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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>McEntyre J, Ostell J, editors. The NCBI Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2002-. </p></div><div class="bk_msg_box bk_bttm_mrgn clearfix bk_noprnt"><div class="iconblock clearfix"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook2e/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook2e-lrg.png" alt="Cover" height="100px" width="80px" /></a><div class="icnblk_cntnt"><ul class="messages"><li class="info icon"><span class="icon"><a href="/books/n/handbook2e/">See "The NCBI Handbook, 2nd Edition"</a></span></li></ul></div></div></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" alt="Cover of The NCBI Handbook" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>The NCBI Handbook [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK21103_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK21103_dtls__"><div>McEntyre J, Ostell J, editors.</div><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2002-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/handbook/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/handbook/ch9/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/handbook/ch11/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK21103_"><span class="label">Chapter 10</span><span class="title" itemprop="name">The SKY/CGH Database for Spectral Karyotyping and Comparative Genomic Hybridization Data</span></h1><p class="contrib-group"><span itemprop="author">Turid Knutsen</span>, <span itemprop="author">Vasuki Gobu</span>, <span itemprop="author">Rodger Knaus</span>, <span itemprop="author">Thomas Ried</span>, and <span itemprop="author">Karl Sirotkin</span>.</p><a data-jig="ncbitoggler" href="#__NBK21103_ai__" style="border:0;text-decoration:none">Author Information and Affiliations</a><div style="display:none" class="ui-widget" id="__NBK21103_ai__"><p class="contrib-group"><h4>Authors</h4><span itemprop="author">Turid Knutsen</span>,<sup>1</sup> <span itemprop="author">Vasuki Gobu</span>,<sup>2</sup> <span itemprop="author">Rodger Knaus</span>,<sup>2</sup> <span itemprop="author">Thomas Ried</span>,<sup>1</sup> and <span itemprop="author">Karl Sirotkin</span><sup>2</sup>.</p><h4>Affiliations</h4><div class="affiliation"><sup>1</sup>
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National Cancer Institute (NCI)
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</div><div class="affiliation"><sup>2</sup>
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National Center for Biotechnology Information (NCBI)
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</div></div><p class="small">Created: <span itemprop="datePublished">October 9, 2002</span>; Last Update: <span itemprop="dateModified">August 13, 2003</span>.</p><p><em>Estimated reading time: 7 minutes</em></p></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="_abs_rndgid_" itemprop="description"><h2 id="__abs_rndgid__">Summary</h2><p>Spectral Karyotyping (<a href="/books/n/handbook/A1237/#app164">SKY</a>) (<a class="bk_pop" href="#A524">1</a>–<a class="bk_pop" href="#A530">7</a>) and Comparative Genomic Hybidization (<a href="/books/n/handbook/A1237/#app24">CGH</a>) (<a class="bk_pop" href="#A531">8</a>–<a class="bk_pop" href="#A534">11</a>) are complementary fluorescent molecular cytogenetic techniques that have revolutionized the detection of chromosomal abnormalities. <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a> permits the simultaneous visualization of all human or mouse chromosomes in a different color, facilitating the detection of chromosomal translocations and rearrangements (<a class="figpopup" href="/books/NBK21103/figure/A499/?report=objectonly" target="object" rid-figpopup="figA499" rid-ob="figobA499">Figure 1</a>). <a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> uses the hybridization of differentially labeled tumor and reference <a class="def" href="/books/n/handbook/A1237/def-item/app37/">DNA</a> to generate a map of DNA copy number changes in tumor genomes.