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<li><a href="#">Overview</a><ul>
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<li><a href="/gtr/docs/about/">About GTR</a></li>
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<li><a title="Submission overview" href="/gtr/docs/submit/">Submission to GTR</a></li>
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<li><a title="Resources included in GTR and where to locate a genetics professional" href="/gtr/docs/resources/">GTR resources</a></li>
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<li><a href="/gtr/docs/linking/">How to create links to GTR</a></li>
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</ul>
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<li><a href="/gtr/docs/login/">Login</a></li>
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<li><a title="Overview of how to submit novel laboratory information" href="/gtr/docs/submit/add_lab/">Register a new lab</a></li>
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<li><a title="Instructions for performing the annual review" href="/gtr/docs/annual_review/">Annual review</a></li>
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<li><a title="Instructions for managing the group account for submitters" href="/gtr/docs/manage_permissions/">Groups: Manage person permissions</a></li>
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<li><a title="Instructions for submitters about updating and deleting records" href="/gtr/docs/manage_records/">Manage records</a></li>
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</ul>
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</li>
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<li><a href="#">Genetic Test Submission</a><ul>
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<li><a title="Overview of genetic test submissions" href="/gtr/docs/submit/">Getting started</a></li>
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<li><a title="Instructions for clinical genetic test submissions" href="/gtr/docs/submit/add_test/">Clinical tests</a></li>
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<li><a title="Instructions for spreadsheet submissions for clinical genetic tests" href="/gtr/docs/fulltest/">Clinical tests by spreadsheet</a></li>
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<li><a title="Instructions for API submissions for clinical genetic tests" href="/gtr/docs/gtr_api_http/">Clinical tests by api</a></li>
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<li><a title="Instructions for research genetic test submissions" href="/gtr/docs/submit/add_research/">Research tests</a></li>
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</ul>
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</li>
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<li><a href="#">Microbe Test Submission</a><ul>
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<li><a title="Overview of microbe test submissions" href="/gtr/docs/microbe_test/">Getting started</a></li>
|
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<li><a title="Instructions for clinical microbe test submissions" href="/gtr/docs/submit/add_microbe_clinical/">Clinical tests</a></li>
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<li><a title="Instructions for spreadsheet submissions for clinical microbe tests" href="/gtr/docs/microbe_fulltest/">Clinical tests by spreadsheet</a></li>
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<li><a title="Instructions for API submissions for clinical microbe tests" href="/gtr/docs/gtr_api_http/">Clinical tests by api</a></li>
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<li><a title="Instructions for research microbe test submissions" href="/gtr/docs/submit/add_microbe_research/">Research tests</a></li>
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</ul>
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</li>
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<li><a href="#">Search GTR</a><ul>
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<li><a title="How to use and search the GTR website" href="/gtr/docs/help/">Search tips</a></li>
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<li><a href="/gtr/docs/advanced_search">Advanced search</a></li>
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<li><a href="/gtr/docs/common_searches/">Common searches</a></li>
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<li><a href="https://www.youtube.com/playlist?list=PL7dF9e2qSW0a1b37gVee-pYFZ4AEOGvqw">YouTube library</a>
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<span id="shared-content-1"></span></li>
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<div><div id="static-page-tools"><div style="display:inline-block;"><form id="form-helpdocs" action="/gtr/docs/" method="get"><label class="ui-helper-hidden-accessible" for="helpdocs-search-term">Search GTR Help Documents</label><input autocomplete="off" value="" placeholder="Search GTR Help Documents" name="term" id="helpdocs-search-term" style="width:30em;" /><button id="search">Search GTR help documents</button></form></div><ul><li class="print"><a href="#" id="print-this" title="Print this document">Print this document</a></li><li class="print"><a href="/gtr/docs/submission/">View and print all related documents</a></li></ul></div>
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<div class="fl_right">
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<div><div><b>OMB NO: 0925-0651</b></div><div><b>EXPIRATION DATE: 01/31/2025</b>*</div><div><a href="/gtr/docs/omb_approval/">Burden Statement</a></div><div style="font-size: 0.9em;">* Renewal in process</div></div>
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</div>
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<div class="title_sec">
