

    + +
    • U.S. Army
      • Director of Operations, 21st Strategic Signal Brigade
      • Senior Signal Program Analyst, 3rd Infantry Division
      • Director of Operations, 52nd Strategic Signal Battalion
      • Retired with rank of Command Sergeant Major
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    Recent Awards

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    • Legion of Merit
    • Bronze Star (x3)
    • Meritorious Service Medal (x4)
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Follow Us on LinkedIn

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Daoud Meerzaman, Ph.D.

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Branch Chief

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Denise Warzel, M.Sc.

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Science Program Analyst

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    I’m a science program analyst who leads the design and development of the Cancer Data Standards Registry and Repository (caDSR) infrastructure, where machine-readable definitions of Common Data Elements (CDEs), case report forms (CRFs), and data models are created, maintained, and distributed. I specialize in systems that leverage machine-readable data semantics based on common concepts to ensure data descriptions can be easily understood at all levels and are useful throughout the data lifecycle.

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    My area of expertise is management and information systems. We have been using Agile development in our current caDSR projects. I also specialize in data management practices, specifically around the creation and management of information needed to accurately describe data elements and models (i.e., metadata), which is the primary mission of caDSR.

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    In addition to a masters in computer science, I am certified as a COR II and SOA Analyst.

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    I also serve on the NIH CDE Governance Group reviewing submissions of CDEs for NIH Endorsement, and I am Convenor JTC1 SC32 Data Management and Interchange, WG2 Metadata Standards, International Organization for Standardization (ISO).

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    Projects

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    + + Scientist, sitting in a lab, looking at bar chart displayed on a computer screen. + +
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    + Cancer Data Standards Registry and Repository +
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    + Provides access to oncology research, common data elements, and forms. + +
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    Publications

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    View Denise’s PubMed Summary
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    Featured Publications

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    FAIR Data Sharing: The Roles of Common Data Elements and Harmonization. Journal of Biomedical Informatics, 2020.

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    Composite CDE: Modeling Composite Relationships Between Common Data Elements for Representing Complex Clinical Data. BMC Medical Informatics and Decision Making, 2020.

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    Call for Data Standardization: Lessons Learned and Recommendations in an Imaging Study. JCO Clinical Cancer Informatics, 2019.

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    In the News

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    Semantics Series—The Role of Common Data Elements and Artificial Intelligence
    Common Data Elements (CDEs) enrich and standardize data through consistent and accurate metadata, helping to make data ready for use in training artificial intelligence (AI) models. In this blog, Ms. Denise Warzel discusses the role of CDEs and AI in CBIIT’s Semantic Infrastructure.
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    The Quest for Harmonized Data
    The quest to harmonize data has ushered in a new way of thinking about standardization. Now, rather than expecting everyone to adopt a particular model or standard, we’re seeking to leverage technology that can do some of this work for us. The DREAM Challenge was designed to make aggregating and mapping data to the correct lexicon of terms and metadata a nearly seamless step for researchers. Read more about the Challenge that’s currently underway and how we hope to address harmonization in the future.
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    Education

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    • M.Sc., Computer Science, University of Oxford
    • B.B.A., Management Information Systems and Services, University of Georgia
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    Previous Work

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    • Independent Consultant, ISO and the International Electrotechnical Commission
    • Independent Consultant, Office of Informatics and Organ Systems Branch, SPORE Programs
    • Senior Research Associate, University of Colorado Health Sciences Center, Cancer Center
    • Manager, International Business Machines (IBM) Corporation
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Dianna Kelly, M.P.H.

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IT Project Manager, Advisor for Strategy and Organization

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    I focus on strategic planning, with the aim of improving non-technical IT business and process methodologies, optimizing the governance process, and raising awareness of NCI’s IT projects. I also have a master’s certificate for federal acquisition management.

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    Background

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    Education

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    • M.P.H., University of Pittsburgh
    • B.S., Health Science, Slippery Rock University
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    Previous Work

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    • IT Program Manager, Scientific Program Analyst, NCI at Frederick
    • Communications Manager, Aspen Systems Corporation
    • Project Manager, Public Health Foundation
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    Recent Awards

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    • 2021 NCI Director’s Award, for supporting the NCI Federal Information Technology Acquisition Reform Act Clearance Strategy Package Team
    • 2020 NCI Director’s Award, as a member of the NCI IT Onsite and Remote Computer Deployment Brigade
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Donald E. Hall II, D.B.A.

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Supervisory Program Analyst

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    I’m responsible for financial management, contract management, portfolio management, and centralized procurement.