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA499" co-legend-rid="figlgndA499"><a href="/books/NBK21103/figure/A499/?report=objectonly" target="object" title="Figure 1" class="img_link icnblk_img figpopup" rid-figpopup="figA499" rid-ob="figobA499"><img class="small-thumb" src="/books/NBK21103/bin/ch10f1.gif" src-large="/books/NBK21103/bin/ch10f1.jpg" alt="Figure 1. A metaphase spread after SKY hybridization." /></a><div class="icnblk_cntnt" id="figlgndA499"><h4 id="A499"><a href="/books/NBK21103/figure/A499/?report=objectonly" target="object" rid-ob="figobA499">Figure 1</a></h4><p class="float-caption no_bottom_margin">A metaphase spread after SKY hybridization. The RGB image demonstrates cytogenetic abnormalities in a cell from a secondary leukemia cell line. <i>Arrows</i> indicate some of the many chromosomal translocations in this cell line. </p></div></div><p>The goal of the <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a>/<a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> database is to allow investigators to submit and analyze both clinical and research (e.g., cell lines) SKY and CGH data. The database is growing and currently has a total of about 700 datasets, some of which are being held private until published. Several hundred labs around the world use this technique, with many more looking at the data they generate. Submitters can enter data from their own cases in either of two formats, public or private; the public data is generally that which has already been published, whereas the private data can be viewed only by the submitters, who can transfer it to the public format at their discretion. The results are stored under the name of the submitter and are listed according to case number. The <a href="/sky/" ref="pagearea=abstract&targetsite=external&targetcat=link&targettype=uri">homepage</a> includes a basic description of SKY and CGH techniques and provides links to a more detailed explanation and relevant literature.</p></div><div id="A500"><h2 id="_A500_">Database Content</h2><p>Detailed information on how to submit data either to the <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a> or <a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> sectors of the database can be found through links on the <a href="/sky/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">homepage</a>. What follows is a brief outline.</p><div id="A501"><h3>Spectral Karyotyping</h3><p>The submitter enters the written <a href="/books/n/handbook/A1237/#app91">karyotype</a>, the number of normal and abnormal copies for each chromosome, and the number of cells for each clone. Each abnormal chromosome segment is then described by typing in the beginning and ending bands, starting from the top of the chromosome (<a class="figpopup" href="/books/NBK21103/figure/A502/?report=objectonly" target="object" rid-figpopup="figA502" rid-ob="figobA502">Figure 2</a>); the computer then builds a colored <a href="/books/n/handbook/A1237/#app203">ideogram</a> of this chromosome and eventually a full <a class="def" href="/books/n/handbook/A1237/def-item/app91/">karyotype</a> (<a href="/books/n/handbook/A1237/#app165">SKYGRAM</a>) with each normal and abnormal chromosome displayed in its unique <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a> classification color, with band overlay (<a class="figpopup" href="/books/NBK21103/figure/A503/?report=objectonly" target="object" rid-figpopup="figA503" rid-ob="figobA503">Figure 3</a>). Each breakpoint submitted is automatically linked by a button marked <a href="/books/n/handbook/A1237/#app56">FISH</a> to the human <a class="def" href="/books/n/handbook/A1237/def-item/app99/">Map Viewer</a> (<a class="figpopup" href="/books/NBK21103/figure/A504/?report=objectonly" target="object" rid-figpopup="figA504" rid-ob="figobA504">Figure 4</a>; <a href="/books/n/handbook/ch20/">Chapter 20</a>), which provides a list of genes at that site and available <a class="def" href="/books/n/handbook/A1237/def-item/app56/">FISH</a> clones for that breakpoint.