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<h1 id="submitting-test-data-to-gtr-in-b">Submitting Test data to GTR in Bulk using an Excel Submission Spreadsheet</h1>
|
||
</div>
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|
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<div class="toc">
|
||
<ul>
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||
<li><a href="#general-requirements">General Requirements</a><ul>
|
||
<li><a href="#download-the-gtr-full-test-submi">Download the GTR full test submission template</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#download-previously-submitted-cl">Download Previously Submitted Clinical Genetic Test Data</a><ul>
|
||
<li><a href="#prepare-a-submission-using-the-g">Prepare a submission using the GTR full test submission template with all Clinical Test Fields</a></li>
|
||
<li><a href="#using-the-gtr-minimal-fields-tes">Using the GTR minimal fields test submission template</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#instructions">Instructions for completing the full test submission file</a><ul>
|
||
<li><a href="#general-features-of-the-test-sub">General features of the test submission file</a></li>
|
||
<li><a href="#how-to-enter-data">How to enter data</a></li>
|
||
<li><a href="#novel-conditions">Novel conditions worksheet</a></li>
|
||
<li><a href="#sample-tests">Sample tests</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#definitions">Definitions and column values</a><ul>
|
||
<li><a href="#key-for-status">Key for Status column</a></li>
|
||
<li><a href="#lab-test-tab">Lab Test Tab</a></li>
|
||
<li><a href="#novel-condition-tab">Novel Condition Tab</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#bulk-submit">Upload your completed spreadsheet.</a><ul>
|
||
<li><a href="#submission-notifications">Submission notifications</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#submission_tips">Submission tips</a><ul>
|
||
<li><a href="#variants">Variants</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#errors">Validation error messages</a></li>
|
||
</ul>
|
||
</div>
|
||
|
||
|
||
<p>This document provides detailed information about how to submit data to GTR describing the clinical tests you offer, via files you prepare in advance. Templates for the files to be uploaded are available from <a href="https://ftp.ncbi.nlm.nih.gov/pub/GTR/submission_templates/">GTR's FTP site</a> and from your laboratory home page in Submission Portal. Bulk submission of research tests is not enabled. For information on the other submission scenarios and formats available, please see <a href="https://www.ncbi.nlm.nih.gov/gtr/docs/submit/#scenarios">http://www.ncbi.nlm.nih.gov/gtr/docs/submit/#scenarios</a>.</p>
|
||
|
||
|
||
<h2 id="general-requirements">General Requirements</h2>
|
||
|
||
|
||
<p>All submission scenarios require that you first register your laboratory in the GTR using the interactive submission website.</p>
|
||
|
||
|
||
<ul>
|
||
<li><a href="/gtr/docs/login#login">Log into the NCBI Submission Portal</a></li>
|
||
<li><a href="/gtr/docs/submit/add_lab/">Register a new laboratory</a></li>
|
||
<li>If a member of your lab needs access to the Submission Portal group account for your lab, please <a href="mailto:tkt-tryhd@ncbi.nlm.nih.gov?subject=Account%20in%20GTR%20Submission%20Portal"><span>contact GTR staff</span></a>.</li>
|
||
</ul>
|
||
|
||
|
||
<h3 id="download-the-gtr-full-test-submi">Download the GTR full test submission template</h3>
|
||
|
||
|
||
<p>There are two ways to download the submission template with all clinical tests fields:</p>
|
||
|
||
|
||
<ul>
|
||
<li>From the GTR FTP site, download the <a href="https://ftp.ncbi.nlm.nih.gov/pub/GTR/submission_templates/gtr_full_test_submission_template.xlsx">full test submission template file</a></li>
|
||
<li>To download your lab-specific template, from your home page in Submission Portal, go to the section 'Tests in this lab'. Then click on 'Submit tests' to go to the test submission page. See <a href="/gtr/docs/submit_tests/#multiple_tests">Submit multiple tests</a>.</li>
|
||
</ul>
|
||
|
||
|
||
<h2 id="download-previously-submitted-cl">Download Previously Submitted Clinical Genetic Test Data</h2>
|
||
|
||
|
||
<p>From your home page in Submission Portal, go to the section 'Tests in this lab'. Click on 'Download tests' to download your data. Clinical genetic tests and clinical microbe tests will be downloaded in separate spreadsheets to your Downloads folder. You will also receive an email, one for each test type, with a link to download the file. If you have only one test type (e.g., clinical genetic tests), then you will be reminded that there are no tests in the other category (ie., clinical microbe tests). You can use the data in the spreadsheet to submit updates to the tests. </p>
|
||
|
||
|
||
<h3 id="prepare-a-submission-using-the-g">Prepare a submission using the GTR full test submission template with all Clinical Test Fields</h3>
|
||
|
||
|
||
<ul>
|
||
<li>Review the <a href="#instructions">instructions for completing the full test submission file</a>. You may use the spreadsheet to:<ul>
|
||
<li>Add a new test</li>
|
||
<li>Edit an existing test</li>
|
||
<li>Delete an existing test</li>
|
||
</ul>
|
||
</li>
|
||
<li>Complete the file according to instructions.</li>
|
||
<li><a href="#bulk-submit">Upload your file</a></li>
|
||
<li>Correct processing errors, if any are found. The entire spreadsheet must pass validation; specific error-free tests will not be processed separately. See <a href="#errors">possible error messages</a>.</li>
|
||
<li>Review the submitted test records on the GTR public web site. A GTR test record becomes available on the GTR public website following indexing, usually within 24-48 hours after successfully submitting the test.</li>
|
||