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    Background

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    Education

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    • D.B.A., M.A., B.A., Business Administration, Trident University International
    • Military Education: Primary Leadership Development Course, Basic Non-Commissioned Officers Course, Advanced Non-commissioned Officers Course, First Sergeant Course, and Sergeant Major Course
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    Previous Work

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    • U.S. Army
      • 3rd Armored Division
      • 1st Armored Division
      • U.S. Army Recruiting Command
      • Retired with rank of Command Sergeant Major
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    Recent Awards

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    • Legion of Merit
    • Meritorious Service Medals (x2)
    • Army Commendation Medals (x6)
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  • + My Team +
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    Federal Staff

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    My Team

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    Brent Reynolds

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    + Program Specialist +
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    + Office of Business Operations +
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Follow Us on LinkedIn

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Doug Hosier

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IT Specialist (Systems Analysis)

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    As an IT Specialist, I support both the NCI Network Service at CBIIT and the NCI Server Service.

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    Background

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    Education

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    • B.S., Diplomacy and Foreign Affairs, Miami University
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Follow Us on LinkedIn

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Esmeralda “Emi” Casas-Silva, Ph.D.

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Health Science Administrator

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    Current Role

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    As a health science administrator and program director, I apply my biomedical sciences and policy background in support of the Cancer Research Data Commons (CRDC), including development oversight of NCI’s Clinical Trials Data Commons. I also co-lead NCI’s Ethical and Regulatory Issues in Cancer Research (ENRICH) forum, and I contribute to the Global Alliance for Genomics and Health’s (GA4GH’s) efforts to enable genomic data sharing for the benefit of human health.

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    Projects

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    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
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    + Cancer Research Data Commons +
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    + Connects you to the data ecosystem, NCI's primary platform for cancer research. + +
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    + + Image shows cells treated with hematoxylin and eosin staining (H&amp;E), a process that helps scientists differentiate between normal and diseased cell structures. Here H&amp;E staining shows several bright pink cells, many of which are in the process of dividing, indicating the presence of cancer cells. + +
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    + National Clinical Trials Network/NCI Community Oncology Research Program Data Archive +
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    + Stores and shares data sets generated from National Clinical Trials Network and NCI Community Oncology Research Program clinical trials. + +
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  • + Publications +
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    Publications

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    View Emi’s PubMed Summary
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    + +
    +
    • +
  • + In the News +
    +

    In the News

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    + + + + + + + + + +
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    NCI’s Clinical and Translational Data Commons Has Launched!
    Explore the NCI Cancer Research Data Commons’s latest portal to find clinical and translational data from NCI-funded studies!
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    NCI Data Science at the 2024 AACR Annual Meeting
    Are you planning to attend this year’s American Association for Cancer Research (AACR) Annual Meeting? Make sure to add these NCI-affiliated data science activities to your schedule!
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    Award-Winning Commitment to Innovation: NCI’s CPTAC and PDC Team Recognized by FedHealthIT
    Celebrate the NCI team that recently received a 2022 FedHealthIT Innovation Award for their commitment to advancing cancer research through work proteomics efforts such as the Proteomic Data Commons.
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    Background

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    Education

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    • Post-Doctoral Fellow, The Scripps Research Institute (La Jolla, CA)
    • Ph.D., Biomedical Sciences, University of California, San Diego
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    Previous Work

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    • Scientific Program Manager/Science Policy, Biorepositories and Biospecimen Branch, NCI’s Division of Cancer Treatment and Diagnosis
    • American Association for the Advancement of Science (AAAS) Science & Technology Policy Fellow, NCI
    • Research Technician, The Salk Institute for Biological Studies
    • Program Manager, American Red Cross (San Diego, CA)
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Follow Us on LinkedIn

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+

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Emily Boja, Ph.D.

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Branch Chief, Supervisory Health Scientist Administrator

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Emily Greenspan, Ph.D.

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Health Science Administrator

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Eric Williams

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Supervisory IT Specialist

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    Current Role

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    As a supervisory IT specialist for NCI’s IT Services and Support Branch, I lead efforts to enhance customer service in support of NCI’s internal information technology needs. In my capacity as the “voice of the customer,” I also focus on building relationships with our divisions to consult and advise on IT services that could assist projects needing technical support. I am currently a member of the NCI Trans Extramural Advisory Group (TEAG), the Informatics and Information Technology Advisory Group (IITAG) and the Information Technology Ambassadors.

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    Background

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    Education

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    • B.A., Urban Studies, University of Maryland
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    Previous Work

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    • Acting Chief, IT Services and Support Branch, NCI CBIIT
    • IT Operations Manager, NCI Center for Bioinformatics and Information Systems and Computer Services (what is now present-day CBIIT)
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    Recent Awards

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    • 2020 NCI Director’s Award, for work with the NCI IT AV/UC Dream Team
    • 2014 NIH Director’s Award, as a member of the Shady Grove Facility and IT Infrastructure Team
    • 2014 NIH Award of Merit, for the NCI CBIIT-OCE Data Center Consolidation Team Leads
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    Federal Staff

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    My Team

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    Doug Hosier

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    + IT Specialist (Systems Analysis) +
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    + IT Services and Support Branch +
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    Paul Von Stein

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    + IT Project Manager +
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Erika M. Kim (Kwon), Ph.D.

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Supervisory Health Science Administrator

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Erin Beck

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Biomedical Informatics Project Manager

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    I lead the NCI Cloud Resources components of the NCI Cancer Research Data Commons (CRDC). Using my informatics background, I work to ensure that the cloud resources are providing researchers a way to access and analyze large data sets in a secure and user-friendly environment.