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</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA502" co-legend-rid="figlgndA502"><a href="/books/NBK21103/figure/A502/?report=objectonly" target="object" title="Figure 2" class="img_link icnblk_img figpopup" rid-figpopup="figA502" rid-ob="figobA502"><img class="small-thumb" src="/books/NBK21103/bin/ch10f2.gif" src-large="/books/NBK21103/bin/ch10f2.jpg" alt="Figure 2. SKY data entry form for two different abnormal chromosomes, built segment by segment, for the SKYGRAM image." /></a><div class="icnblk_cntnt" id="figlgndA502"><h4 id="A502"><a href="/books/NBK21103/figure/A502/?report=objectonly" target="object" rid-ob="figobA502">Figure 2</a></h4><p class="float-caption no_bottom_margin">SKY data entry form for two different abnormal chromosomes, built segment by segment, for the SKYGRAM image. Chromosome images on the <i>left</i> are the result of entering the start (<i>top</i>) and stop (<i>bottom</i>) band for each segment. </p></div></div><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA503" co-legend-rid="figlgndA503"><a href="/books/NBK21103/figure/A503/?report=objectonly" target="object" title="Figure 3" class="img_link icnblk_img figpopup" rid-figpopup="figA503" rid-ob="figobA503"><img class="small-thumb" src="/books/NBK21103/bin/ch10f3.gif" src-large="/books/NBK21103/bin/ch10f3.jpg" alt="Figure 3. A SKYGRAM from the SKY/CGH database demonstrating cytogenetic abnormalities in a transitional cell carcinoma of the bladder cell line." /></a><div class="icnblk_cntnt" id="figlgndA503"><h4 id="A503"><a href="/books/NBK21103/figure/A503/?report=objectonly" target="object" rid-ob="figobA503">Figure 3</a></h4><p class="float-caption no_bottom_margin">A SKYGRAM from the SKY/CGH database demonstrating cytogenetic abnormalities in a transitional cell carcinoma of the bladder cell line. The written karyotype and a one-line case summary are also provided. </p></div></div><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA504" co-legend-rid="figlgndA504"><a href="/books/NBK21103/figure/A504/?report=objectonly" target="object" title="Figure 4" class="img_link icnblk_img figpopup" rid-figpopup="figA504" rid-ob="figobA504"><img class="small-thumb" src="/books/NBK21103/bin/ch10f4.gif" src-large="/books/NBK21103/bin/ch10f4.jpg" alt="Figure 4. Map Viewer image depicting the information on genes, clones, FISH clones, map sequences, and STSs for a specific chromosomal breakpoint (5q13) identified in a SKYGRAM image." /></a><div class="icnblk_cntnt" id="figlgndA504"><h4 id="A504"><a href="/books/NBK21103/figure/A504/?report=objectonly" target="object" rid-ob="figobA504">Figure 4</a></h4><p class="float-caption no_bottom_margin">Map Viewer image depicting the information on genes, clones, FISH clones, map sequences, and STSs for a specific chromosomal breakpoint (5q13) identified in a SKYGRAM image. </p></div></div></div><div id="A505"><h3>Comparative Genomic Hybridization</h3><p>The <a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> database displays gains, losses, and amplification of chromosomes and chromosome segments. The data are entered either by hand or automatically from various CGH software programs. In the manual format, the submitter enters the band information for each affected chromosome, describing the start band and stop band for each gain or loss, and the computer program displays the final <a class="def" href="/books/n/handbook/A1237/def-item/app91/">karyotype</a> with vertical bars to the left or right of each chromosome, indicating loss or gain, respectively (<a class="figpopup" href="/books/NBK21103/figure/A506/?report=objectonly" target="object" rid-figpopup="figA506" rid-ob="figobA506">Figure 5</a>).