<li><a href="#definitions">Test field definitions and column values</a></li>
|
||
</ul>
|
||
|
||
|
||
<p><em>Notes:
|
||
Supporting documents, such as FDA approval documents and sample reports cannot be uploaded via the full test submission template. If you wish to add these files, please do so manually within the GTR submission interface found at https://submit.ncbi.nlm.nih.gov/subs/gtr.</em></p>
|
||
|
||
|
||
<h3 id="using-the-gtr-minimal-fields-tes">Using the GTR minimal fields test submission template</h3>
|
||
|
||
|
||
<p>For instructions on how to use the GTR minimal fields submission template, which contains a subset of fields, refer to <a href="/gtr/docs/submit/semiautomatic/">Submitting data to GTR in bulk using an excel file with a subset of fields</a>.</p>
|
||
|
||
|
||
<h2 id="instructions">Instructions for completing the full test submission file</h2>
|
||
|
||
|
||
<h3 id="general-features-of-the-test-sub">General features of the test submission file</h3>
|
||
|
||
|
||
<p>This spreadsheet is used to provide the full set of test-specific data for clinical tests to GTR. The template includes minimal, recommended, and optional fields. Registration of each test is complete after the spreadsheet is successfully uploaded. You can add or edit fields at a later time using either the full test submission template, or by using the GTR submission user interface. For definitions of minimal, recommended, and optional fields, please go <a href="#key-for-status">here</a>.</p>
|
||
|
||
|
||
<p>The file does not have to reflect all tests offered by your laboratory. You can prepare and submit multiple test submission files. You can also enter and/or edit tests by using the interactive submission site.</p>
|
||
|
||
|
||
<p>Please do not edit rows that start with a # or that have a colored background.</p>
|
||
|
||
|
||
<p>A red triangle in the upper right of a cell indicates there is a comment. Hover over these cells to see abbreviated instructions on how to complete that cell.</p>
|
||
|
||
|
||
<p>Columns C, J, M, N, O, Q, R, U, X, AD, AE, AF, AG, AK, AN, AT, AU, AW, AX, AZ, BB, BN, BR, BU, BX, CD, CF, CI, CJ, CL, CR, CS, CT, provide pull-down menus. To complete those fields, first click the cell. A gray arrow will appear to the right of the cell. Click on the arrow to see the menu of allowed values and select from it. If you need to select multiple values click on the cell below to add another value. Please note carefully how to manage definitions of a test using multiple rows in the spreadsheet.</p>
|
||
|
||
|
||
<p>If order codes are unique for each test in your lab, and your lab does not have an internal tracking identifier, you can use the order code as your Test tracking ID.</p>
|
||
|
||
|
||
<p>The first column and the first row are frozen as default. However, you may want to unfreeze the first column or freeze another column (<em>e.g.</em> order code) to help keep track of which test you are working on. To do this go to the 'View' tab of the spreadsheet and click the freeze panes icon.</p>
|
||
|
||
|
||
<h3 id="how-to-enter-data">How to enter data</h3>
|
||
|
||
|
||
<p>The form contains all available columns, or data fields, which you can use to provide data for a test. <strong>The first column is critical, because if your submission requires more than one row to describe a test completely, the value in the first column is used to recognize that these data all belong to the same test.</strong> In general, each row corresponds to a test target description. A test target is what the test interrogates (e.g., for clinical genetic tests, the analyte, chromosomal region/mitochondrion, gene or protein). For simple tests (i.e., one test target), one row corresponds to one test you want to register in GTR. Each set of test targets and linked attributes (e.g., condition the target is assessing, target category, name of what is tested, variants, RefSeq:exons) must be entered in one row so GTR can identify their interrelationship. Thus, a test with multiple test targets will have multiple rows, each with the same value in column A.</p>
|
||
|
||
|
||
<p>Each set of rows with the same Test tracking ID is processed as one test. For single tests that are described using multiple rows, please enter the same Test tracking ID in column A for each applicable row. GTR identifies specific tests via the Test tracking ID, therefore it is crucial that each test be assigned a unique id of your choosing.</p>
|
||
|
||
|
||
<p>The action column designates whether you are adding a new test, or editing or deleting an existing registered GTR test. If you are editing or deleting an existing GTR test, you MUST include the GTR test accession in column B. You can find the test accession number in your list of tests on the GTR submission site (far right column).</p>
|
||
|
||
|
||
<p>Each test target must be linked to at least one indication (condition or phenotype name). Multiple indications for the same test target can be separated by |. Indications placed in the same row as a test target will be connected to that specific target.</p>
|
||
|
||
|
||
<p>If the same indication (condition or phenotype) relates to more than one test target it must be repeated for each appropriate test target row.</p>
|
||
|
||
|
||
<p>Indications (condition or phenotypes) may be entered either as names or MIM numbers. We recommend that you <a href="/gtr/conditions/">search GTR</a> to find condition/phenotype names recognized by GTR. Use of a recognized condition/phenotype name facilitates discovery of your test through the autocomplete dictionary and disease hierarchies, and enables your test to be linked to clinical, literature and consumer resources.</p>
|
||
|
||
|
||