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  • + Projects +
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    Projects

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    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
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    + Cancer Research Data Commons +
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    + Connects you to the data ecosystem, NCI's primary platform for cancer research. + +
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    Publications

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    Featured Publications

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    Therapeutic Targeting of ATR Yields Durable Regressions in Small Cell Lung Cancers with High Replication Stress. Cancer Cell, 2021.

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    Background

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    Education

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    • M.S., Bioinformatics, The Johns Hopkins University
    • B.S., Bioinformatics & Computational Biology, The University of Maryland, Baltimore County
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    Previous Work

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    • Informatics Support, Axle Informatics (supporting NIH’s National Center for Advancing Translational Sciences [NCATS])
    • Senior Bioinformatics Engineer, J. Craig Venter Institute
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Fatma Onmus

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Clinical Bioinformatician

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    Current Role

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    As a clinical bioinformation for the Clinical and Translational Research Informatics Branch, I’m responsible for the oversight of the CIDC part of the CIMAC-CIDC network (CIDC being the “Cancer Immunologic Data Commons,” while CIMAC stands for “Cancer Immune Monitoring and Analysis Centers”). This network addresses the critical importance of improving the management of cancer patients receiving immunotherapy by identifying biomarkers for optimizing immunotherapeutic strategies. The CIMAC-CIDC network involves a collaborative effort among various stakeholders, such as NCI, Clinical Trial Teams, CIMACs, the Partnership for Accelerating Cancer Therapies collaboration, and Foundation NIH. Together, we can collect, analyze, and share the data from various clinical trials that use analytically validated and standardized platforms.

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    • +
  • + Projects +
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    Projects

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    + + Cloud technology. Polygonal wireframe cloud storage sign with two arrows up and down on dark blue. + +
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    + Cancer Immunologic Data Center +
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    + Enables you to analyze a variety of clinical, specimen, and molecular data for biomarker discovery. + +
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    + + Photo of a doctor sitting next to a younger woman. The doctor is speaking to the woman and the woman is looking at the doctor and smiling. + +
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    + Molecular Analysis for Therapy Choice +
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    + Enrolls patients to determine whether treating cancer based on their genome is effective. + +
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    • +
  • + Publications +
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    Publications

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    View Fatma’s PubMed Summary
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    + +
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    • +
  • + Background +
    +

    Background

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    Education

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    • Graduate Certificate Bioinformatics, University of Maryland Global Campus
    • M.S., Biology, Ege Üniversitesi (Turkey)
    • B.S., Biology, Ege Üniversitesi  (Turkey)
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    +
    +

    Previous Work

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    • Biologist, U.S. Department of Health and Human Services, Food and Drug Administration (FDA)
    • Senior Scientific Computer Engineer, Science Applications International Corporation
    • Bioinformatician, Contractor for Walter Reed Army Institute of Research
    • Research Associate/Lab Manager, J. Craig Venter Institute
    • Supervisor/Project Manager, Gene Logic
    • Associate Scientist, Metrigenix
    • Associate Scientist, Digene Corporation
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    +

    Recent Awards

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    • 2024 FDA CDRH Excellence in Communications and Education Award, for exceptional leadership in advancing Artificial Intelligence (AI) training for reviewers and others interested in AI to help dive consistent understanding communication and collaboration.
    • 2024 FDA CDRH Excellence in Communications and Education Award, for exceptional leadership in advancing Digital Health review training, consistent policy implementation, and cross-Office communication and collaboration.
    • 2022 FDA Commissioner’s Special Citation (Paige Prostate De Novo Review Team), for excellent collaboration and coordination that led to the authorization of the first artificial intelligence-based software in digital pathology
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Freddie L. Pruitt III, Ph.D.

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Health Science Administrator

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  • Center for Biomedical Informatics & Information Technology
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  • Office of Data Sharing
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Staff Directory

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To find a federal staff member, select a branch/office or search by name. 

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+ + Kanakadurga “Durga” Addepalli, Ph.D. + +

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+ Health Scientist (Bioinformatics) +
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+ Data Ecosystems Branch +
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+ + Jill S. Barnholtz-Sloan, Ph.D. + +

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+ CBIIT Acting Director, IDS Associate Director +
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+ Informatics and Data Science Program +
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+ + Heather K. Basehore, Ph.D. + +

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+ Health Science Administrator +
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+ Scientific Policy and Program Branch B +
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+ + Erin Beck + +

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+ Biomedical Informatics Project Manager +
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+ Data Ecosystems Branch +
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+ + Emily Boja, Ph.D. + +

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+ Branch Chief, Supervisory Health Scientist Administrator +
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+ Scientific Policy and Program Branch B +
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+ + Nathan Boyd, Ph.D. + +

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+ Health Science Administrator +
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+ Scientific Policy and Program Branch A +
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+ + Lawrence “Larry” Brem, M.S. + +

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+ Computer Scientist (Configuration Manager, Code 4 Supervisor) +
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+ Digital Services and Solutions Branch +
+ + + + + (240) 276-5276 + +
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+ + Javis Brown + +

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+ IT Specialist (Information Security) +
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+ IT Services and Support Branch +
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+ + Brian Capaldo, Ph.D. + +

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+ Bioinformatics Specialist +
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+ Computational Genomics & Bioinformatics Branch +
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+ + Esmeralda “Emi” Casas-Silva, Ph.D. + +

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+ Health Science Administrator +
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+ Data Ecosystems Branch +
+ + + + + (240) 276-6989 + +
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Granger Sutton, Ph.D.