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</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA506" co-legend-rid="figlgndA506"><a href="/books/NBK21103/figure/A506/?report=objectonly" target="object" title="Figure 5" class="img_link icnblk_img figpopup" rid-figpopup="figA506" rid-ob="figobA506"><img class="small-thumb" src="/books/NBK21103/bin/ch10f5.gif" src-large="/books/NBK21103/bin/ch10f5.jpg" alt="Figure 5. A CGH profile from the SKY/CGH database demonstrating copy number gains and losses in a tumor cell line established from a metastatic lymph node in von Hippel-Lindau renal cell carcinoma." /></a><div class="icnblk_cntnt" id="figlgndA506"><h4 id="A506"><a href="/books/NBK21103/figure/A506/?report=objectonly" target="object" rid-ob="figobA506">Figure 5</a></h4><p class="float-caption no_bottom_margin">A CGH profile from the SKY/CGH database demonstrating copy number gains and losses in a tumor cell line established from a metastatic lymph node in von Hippel-Lindau renal cell carcinoma. </p></div></div></div><div id="A507"><h3>Case Information</h3><p>Clinical data submitted include case identification, World Health Organization (<a class="def" href="/books/n/handbook/A1237/def-item/app196/">WHO</a>) disease classification code, diagnosis, organ, tumor type, and disease stage. To obtain the correct classification code, a link is provided to the <a class="def" href="/books/n/handbook/A1237/def-item/app118/">NCI</a>'s <a href="/books/n/handbook/A1237/#app105">Metathesaurus</a>
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<sup>TM</sup>
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<a href="http://ncievs.nci.nih.gov/NCI-Metaphrase.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">site</a>, which includes, among its many systems, the codes developed by the WHO and NCI, and published as the International Classification of Diseases, 3rd edition (<a class="def" href="/books/n/handbook/A1237/def-item/app79/">ICD-O-3</a>).</p></div><div id="A508"><h3>Reference Information</h3><p>The references for the published cases are entered into the Case Information page and are linked to their abstracts in <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>.</p></div><div id="A509"><h3>Tools for Data Entry</h3><div id="A510"><h4>SKYIN</h4><p>A colored <a class="def" href="/books/n/handbook/A1237/def-item/app91/">karyotype</a> with band overlay is presented to the submitter, who then builds each aberrant chromosome by cutting and pasting (by clicking with the mouse at appropriate breakpoints) (<a class="figpopup" href="/books/NBK21103/figure/A511/?report=objectonly" target="object" rid-figpopup="figA511" rid-ob="figobA511">Figure 6</a>). Each aberrant chromosome is then inserted into the full karyotype, which is displayed as a <a class="def" href="/books/n/handbook/A1237/def-item/app165/">SKYGRAM</a>.
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</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA511" co-legend-rid="figlgndA511"><a href="/books/NBK21103/figure/A511/?report=objectonly" target="object" title="Figure 6" class="img_link icnblk_img figpopup" rid-figpopup="figA511" rid-ob="figobA511"><img class="small-thumb" src="/books/NBK21103/bin/ch10f6.gif" src-large="/books/NBK21103/bin/ch10f6.jpg" alt="Figure 6. SKYIN format." /></a><div class="icnblk_cntnt" id="figlgndA511"><h4 id="A511"><a href="/books/NBK21103/figure/A511/?report=objectonly" target="object" rid-ob="figobA511">Figure 6</a></h4><p class="float-caption no_bottom_margin">SKYIN format. Clicking on a chromosome brings up that chromosome with band overlay. Using the cursor, the operator cuts and pastes together each abnormal chromosome. The abnormal chromosome shown is a combination of chromosomes 10, 16, and 22. <i>Inset,</i> <a href="/books/NBK21103/figure/A511/?report=objectonly" target="object" rid-ob="figobA511">(more...)</a></p></div></div></div><div id="A512"><h4>Karyotype Parser</h4><p>To speed up the entry of cytogenetic data into the database, <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> has built a computer program to automatically read short-form karyotypes, extract the information therein, and insert it into the <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a> database (<a class="figpopup" href="/books/NBK21103/figure/A513/?report=objectonly" target="object" rid-figpopup="figA513" rid-ob="figobA513">Figure 7</a>). Karyotypes are written according to specific rules described in <i>An International System for Human Cytogenetic Nomenclature (1995)</i> (<a class="bk_pop" href="#A535">12</a>). Using these rules, the parser (1) breaks the <a class="def" href="/books/n/handbook/A1237/def-item/app91/">karyotype</a> into small syntactic components, (2) assembles information from these components into an information structure in computer memory, (3) transforms this information into the formats required for an application, and (4) uses the information in the application, i.e., inserts it into the database. To accomplish this, the syntactic parser first extracts the information out of each piece of the input; the pieces are then put directly into a tree structure that represents karyotype semantics. For insertion into the SKY database, the karyotype information is transformed into <a class="def" href="/books/n/handbook/A1237/def-item/app5/">ASN.1</a> structures that reflect the design of the database.