<p>GTR does not accept registration of send-out tests (i.e. tests that are performed entirely at an outside laboratory/facility as explained <a href="/gtr/docs/submit/test_performance/#availability">here</a>). At least one test component must be performed at the laboratory that is registering the test. If any part of the test is performed at an outside facility, you may enter 'No' for 'Test performance location' on the spreadsheet. In the next column, you should specify which components of the test are performed at an outside facility and subsequently provide additional information in the following comment cell.</p>
|
||
|
||
|
||
<p>For column/fields that have menu choices, you must select from the choices provided. If multiple choices are applicable, each must be entered in the row(s) below.</p>
|
||
|
||
|
||
<h3 id="novel-conditions">Novel conditions worksheet</h3>
|
||
|
||
|
||
<p>The ‘Novel conditions’ worksheet should only be used if the condition for the test does not exist in GTR, that is, if it is a truly novel condition. To help prevent duplicate entries, please search <a href="/gtr/">GTR</a> for the condition name before creating a new entry. Note that the condition name for your test may be listed as an alternate name for a GTR condition name. If the condition exists in GTR, submission processing will preferentially capture data stored in the GTR database from sources such as OMIM, HPO, GeneReviews, Orphanet, and Monarch/MONDO, and will ignore data provided in this worksheet for mode of inheritance, prevalence, and other fields.</p>
|
||
|
||
|
||
<h3 id="sample-tests">Sample tests</h3>
|
||
|
||
|
||
<p>A file with sample tests in the full test submission template can be downloaded <a href="https://ftp.ncbi.nlm.nih.gov/pub/GTR/submission_templates/gtr_submission_examples_v1.xlsx">here</a>.</p>
|
||
|
||
|
||
<p>The sample tests are as follows:</p>
|
||
|
||
|
||
<p>Test 10001 demonstrates completion of all fields except for those recommended or optional fields which are not applicable</p>
|
||
|
||
|
||
<p>Test 10002 demonstrates completion of minimal fields only</p>
|
||
|
||
|
||
<p>Test 10003 demonstrates completion of minimal and applicable recommended fields</p>
|
||
|
||
|
||
<h2 id="definitions">Definitions and column values</h2>
|
||
|
||
|
||
<p>This table describes each value in the columns of the test submission file. The status column below (see key) indicates whether the field must be supplied to enable successful upload of the file and the impact on public display. On the full test submission template, minimal fields are highlighted so that they are differentiated from recommended and optional fields.</p>
|
||
|
||
|
||
<p>Four columns pertain to the spreadsheet submission process: (A) <em>Test tracking ID</em>, (B) <em>GTR accession</em>, (C) <em>Action</em> and (BS) <em>Condition/phenotype: choose name or identifier source</em>. All of the remaining columns correspond to fields that are part of overall GTR test submission.</p>
|
||
|
||
|
||
<h3 id="key-for-status">Key for Status column</h3>
|
||
|
||
|
||
<p>Private = field will not display to the public</p>
|
||
|
||
|
||
<p>Public = field will be viewable by GTR users</p>
|
||
|
||
|
||
<p>Minimal = field must be completed for this file to be processed successfully</p>
|
||
|
||
|
||
<p>Recommended = field will display as 'Not provided' if left blank</p>
|
||
|
||
|
||
<p>Optional = field will not display to the public if left blank (<em>i.e.</em> if not applicable for the test)</p>
|
||
|
||
|
||
<h3 id="lab-test-tab"><em>Lab Test Tab</em></h3>
|
||
|
||
|
||
<p><table>
|
||
<thead>
|
||
<tr>
|
||
<th scope="col">Column</th>
|
||
<th scope="col">Status</th>
|
||
<th scope="col">Description</th>
|
||
<th scope="col">Hints</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>A</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Test tracking ID</em>
|
||
</td>
|
||
<td>ID to distinguish one test from another on this spreadsheet. This field must be completed for each line. If a single test has multiple lines of data, this field <strong><em>must</em></strong> have the same value for all lines of that test. If you have an internal ID, which will help you track your submission, provide it here. You can use your order code if unique for each test or you can come up with your own unique tracking code (<em>e.g.</em> 1,2,3,4,...)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>B</td>
|
||
<td>
|
||
<p>Minimal* (if updating or deleting)</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>GTR Accession</em>
|
||
</td>
|
||
<td>Test ID to identify the GTR test you wish to edit or delete. This field should be empty if you are adding a new test, and must be completed if you are updating or deleting a test previously registered in the GTR.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>C</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Action</em>
|
||
</td>
|
||
<td>
|
||
<p>Field used to determine which action to perform on the row(s) corresponding to a single test. Only enter once per test. Selections include:</p>
|
||
<ul>
|
||
<li>Update: Edit an existing GTR test</li>
|
||
<li>Delete: Permanently remove an existing GTR test</li>
|
||
<li>Add New: Create a new test registration</li>
|
||
<li>No Change: Do nothing to the existing test registration</li>
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>D</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test order code</em>
|
||
</td>
|
||
<td>Enter the test order code, commonly found on the laboratory's requisition form, test menu or test catalog. This is the code health care providers (for example) would use to order the test through the laboratory. Complete this field only for the first line of data for each test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>E</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Laboratory test name</em>
|
||
</td>
|
||