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Data Scientist

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    Current Role

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    As a data scientist in the Data Ecosystems Branch, I focus on artificial intelligence (AI) and imaging to support the Cancer Research Data Commons (CRDC) and related projects. I also work as a computer scientist, bioinformatician, and computational biologist with research interests in cancer, infectious diseases, biological databases, imaging, AI, cloud applications, genome assembly, pan-genome analysis, and large-scale genomic analysis.

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    Projects

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    + + Stylized image of a brain as viewed from the top. Instead of brain structures the brain is portrayed as a series of interconnected lines and dots. + +
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    + Artificial Intelligence in Medical Imaging +
    +
    + Focuses on both imaging data artificial intelligence-readiness and the curation of harmonized tools/models in a central repository. + +
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    + + Stylized photo of a scientist peering at a computer screen showing different views of a brain image. The doctor is wearing a lab coat, surgical mask, surgical gloves, and surgical cap. To the left of the image is another graphic showing a locked padlock against a background of interconnected lines and dots. + +
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    + Medical Image De-identification Initiative +
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    + Addresses and implements best practices for the protection of patient privacy in clinical image sharing. + +
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    +
    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
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    + Cancer Research Data Commons +
    +
    + Connects you to the data ecosystem, NCI's primary platform for cancer research. + +
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    • +
  • + Publications +
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    Publications

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    View Granger’s PubMed Summary
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    Featured Publications

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    A Pan-genome Method to Determine Core Regions of the Bacillus subtilis and Escherichia coli Genomes. F1000 Research, 2021.

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    Gene and Alternative Splicing Annotation with AIR. Genome Research, 2005.

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    Background

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    Education

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    • Ph.D., Computer Science, University of Maryland, College Park
    • M.S., Computer Engineering, Stanford University
    • B.S., Electrical Engineering, University of Maryland, College Park
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    Previous Work

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    • Bioinformatics Consultant
    • Expert Witness
    • Professor, Informatics, J. Craig Venter Institute
    • Senior Director of Informatics, J. Craig Venter Institute
    • Senior Computational Scientist, J. Craig Venter Institute
    • Principal Scientist/Director, Informatics Research, Celera Genomics
    • Computer Scientist, The Institute for Genomic Research
    • Technical Staff Member, AT&T Bell Labs
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Heather K. Basehore, Ph.D.

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Health Science Administrator

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  • Center for Biomedical Informatics & Information Technology
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  • Office of Data Sharing
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  • Scientific Policy and Program Branch B
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    Current Role

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    As a health science administrator, I apply my background in biomedical sciences and research administration to support the Office of Data Sharing (ODS), serving as a member of the NCI data access committee and providing program support to large projects such as the Childhood Cancer Data Initiative (CCDI). The ODS team coordinates NCI’s approach to the development and implementation of data sharing and public access policies.

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    • +
  • + Projects +
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    Projects

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    + + Childhood cancer patient smiling and talking with her physician. + +
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    + Childhood Cancer Data Initiative +
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    + Develops means to collect and share childhood cancer data to learn from every child with cancer. + +
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    • +
  • + Publications +
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    Publications

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    View Heather’s PubMed Summary
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    Featured Publications

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    Genetic Variation in PADI6-PADI4 on 1p36.13 Is Associated with Common Forms of Human Generalized Epilepsy. Genes, 2021.

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    • +
  • + In the News +
    +

    In the News

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    + + + + + + + + + +
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    Your Guide to the 2023 NIH Data Management and Sharing Policy
    Do you know how the 2023 NIH Data Management and Sharing Policy will impact your work? If you are seeking NCI funding, this blog is for you. We cover the key policy distinctions, implementation changes, and resources to help you navigate the process.
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    Background

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    Education

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    • Ph.D., Integrative Biosciences, The Pennsylvania State University
    • B.S., Chemistry, Mansfield State University
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    Previous Work

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    • Program Coordinator for Research and Development, Department of Veterans Affairs Medical Center, Coatesville, PA
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Heather Creasy

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Biomedical Informatics Project Manager

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    Current Role

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    As a CBIIT biomedical informatics project manager, I ensure that data across the NCI Cancer Research Data Commons (CRDC) adheres to the FAIR (findable, accessible, interoperable, reusable) guiding principles for scientific data management. I lead the CRDC Data Standards Services and Cancer Data Aggregator teams to enable interoperability across CRDC data repositories. In addition, I serve as the CRDC driver project champion and NIH Cloud Platform Interoperability (NCPI) contributor to the Global Alliance for Genomics and Health (GA4GH). In this capacity, I promote GA4GH products and ensure that they are serving real world needs. All of this is with the intent to unlock the power of genomic data to benefit human health.