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</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figA513" co-legend-rid="figlgndA513"><a href="/books/NBK21103/figure/A513/?report=objectonly" target="object" title="Figure 7" class="img_link icnblk_img figpopup" rid-figpopup="figA513" rid-ob="figobA513"><img class="small-thumb" src="/books/NBK21103/bin/ch10f7.gif" src-large="/books/NBK21103/bin/ch10f7.jpg" alt="Figure 7. Karyotype Parser." /></a><div class="icnblk_cntnt" id="figlgndA513"><h4 id="A513"><a href="/books/NBK21103/figure/A513/?report=objectonly" target="object" rid-ob="figobA513">Figure 7</a></h4><p class="float-caption no_bottom_margin">Karyotype Parser. The short-form written karyotype, entered in the karyotype field in (<i>a</i>), has been converted into a modified long-form karyotype (<i>b</i>), which describes each abnormal chromosome from <i>top</i> to <i>bottom</i>. Both short and long terms use standardized <a href="/books/NBK21103/figure/A513/?report=objectonly" target="object" rid-ob="figobA513">(more...)</a></p></div></div></div><div id="A514"><h4>NCI Metathesaurus</h4><p>Data submitters must use the same terminology for diagnosis (morphology) and organ site (topography) to permit comparison or combination of the data in the <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a>/<a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> database. From the many different disease classification systems, the <i>International Classification of Diseases for Oncology</i>, 3rd edition (<a class="def" href="/books/n/handbook/A1237/def-item/app79/">ICD-O-3</a>)(<a class="bk_pop" href="#A536">13</a>) was selected as the database's standard. It contains a morphology tree and a topography tree. In most cases, the submitter must select one term from each tree to fully classify a case. To find and select the correct ICD-O-3 morphology and topography terms, the user is referred to <a href="http://ncievs.nci.nih.gov/NCI-Metaphrase.html" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">NCI Metathesaurus</a>, a comprehensive biomedical terminology database, produced by the NCI Center for Bioinformatics Enterprise Vocabulary Service. This tool facilitates mapping concepts from one vocabulary to other standard vocabularies.</p></div></div></div><div id="A515"><h2 id="_A515_">Data Analysis: Query Tools</h2><div id="A516"><h3>Quick Search Format</h3><p>Quick Search can be found at the top of the <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a>/<a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> <a href="/sky/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">homepage</a> and can be used for several types of information in the database; these are defined in Searchable Topics in the <a href="/sky/help.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Help</a> section. Topics include cytogenetic information (whole chromosome, chromosome arm, or chromosome breakpoint), submitter name, case name, cell line by name, diagnosis, site of disease, treatment, hereditary disorders, mouse strain, and <a class="def" href="/books/n/handbook/A1237/def-item/app65/">genotype</a>. One or more terms can be entered, and there are options to search SKY alone, CGH alone, SKY AND CGH, or the default, SKY OR CGH.</p><p>The query results page displays information on all relevant cases, clones, and cells, along with details of <a class="def" href="/books/n/handbook/A1237/def-item/app164/">SKY</a> and/or <a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> studies and clinical information for each case.</p></div><div id="A517"><h3>Advanced Search Format</h3><p>All of the public clinical and cytogenetic information can be searched. This format is currently under development.</p></div><div id="A518"><h3>The CGH Case Comparison Tool</h3><p>This <a href="/sky/webcghdrawing.cgi" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">tool</a> compares and summarizes the <a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> profiles from multiple cases on one <a class="def" href="/books/n/handbook/A1237/def-item/app203/">ideogram</a>. There are numerous criteria that can be used for comparison, such as diagnosis, tumor site, mouse strain, and gain or loss of specific chromosomes, chromosome arms, or chromosome bands.