<td>Test name as found on the lab test menu or requisition form. By default, test name is the record name in GTR and this is how you can easily identify your tests in your submission homepage. Complete this field only for the first line of data for each test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>F</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Laboratory test short name</em>
|
||
</td>
|
||
<td>The short test name is the shortened name or mneumonic used by the lab to identify the test. This may be a test name used in conjunction with a test order code for quick test menus, electronic medical records or HL7 systems and programs. Examples include: CHD7Full. Complete this field only for the first line of data for each test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>G</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Manufacturer's test name</em>
|
||
</td>
|
||
<td>Enter the manufacturer's name of the commerical test or kit used if in the submitted assay. If the test is an entirely laboratory developed test, there should not be a manufacturer's test name. Complete this field only for the first line of data for each test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>H</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>URL for the test</em>
|
||
</td>
|
||
<td>Enter the URL for test-specific information on your laboratory's website. URLs should be entered with the appropriate prefix, <em>i.e.</em>, http:// or https://. Complete this field only for the first line of data for each test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>I</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Search terms</em>
|
||
</td>
|
||
<td>Enter any search terms you wish to be associated with your submitted test. You do not need to enter keywords such as the disease/condition, gene, variant or test name. These will all automatically be included in a search. Relevant terms may include keywords such as archived or previously used test names. Limit to one search term per cell. Multiple search terms should be entered on multiple lines.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>J</td>
|
||
<td>
|
||
<p>Minimal </p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Purpose of the test</em>
|
||
</td>
|
||
<td>
|
||
<p>Select the appropriate purpose or indication of the test. If you need to add multiple test purposes, use a new line for each purpose added. Definitions of choices can be found <a href="/gtr/docs/submit/test_basics/#purpose">here</a>. In the spreadsheet, you can select from the following list:</p>
|
||
<em>Diagnosis<br />Drug response<br />Monitoring<br />Mutation confirmation<br />Pre-implantation genetic diagnosis<br />Pre-symptomatic<br />Predictive<br />Prognostic<br />Recurrence<br />Risk assessment<br />Screening<br />Therapeutic management</em>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>K</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>
|
||
<em>Target population for this test</em>
|
||
</em>
|
||
</td>
|
||
<td>Provide information on which population segment(s) the test is appropriate for and why. Complete this field once for each test. Example: Individuals with clinical symptoms consistent with Noonan syndrome.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>L</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations for target population</em>
|
||
</td>
|
||
<td>PubMed identifiers preferred; otherwise, full citations or URLs. If multiple, separate by '|'. This will allow GTR to provide a link for users to have easy access to the citation. You can also provide a link to your lab's webpage with information about the target population for this test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>M</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Has there been FDA review of this test?</em>
|
||
</td>
|
||
<td>Select the option (Y/N) corresponding to if the test or any portion of the test including reagents has been reviewed or is pending review by the FDA. This field should only be completed once per test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>N</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>If no FDA review, FDA category designation</em>
|
||
</td>
|
||
<td>
|
||
<p>Select the appropriate option from the available choices:</p>
|
||
<p class="rteindent1">
|
||
<em>FDA exercises enforcement discretion</em>
|
||
<br />
|
||
<em>Not applicable</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>O</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>If FDA review, item reviewed</em>
|
||
</td>
|
||
<td>This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. From the options indicated, select the portion of the test that has been reviewed or is pending review by the FDA. If multiple items reviewed, enter each item on a new line. Choices include:
|
||
<p class="rteindent1">
|
||
<em>ASR - Analyte-specific reagents</em>
|
||
<br />
|
||
<em>Assay(s)</em>
|
||
<br />
|
||
<em>IVDMIA - In Vitro Diagnostic Multivariate Assay(s)</em>
|
||
<br />
|
||
<em>Instrument(s)</em>
|
||
<br /><em>Test kit(s)</em>
|
||
<br />
|
||
<em>Other</em>- Please specify</p></td>
|
||
</tr>
|
||
<tr>
|
||
<td>P</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' selected in item reviewed)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Item reviewed, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the text corresponding to the 'Other' value for Item reviewed.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Q</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>If FDA review, FDA category designation</em>
|
||
</td>
|
||
<td>This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. From the options indicated, select the category of FDA review. Choices include:<p class="rteindent1">
|
||
<em>IUO - Investigational Use Only -</em>The performance characteristics of this product have not been established.