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    • +
  • + Projects +
    +

    Projects

    + +
    +
    +
    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
    +
    + Cancer Research Data Commons +
    +
    + Connects you to the data ecosystem, NCI's primary platform for cancer research. + +
    +
    +
    + +
    +
    • +
  • + Publications +
    +

    Publications

    + +
    +
    +
    View Heather’s PubMed Summary
    +
    +
    + +

    Featured Publications

    +
    + +
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    + +

    Making Common Fund Data More Findable: Catalyzing a Data Ecosystem. GigaScience, 2022.

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    • +
  • + Background +
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    Background

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    Education

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    • M.S., Molecular Biology, Boston College
    • B.S., Biology, Providence College
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    Previous Work

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    • Lead Bioinformatics Analyst, Institute for Genome Sciences (IGS), University of Maryland School of Medicine
    • Bioinformatics Analyst, The Institute for Genomic Research (TIGR)
    • Senior Research Technician, Division of Molecular Genetics, Boston University School of Medicine
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Staff Directory

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To find a federal staff member, select a branch/office or search by name. 

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+ + Kanakadurga “Durga” Addepalli, Ph.D. + +

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+ Health Scientist (Bioinformatics) +
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+ Data Ecosystems Branch +
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+ + Jill S. Barnholtz-Sloan, Ph.D. + +

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+ CBIIT Acting Director, IDS Associate Director +
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+ Informatics and Data Science Program +
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+ + Heather K. Basehore, Ph.D. + +

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+ Health Science Administrator +
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+ Scientific Policy and Program Branch B +
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+ + Erin Beck + +

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+ Biomedical Informatics Project Manager +
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+ Data Ecosystems Branch +
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+ + Emily Boja, Ph.D. + +

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+ Branch Chief, Supervisory Health Scientist Administrator +
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+ Scientific Policy and Program Branch B +
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+ + Nathan Boyd, Ph.D. + +

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+ Health Science Administrator +
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+ Scientific Policy and Program Branch A +
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+ + Lawrence “Larry” Brem, M.S. + +

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+ Computer Scientist (Configuration Manager, Code 4 Supervisor) +
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+ Digital Services and Solutions Branch +
+ + + + + (240) 276-5276 + +
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+ + Javis Brown + +

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+ IT Specialist (Information Security) +
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+ IT Services and Support Branch +
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+ + Brian Capaldo, Ph.D. + +

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+ Bioinformatics Specialist +
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+ Computational Genomics & Bioinformatics Branch +
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+ + Esmeralda “Emi” Casas-Silva, Ph.D. + +

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+ Health Science Administrator +
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+ Data Ecosystems Branch +
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Ina Felau

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Health Science Administrator

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  • + Current Role +
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    Current Role

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    I support various efforts related to the NCI Cancer Research Data Commons (CRDC). This includes coordinating activities specific to the Data Hub, serving as the central coordinator for all CRDC components, and supporting outreach and communications activities. I also serve as a CRDC liaison to the NIH Cloud Platform Interoperability Team.

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    +
    • +
  • + Projects +
    +

    Projects

    + +
    +
    +
    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
    +
    + Cancer Research Data Commons +
    +
    + Connects you to the data ecosystem, NCI's primary platform for cancer research. + +
    +
    +
    + +
    +
    • +
  • + Publications +
    +

    Publications

    +

    Featured Publications

    +
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    + +

    Whole-genome Characterization of Lung Adenocarcinomas Lacking Alterations in the RTK/RAS/RAF Pathway. Cell Reports, 2021.

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    Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell, 2020.

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    Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data. Cell Systems, 2019.

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    • +
  • + In the News +
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    In the News

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    + + + + + + + + + +
    +
    NCI Data Science at the 2024 AACR Annual Meeting
    Are you planning to attend this year’s American Association for Cancer Research (AACR) Annual Meeting? Make sure to add these NCI-affiliated data science activities to your schedule!
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    Up to $50k in Prizes for AI-Readiness Challenge on NCI Data
    Participate in the upcoming challenge to assess NCI Cancer Research Data Commons' compatibility with AI/ML technologies.
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  • + Background +
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    Background

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    Education

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    • M.S., Biology, Towson University
    • B.S., Biology, Loyola College
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    Previous Work

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    • Genome Data Analysis Network Program Manager, Center for Cancer Genomics Office, NCI
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    Recent Awards

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    • 2020 AACR Team Science Award, for work with The Cancer Genome Atlas (TCGA) Current Project Team to advance and functionalize data generated by the TCGA
    • 2015 NCI Award of Merit, for exceptional and sustained performance in the monitoring and contractual administration of the TCGA Tissue Acquisition Project
    • 2014 NIH Director’s Award, for work with the TCGA Project Team to successful plan, manage, and operate one of the largest cancer genomics projects to date (which is transforming the diagnosis and treatment of patients)
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Follow Us on LinkedIn

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Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

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+

+

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Jane Pollack

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Clinical Bioinformatician

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  • + Current Role +
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    Current Role

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    As a clinical bioinformatician in semantic infrastructure, I’m creating a common entry point for the NCI Cancer Research Data Commons to make content more accessible, as well as incorporating content from the caDSR and EVS. I’m also leveraging my graph database expertise to support the Shared Semantic Infrastructure Services project as well as a project that semi-automatically matches patients to clinical trials using electronic health record data.