</p></div></div><div id="A519"><h2 id="_A519_">Data Integration</h2><div id="A520"><h3>Integration with the NCBI Map Viewer</h3><p>All chromosomal bands, including breakpoints involved in chromosomal abnormalities, are linked to the <a class="def" href="/books/n/handbook/A1237/def-item/app99/">Map Viewer</a> database (<a class="figpopup" href="/books/NBK21103/figure/A504/?report=objectonly" target="object" rid-figpopup="figA504" rid-ob="figobA504">Figure 4</a> ; see also <a href="/books/n/handbook/ch20/">Chapter 20</a>) The <a href="/mapview" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Map Viewer</a> provides graphical displays of features on <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a>'s assembly of human genomic sequence data as well as cytogenetic, genetic, physical, and radiation hybrid maps. Map features that can be seen along the sequence include NCBI contigs, the <a class="def" href="/books/n/handbook/A1237/def-item/app6/">BAC</a> <a href="/books/n/handbook/A1237/#app182">tiling path</a>, and the location of genes, STSs, <a class="def" href="/books/n/handbook/A1237/def-item/app56/">FISH</a> mapped clones, ESTs, <a href="/books/n/handbook/A1237/#app64">GenomeScan</a> models, and variation (SNPs; see <a href="/books/n/handbook/ch5/">Chapter 5</a>).</p></div><div id="A521"><h3>SKY/CGH Database Links</h3><p>Links are provided to related Web sites including: chromosome databases (e.g., the Mitelman database); other <a class="def" href="/books/n/handbook/A1237/def-item/app118/">NCI</a> (e.g., <a href="/books/n/handbook/A1237/#app23">CGAP</a> and <a href="/books/n/handbook/A1237/#app17">CCAP</a>) and <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> [e.g., the <a class="def" href="/books/n/handbook/A1237/def-item/app99/">Map Viewer</a> (<a href="/books/n/handbook/ch20/">Chapter 20</a>), <a class="def" href="/books/n/handbook/A1237/def-item/app97/">Entrez Gene</a> (<a href="/books/n/handbook/ch19/">Chapter 19</a>) resources; and <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> (<a href="/books/n/handbook/ch2/">Chapter 2</a>)] sites; The Jackson Laboratory; and several other <a class="def" href="/books/n/handbook/A1237/def-item/app24/">CGH</a> sites.</p></div></div><div id="A522"><h2 id="_A522_">Contributors</h2><p><b><a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a>:</b> Karl Sirotkin, Vasuki Gobu, Rodger Knaus, Joel Plotkin, Carolyn Shenmen, and Jim Ostell</p><p><b><a class="def" href="/books/n/handbook/A1237/def-item/app118/">NCI</a>:</b> Turid Knutsen, Hesed Padilla-Nash, Meena Augustus, Evelin Schröck, Ilan R. Kirsch, Susan Greenhut, James Kriebel, and Thomas Ried</p></div><div id="A523"><h2 id="_A523_">References</h2><dl class="temp-labeled-list"><dt>1.</dt><dd><div class="bk_ref" id="A524">Schröck E , du Manoir S , Veldman T , Schoell B , Wienberg J , Ferguson-Smith MA , Ning Y , Ledbetter DH , Bar-Am I , Soenksen D , Garini Y , Ried T . Multicolor spectral karyotyping of human chromosomes. <span><span class="ref-journal">Science. </span>1996;<span class="ref-vol">273</span>:494–497.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/8662537" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 8662537</span></a>]</div></dd><dt>2.</dt><dd><div class="bk_ref" id="A525">Liyanage M , Coleman A , du Manoir S , Veldman T , McCormack S , Dickson RB , Barlow C , Wynshaw-Boris A , Janz S , Wienberg J , Ferguson-Smith MA , Schröck E , Ried T . Multicolour spectral karyotyping of mouse chromosomes. <span><span class="ref-journal">Nat Genet. </span>1996;<span class="ref-vol">14</span>:312–315.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/8896561" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 8896561</span></a>]</div></dd><dt>3.</dt><dd><div class="bk_ref" id="A526">Ried T , Liyanage M , du Manoir S , Heselmeyer K , Auer G , Macville M , Schröck E . Tumor cytogenetics revisited: comparative genomic hybridization and spectral karyotyping. <span><span class="ref-journal">J Mol Med. </span>1997;<span class="ref-vol">75</span>:801–814.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/9428610" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 9428610</span></a>]</div></dd><dt>4.