|
||
<br />
|
||
<em>IVD - In Vitro Device</em>
|
||
<br />
|
||
<em>RUO - Research Use Only</em>- Not for use in diagnostic procedures.
|
||
<br /></p></td>
|
||
</tr>
|
||
<tr>
|
||
<td>R</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>If FDA review, FDA regulatory status</em>
|
||
</td>
|
||
<td>This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. From the options provided, select the status of the item reviewed. Choices include:<p class="rteindent1">
|
||
<em>FDA cleared/approved</em>
|
||
<br />
|
||
<em>FDA exempt</em>
|
||
<br />
|
||
<em>Pending</em>
|
||
<br />
|
||
<em>Not submitted</em>
|
||
<br />
|
||
<em>Other</em>-<em>Please specify</em></p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>S</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' selected in regulatory status)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Regulatory status, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for regulatory status.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span>T</span>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<span>Optional</span>
|
||
</p>
|
||
<p>
|
||
<span>Public</span>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<em>
|
||
<span>If FDA review, application number</span>
|
||
</em>
|
||
</td>
|
||
<td>
|
||
<span>This field is completed only when 'yes' is selected from the 'Has there been FDA review of this test?'. Enter the FDA application number associated with the item reviewed.</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>U</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>NYS CLEP status</em>
|
||
</td>
|
||
<td>This field is required if 'NYS CLEP' is a valid certification for the specific test. Enter the status of the NYS CLEP <u>approval for the test</u>. This field should only be completed once per test. Options include:<p class="rteindent1">
|
||
<em>Approved</em>
|
||
<br />
|
||
<em>Not approved</em>
|
||
<br />
|
||
<em>Pending</em>
|
||
<br />
|
||
<em>Grandfathered</em>
|
||
<br />
|
||
<em>Exempt</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>V</td>
|
||
<td>
|
||
<p>Minimal* (if licensed by NYS)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>NYS CLEP license number</em>
|
||
</td>
|
||
<td>This field is required if 'NYS CLEP' is a valid certification for the specific test. Enter the license number provided by NYS CLEP <u>for the approved test</u>. This field should only be completed once per test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>W</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test development</em>
|
||
</td>
|
||
<td>Select a single option for how the test was developed. Intended to help delineate the differences in certification requirements between the test types. Do not include reflex tests here. Options include:<p class="rteindent1">
|
||
<em>FDA-reviewed (has FDA test name) -</em>The test, test kit or reagents either have FDA approval or are currently in FDA review.<br />
|
||
<em>Manufactured (research use only; not FDA-reviewed) -</em>The test or primary parts of the test are purchased from a commercial entity and have not gone through FDA review.<br />
|
||
<em>Modified FDA (has FDA-reviewed entry, but with lab modifications/field changes) -</em>The test, test kit or reagents used in the test have undergone FDA review and are approved, however the submitting laboratory has augmented some part of the test or testing protocol.<br />
|
||
<em>Test developed by laboratory (no manufacturer test name) -</em>This test is developed, produced and performed by the submitting laboratory. Also known as LDT.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>X</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>How to order (text description)</em>
|
||
</td>
|
||
<td>Enter a description of the test ordering procedure, such as required forms, specimen handling/shipping instructions, etc. Requirements and recommendations about informed consent and genetic counseling can be discussed here. If applicable, a statement similar to the following can be used: “The laboratory recommends that pre- and post-test genetic counseling be offered and informed consent be obtained for this test but does not require documentation to accept and process the sample.” Complete this field only for the first line of data for this test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Y</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>How to order (URL)</em>
|
||
</td>
|
||
<td>Enter the URL for information on how to order the test. URLs should be entered with the appropriate prefix,<em>i.e.</em>, http:// or https://. Complete this field only for the first line of data for this test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Z</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test codes (URL)</em>
|
||
</td>
|
||
<td>Enter the URL for information on corresponding codes related to the test, including CPT, ICD-9, ICD-10 and HCPCS codes. URLs should be entered with the appropriate prefix,<em>i.e.</em>, http:// or https://. Complete this field only for the first line of data for this test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AA</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>LOINC codes</em>
|
||
</td>
|
||