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    Projects

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    + + Scientist, sitting in a lab, looking at bar chart displayed on a computer screen. + +
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    + Cancer Data Standards Registry and Repository +
    +
    + Provides access to oncology research, common data elements, and forms. + +
    +
    +
    +
    + + Photo shows a transparent computer screen portraying icons often associated with cloud computing, including uploading and downloading to the cloud, file transfer, and file saving. A person is sitting at the screen with his hands on the keyboard. Small specks of bright lights appear in the background. + +
    +
    + Enterprise Vocabulary Services +
    +
    + Provides terminology content and tools to code, analyze, and share cancer and biomedical research information. + +
    +
    +
    +
    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
    +
    + Cancer Research Data Commons +
    +
    + Connects you to the data ecosystem, NCI's primary platform for cancer research. + +
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    • +
  • + Background +
    +

    Background

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    Education

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    • M.S., Bioinformatics and Computational Biology, University of Minnesota
    • B.S., Mathematics, Minnesota State University, Mankato
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    Previous Work

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    • Senior Research Informaticist with the Center for International Blood and Marrow Transplant Research, National Marrow Donor Program
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Follow Us on LinkedIn

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+ Join Our Community + No +
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+ +
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+

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Janelle Cortner, Ph.D.

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Bioinformatics Project Manager

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    Current Role

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    I oversee OCIO’s Data Management and Analysis Program (DMAP), which aims to build a highly secure, integrated data infrastructure. The goals of this infrastructure are to accelerate the pace of research by streamlining management and analysis of high value scientific data, promoting resource stewardship, lowering barriers to collaboration and secondary data use, and promoting FAIR (Findable, Accessible, Interoperable, and Reusable) standards.

    + +

    Towards these goals, I work with intramural scientists to identify and develop broadly useful data management and analysis platforms (e.g., the NIH Integrated Data Analysis Portal; the NCI HALO Digital Pathology; and 2D Imaging Resource) and integrate high-impact data resources and new capabilities into the data environment.

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    Background

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    Education

    + +
    • Ph.D., Cellular and Molecular Biology, University of Wisconsin-Madison
    • B.S., Biology, B.S., Chemistry, University of Washington, Seattle
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    Previous Work

    + +
    • Project Manager, NCI Division of Basic Sciences and Center for Cancer Research
    + +
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    Recent Awards

    + +
    • 2021 NIH Director’s Award, for support of the NCATS National COVID Cohort Collaborative (N3C) Team
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  • + My Team +
    +

    Federal Staff

    +

    My Team

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    +
    +

    Ryan Hash

    +
    + Program Analyst +
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    + IT Services and Support Branch +
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Javis Brown

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IT Specialist (Information Security)

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    I am responsible for defining goals that must be met on major program issues. I am also responsible for recommending and implementing courses of action for various administrative areas of the organization, such as budget management, service and equipment procurement, personnel and workforce utilization, contract negotiation, and space management, effectively managing and developing the Service Desk Team. I am a member of the “NCI Gradual Return to On-site Work” working group.

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    Background

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    Education

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    • B.S., Finance, Liberty University
    • U.S. Army certificates of completion: Primary Leadership Development Course, Basic Non-Commissioned Officers Course, Advanced Non-Commissioned Officers Course, and the First Sergeant Course
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    +
    +

    Previous Work

    + +
    • U.S. Army
      • 194th Armored Brigade
      • Armor Center, Ft. Knox, KY
      • U.S. Army Recruiting Command
      • Retired with rank of First Sergeant
    + +
    +
    +

    Recent Awards

    + +
    • 2020 NCI Director’s Award, as a member of the NCI IT Onsite and Remote Computer Deployment Brigade
    • Meritorious Service Medal (x3)
    • Army Commendation Medal (x8)
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Follow Us on LinkedIn

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+

Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

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+
+ Join Our Community + No +
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+

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Jay Spencer

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IT Specialist (Information Security)

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    Current Role

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    As a software and systems lifecycle professional, I lead the remediation of information security vulnerabilities, review security incidents for completeness and accuracy, perform comprehensive and in-depth risk and vulnerability analysis of systems, review system designs from IT security perspectives, and propose well-documented changes.