</dt><dd><div class="bk_ref" id="A527">Weaver ZA , McCormack SJ , Liyanage M , du Manoir S , Coleman A , Schröck E , Dickson RB , Ried T . A recurring pattern of chromosomal aberrations in mammary gland tumors of MMTV–c-myc transgenic mice. <span><span class="ref-journal">Genes Chromosomes Cancer. </span>1999;<span class="ref-vol">25</span>:251–260.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/10379871" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 10379871</span></a>]</div></dd><dt>5.</dt><dd><div class="bk_ref" id="A528">Knutsen T , Ried T . SKY: a comprehensive diagnostic and research tool. A review of the first 300 published cases. <span><span class="ref-journal">J Assoc Genet Technol. </span>2000;<span class="ref-vol">26</span>:3–15.</span></div></dd><dt>6.</dt><dd><div class="bk_ref" id="A529">Padilla-Nash HM , Heselmeyer-Haddad K , Wangsa D , Zhang H , Ghadimi BM , Macville M , Augustus M , Schröck E , Hilgenfeld E , Ried T . Jumping translocations are common in solid tumor cell lines and result in recurrent fusions of whole chromosome arms. <span><span class="ref-journal">Genes Chromosomes Cancer. </span>2001;<span class="ref-vol">30</span>:349–363.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/11241788" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11241788</span></a>]</div></dd><dt>7.</dt><dd><div class="bk_ref" id="A530">Phillips JL , Ghadimi BM , Wangsa D , Padilla-Nash H , Worrell R , Hewitt S , Walther M , Linehan WM , Klausner RD , Ried T . Molecular cytogenetic characterization of early and late renal cell carcinomas in Von Hippel-Lindau (VHL) disease. <span><span class="ref-journal">Genes Chromosomes Cancer. </span>2001;<span class="ref-vol">31</span>:1–9.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/11284029" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 11284029</span></a>]</div></dd><dt>8.</dt><dd><div class="bk_ref" id="A531">Kallioniemi A , Kallioniemi OP , Sudar D , Rutovitz D , Gray JW , Waldman F , Pinkel D . Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. <span><span class="ref-journal">Science. </span>1992;<span class="ref-vol">258</span>:818–821.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/1359641" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 1359641</span></a>]</div></dd><dt>9.</dt><dd><div class="bk_ref" id="A532">Heselmeyer K , Schröck E , du Manoir S , Blegen H , Shah K , Steinbeck R , Auer G , Ried T . Gain of chromosome 3q defines the transition from severe dysplasia to invasive carcinoma of the uterine cervix. <span><span class="ref-journal">Proc Natl Acad Sci U S A. </span>1996;<span class="ref-vol">93</span>:479–484.</span> [<a href="/pmc/articles/PMC40262/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC40262</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/8552665" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 8552665</span></a>]</div></dd><dt>10.</dt><dd><div class="bk_ref" id="A533">Ried T , Liyanage M , du Manoir S , Heselmeyer K , Auer G , Macville M , Schröck E . Tumor cytogenetics revisited: comparative genomic hybridization and spectral karyotyping. <span><span class="ref-journal">J Mol Med. </span>1997;<span class="ref-vol">75</span>:801–814.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/9428610" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 9428610</span></a>]</div></dd><dt>11.</dt><dd><div class="bk_ref" id="A534">Forozan F , Karhu R , Kononen J , Kallioniemi A , Kallioniemi OP . Genome screening by comparative genomic hybridization. <span><span class="ref-journal">Trends Genet. </span>1997;<span class="ref-vol">13</span>:405–409.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/9351342" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 9351342</span></a>]</div></dd><dt>12.</dt><dd><div class="bk_ref" id="A535">ISCN: An International System for Human Cytogenetic Nomenclature. In: Mitelman F, editor. Basel: S. Karger; 1995.
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</div></dd><dt>13.</dt><dd><div class="bk_ref" id="A536">Fritz A, Percy C, Jack Andrew, Shanmugaratnam K, Sobin L, Parkin DM, Whelan S, editors. International Classification of Diseases for Oncology, 3rd ed. Geneva: World Health Organization; 2000.
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