<td>The LOINC (Logical Observation Identifiers Names and Codes) database provides a set of universal names and ID codes for identifying laboratory and clinical test results. Enter the LOINC code. If applicable, the LOINC code can be found by using the 'Search' link, which will take you to the official LOINC website. The LOINC code must be entered manually, even if the submitter searches for the code using the link provided. Multiple codes should be entered on the same line, separated by '|'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AB</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>CPT codes</em>
|
||
</td>
|
||
<td>Enter a molecular pathology CPT code. Enter one CPT code per line. If you do not know which code(s) are appropriate for your test, you can review code descriptors on the GTR submission site by clicking edit on your test (once submitted) and navigating to the 'How to Order' tab. You will have to review and accept the AMA CPT code agreement before accessing the code descriptors.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AC</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Who can order this test?</em>
|
||
</td>
|
||
<td>Identify who can order the test based on the laboratory's policy on how the test can be ordered. Multiple selections should be made on multiple lines for the test.<p>Choose from the following options:</p><p class="rteindent1"><em>Genetic counselor</em><br /><em>Health care provider</em><br /><em>In-state patients</em><br /><em>Licensed dentist</em><br /><em>Licensed physician</em><br /><em>Nurse practitioner</em><br /><em>Out-of-state patients</em><br /><em>Physician assistant</em><br /><em>Public health mandate</em><br /><em>Registered nurse</em></p></td>
|
||
</tr>
|
||
<tr>
|
||
<td>AD</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Informed consent required?</em>
|
||
</td>
|
||
<td>
|
||
<p>Identify if the laboratory requires informed consent prior to performing the test. Select from the following choices:</p>
|
||
<p class="rteindent1">
|
||
<em>Decline to answer<br />Required<br />Not required<br />As required by state law</em>
|
||
</p>
|
||
<p>If not required but recommended, you can comment in the 'How to order' text field.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AE</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Pre-test genetic counseling required?</em>
|
||
</td>
|
||
<td>
|
||
<p>Identifiy if the laboratory requires genetic counseling prior to performing the test. Select from the following choices:</p>
|
||
<p class="rteindent1">
|
||
<em>Decline to answer</em>
|
||
<br />
|
||
<em>Required</em>
|
||
<br />
|
||
<em>Not required</em>
|
||
</p>
|
||
<p>If not required but recommended, you can comment in the 'How to order' text field.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AF</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Post-test genetic counseling required?</em>
|
||
</td>
|
||
<td>
|
||
<p>Identify if the laboratory requires genetic counseling after performing the test in order to release test results. Select from the following choices:</p>
|
||
<p class="rteindent1">
|
||
<em>Decline to answer</em>
|
||
<br />
|
||
<em>Required</em>
|
||
<br />
|
||
<em>Not required</em>
|
||
</p>
|
||
<p>If not required but recommended, you can comment in the 'How to order' text field.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AG</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test service</em>
|
||
</td>
|
||
<td>
|
||
<p>If applicable, select the laboratory services that are offered in conjunction with the specific test. Multiple selections are allowed, but enter each on a separate line. Please select each test service only once (you can provide multiple order codes for one service in the order code field). This field is different from 'Laboratory services' which allows submitters to select general services the laboratory provides. Choose from the following options:</p>
|
||
<p class="rteindent1">
|
||
<em>Clinical testing/Confirmation of Mutations Identified Previously<br />
|
||
Confirmation of Research Findings<br />
|
||
Custom Balanced Chromosome Rearrangement Studies<br />
|
||
Custom Deletion/Duplication Testing<br />
|
||
Custom Sequence Analysis<br />
|
||
Data Storage and Backup<br />
|
||
Genetic Counseling<br />
|
||
Identity Testing<br />
|
||
Marker Chromosome Identification<br />
|
||
Preimplantation Genetic Diagnosis (PGD)<br />
|
||
Result Interpretation<br />
|
||
Specimen Source Identification<br />
|
||
Uniparental Disomy (UPD) Testing<br />
|
||
X-Chromosome Inactivation Studies</em>
|
||
</p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AH</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected in test service)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test service, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for test-specific services.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AI</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test service order code</em>
|
||
</td>
|
||