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    Background

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    Education

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    • B.S., Computer Science, Excelsior College
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Follow Us on LinkedIn

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+

Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

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+
+ Join Our Community + No +
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Jennifer Kwok

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Supervisory IT Specialist

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Follow Us on LinkedIn

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+

Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

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+
+ Join Our Community + No +
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Jill S. Barnholtz-Sloan, Ph.D.

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CBIIT Acting Director, IDS Associate Director

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Follow Us on LinkedIn

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+

Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

+
+
+ Join Our Community + No +
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+

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Jim Racheff, M.S., M.B.A.

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Branch Chief

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    Current Role

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    As the chief for NCI’s IT Services and Support Branch, I lead efforts to ensure that NCI’s information and technology infrastructure and services reliably empower the scientific, business, and administrative needs across the entire NCI enterprise and champion the best and highest use of NCI IT capabilities in support of the NCI mission. We work across stakeholders to build relationships that inform our approaches as we provide services that are reliable and resilient while being responsive to the evolving requirements of a complex research organization.

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  • + Background +
    +

    Background

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    Education

    + +
    • M.B.A., Strategy and Organizational Behavior, Hood College
    • M.S., Computer Science (Engineering and Project Management), Hood College
    • B.S., Computer Science, University of Maryland, College Park
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    +
    +

    Previous Work

    + +
    • President, Data Management Services, Inc.
    • Principal Manager, Computer and Statistical Services, Frederick National Laboratory for Cancer Research
    + +
    +
    +

    Recent Awards

    + +
    • 2019 Outstanding Plan of the Year as Chair for Livable Frederick Strategic Master Plan, American Planning Association
    • 2012 Doctorate of Humane Letters (Honoris Causa), Hood College
    • 2011 Entrepreneur of the Year, Entrepreneur Council
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  • + My Team +
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    Federal Staff

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    My Team

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    Stephanie Halling

    +
    + Supervisory IT Specialist +
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    + IT Services and Support Branch +
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    Eric Williams

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    + Supervisory IT Specialist +
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    + IT Services and Support Branch +
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    Cliff Wong

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    + Computer Scientist +
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    + IT Services and Support Branch +
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    • +
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Follow Us on LinkedIn

+
+

Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

+
+
+ Join Our Community + No +
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+

+

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Joe Flores-Toro, Ph.D.

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Health Scientist Administrator

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  • Center for Biomedical Informatics & Information Technology
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  • Office of Data Sharing
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  • Scientific Policy and Program Branch A
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Follow Us on LinkedIn

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+

Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

+
+
+ Join Our Community + No +
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+

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Joe Longo

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Program Analyst

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    Current Role

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    As a program analyst at CBIIT, I am responsible for activities involving the Portfolio Management and Operations Support Program. I’m also the service manager for CBIIT staff salaries, awards, and training support.

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    • +
  • + Background +
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    Background

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    Education

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    • B.S., Human Resource Management, Columbia Southern University
    • U.S. Army certificates of completion: Primary Leadership Development Course, Basic Non-Commissioned Officers Course, Advanced Non-Commissioned Officers Course, Equal Opportunity Leaders Course, and Instructor Training Course
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    Previous Work

    + +
    • U.S. Army
      • 1st Infantry Division, Vilseck, Germany
      • 5th Squadron, 15th Cavalry Regiment, Ft. Knox, KY
      • U.S. Army Recruiting Command
      • Retired with the rank of Master Sergeant
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    Recent Awards

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    • Meritorious Service Medals (x2)
    • Army Commendation Medals (x5)
    • Army Achievement Medals (x6)
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Follow Us on LinkedIn

+
+

Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

+
+
+ Join Our Community + No +
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+ +
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+

+

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Kanakadurga “Durga” Addepalli, Ph.D.

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Health Scientist (Bioinformatics)

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    Current Role

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    As a biomedical informatics scientist, I provide informatics and scientific expertise to the intramural and extramural cancer research communities. I lead the Cancer Data Service by overseeing and managing efforts focused on cancer data governance and management for cloud platforms supporting the NCI Cancer Research Data Commons. I am responsible for programs and projects focused on FAIR (Findable, Accessible, Interoperable, and Reusable) data management, which include data storage, sharing, and analysis on high-performance computing or the cloud. I also manage NCI’s Nanotechnology research data-sharing portal, caNanoLab, which is designed to facilitate information sharing across the international biomedical nanotechnology research community to expedite and validate the use of nanotechnology in biomedicine. I oversee the NCI Containers and Workflows Interest Group (CWIG), and I manage a webinar series that invites researchers and data scientists to discuss the latest advancements in cloud computing and container technologies, workflow, tools, and packages.

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    • +
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    Projects

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    + + Stylized image of a three-dimensional image representing a high-tech cell. The structure is fully transparent and set against a multicolored background. + +
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    + cancer Nanotechnology Laboratory +
    +
    + Facilitates information sharing across the biomedical nanotechnology research community. + +
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    +
    +
    + + Stylized image of a cloud showing repositories of data represented by circles with small icons hovering over top. The repositories include canine, imaging, genomic, and other types of data. + +
    +
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    View Durga’s PubMed Summary
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    Featured Publications

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    Enabling Precision Medicine via Standard Communication of HTS Provenance, Analysis, and Results. PLoS Biology, 2018.

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    Resources for Interpreting Variants in Precision Genomic Oncology Applications. Frontiers in Oncology, 2017.

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    AACR Annual Meeting 2022: NCI Data Science Event Sessions and Posters
    If you’re attending the 2022 American Association for Cancer Research Annual Meeting (either in person or virtual), don’t miss these data science sessions, poster presentations, and the NCI exhibit booth, where you can hear more about our programs and activities!
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    Learn More About the Cloud and Container Technology Driving Cancer Data Science at the Containers and Workflow Interest Group (CWIG) Webinars
    The relaunched monthly CWIG webinar series will invite researchers from across the globe to discuss the latest advancements in cloud computing technologies, workflow, tools, and packages.
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    Background

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    Education

    + +
    • Ph.D., Computational Biology and Bioinformatics, George Mason University
    • M.S., Biochemistry, University of Mumbai
    • Postgraduate Diploma, Bioinformatics, Savitribai Phule University
    + +
    +
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    Previous Work

    + +
    • Senior Biomedical Informatics Specialist, NCI Cancer Research Data Commons (CRDC) Cloud Resources
    • Senior Biomedical Informatics Specialist, dbGaP Backlog, CBIIT Office of Data Sharing
    • Senior Bioinformatics Business Analyst and Requirements Lead, High-Performance Computing (HPC) Data Management Environment
    • Bioinformatics Analyst II, NCI Center for Cancer Research Collaborative Bioinformatics Resource
    • Bioinformatics Business Analyst, NCI Cancer Therapy Evaluation Program
    • Bioinformatics System Analyst, NCICB (what is now present-day CBIIT)
    • Bioinformatics Executive, Dr. Reddy’s Labs, India
    • Bioinformatics Officer, Rajco Infotech, India
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    As the lead of CBIIT’s Security Compliance Team, my teams and I are dedicated to information technology and cybersecurity. A layered approach is applied to security framework services, including application of protocols, policies, and implementation of compliance procedures throughout governance and assessments. I’m also an information security officer (ISO) alternate, so my responsibilities include information assurance for enterprise systems (under the Federal Information Security Management Act, or FISMA), security assessment and authorization, policy, compliance, and oversight of testing protocols, continuous monitoring, and quality assurance. I hold a ISC2 Certified Secure Software Lifecycle Professional (CSSLP) certification, as well as a SANS Institute’s Global Information Assurance Certification (GIAC) Security Essentials (GSEC) Gold certification. I am also a certified Contracting Officer’s Representative level two (COR II) and Federal Acquisition Certification Program level two (FAC II).

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Krish Seshadri

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Senior Cloud Architect

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    As the senior cloud architect/computer scientist of CBIIT’s Digital Services and Solutions Branch, I am responsible for duties as they relate to the cloud—this includes providing technical direction, architecture consultation, containerization, infrastructure automation, migration, optimization, and cost savings. I am the system owner for the CBIIT cloud platform operated in Amazon Web Services (AWS), Google Cloud Platforms. I lead the cloud team to provide the cloud engineering activities, as well as the operations and maintenance of the CBIIT cloud infrastructure.

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    Publications

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    Featured Publication

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    Artificial Intelligence-based Tumor Segmentation in Mouse Models of Lung Adenocarcinoma. Journal of Pathology Informatics, 2022.

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    Background

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    Education

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    • M.S., Computer Application, University of Madras, Chennai, India
    • B.S., Physics, University of Madras, Chennai, India
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    Previous Work

    + +
    • Senior Director, Cloud Projects, Karthik Consulting Inc.
    • Senior Systems Manager, Cloud Projects, GDIT Inc.
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Lawrence “Larry” Brem, M.S.

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Computer Scientist (Configuration Manager, Code 4 Supervisor)

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Lyubov Remennik, Ph.D., M.D.

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    I lead a team that manages the unified communications (i.e., phone services, teleconferencing services) and conference room support projects at NCI. My team and I work to improve these technologies, and we always provide professional support to the community in order to help researchers achieve NCI’s mission.

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    • 2020 NCI Director’s Award, for work with the NCI IT AV/UC Dream Team
    • 2020 NCI Director’s Award, as a member of the NCI IT Onsite and Remote Computer Deployment Brigade
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Scientific Program Analyst

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    Current Role

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    I serve as a member of the Informatics and Data Science (IDS) Leadership team, supporting our Associate Director in managing the strategic and financial plans for the IDS program. In this capacity, I advise on the systems, policies, and processes needed to allocate the necessary resources for IDS activities. Working with my colleagues, we discuss and problem solve critical issues that shape IDS program management needs and strategic direction.

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    Background

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    Education

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    • B.S., Biology, Hood College, Frederick, Maryland
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Find training resources, opportunities to collaborate, advice from NCI data science experts, and ways to network and engage with the cancer data science community on our NCI Cancer Data Science page!

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