<td>If applicable, enter the order code for the test-specific service, commonly found on the laboratory's requisition form, test menu or test catalog. This is the code health care providers (for example) would use to order the service through the laboratory. If multiple services are entered, enter the associated order codes on separate corresponding lines.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AJ</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test service comment</em>
|
||
</td>
|
||
<td>Enter further information to assist health care providers in ordering the test-specific services. An example includes, 'Pre-test and post-test genetic counseling is available for this test'. If multiple services are entered, enter the associated test-specific comment on separate corresponding lines.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AK</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test additional service</em>
|
||
</td>
|
||
<td>
|
||
<p>If applicable, select the additional laboratory services that are offered in conjunction with the specific test. Enter multiple selections on separate lines. Please select each test service only once (you can provide multiple order codes for one service in the order code field). This field is different from 'Laboratory additional services' which allows submitters to select general services the laboratory provides. Options include:</p>
|
||
<p>
|
||
<em>Custom prenatal testing</em>
|
||
<br />
|
||
<em>Custom mutation-specific/Carrier testing</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AL</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test additional service order code</em>
|
||
</td>
|
||
<td>If applicable, enter the order code for the test-specific additional service, commonly found on the laboratory's requisition form, test menu or test catalog. This is the code health care providers (for example) would use to order the service through the laboratory. If multiple services are entered, enter the associated order codes on separate corresponding lines.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AM</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test additional service comment</em>
|
||
</td>
|
||
<td>Enter further information to assist health care providers in ordering the additional test-specific services. An example includes, 'Once a mutation is identified, prenatal testing is available'. If multiple services are entered, enter the associated test-specific additional comment on separate corresponding lines.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AN</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Specimen source</em>
|
||
</td>
|
||
<td>
|
||
<p>Select the specimen type(s) allowed for the test. Multiple selections allowed. Each specimen type should be on a separate line. Choices include:</p>
|
||
<p>
|
||
<em>Amniocytes</em><br />
|
||
<em>Amniotic fluid</em><br />
|
||
<em>Bone marrow</em><br />
|
||
<em>Buccal swab</em><br />
|
||
<em>Buffy coat</em><br />
|
||
<em>Cell culture</em><br />
|
||
<em>Cell-free DNA</em><br />
|
||
<em>Cerebrospinal fluid</em><br />
|
||
<em>Chorionic villi</em><br />
|
||
<em>Cord blood</em><br />
|
||
<em>Cystic hygroma fluid</em><br />
|
||
<em>Dried blood spot (DBS) card</em><br />
|
||
<em>Fetal blood</em><br />
|
||
<em>Fibroblasts</em><br />
|
||
<em>Fresh tissue</em><br />
|
||
<em>Frozen tissue</em><br />
|
||
<em>Isolated DNA</em><br />
|
||
<em>Paraffin block</em><br />
|
||
<em>Peripheral (whole) blood</em><br />
|
||
<em>Plasma</em><br />
|
||
<em>Product of conception (POC)</em><br />
|
||
<em>Saliva</em><br />
|
||
<em>Serum</em><br />
|
||
<em>Skin</em><br />
|
||
<em>Sputum</em><br />
|
||
<em>Urine</em><br />
|
||
<em>White blood cell prep</em><br />
|
||
<em>Other</em>-please specify
|
||
</p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AO</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected for specimen source)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Specimen source, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for specimen source.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AP</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Specimen source URL</em>
|
||
</td>
|
||
<td>Enter the URL to the laboratory's website that describes the specimen requirements and handling for the test. URLs should be entered with the appropriate prefix,<em>i.e</em>., http:// or https://.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AQ</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Testing strategy</em>
|
||
</td>
|
||
<td>Describe the suggested sequence of ordering tests, discuss reflex testing, testing algorithms and related issues. This field is for recommendations on how to order the test in sequence of relevance to the patient (target population) being tested. This field should not include discussion of methodologies or test procedural protocols. If describing reflex tests, each test component should be delineated. If a test is ordered, additional tests may be performed as necessary under certain circumstances based on initial results and that should be described in this field.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AR</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support testing strategy</em>
|
||
</td>
|
||
<td>Enter references and/or URLs as appropriate to further describe the testing strategy/algorithm. If entering an URL, please specify the appropriate prefix, http:// or https://. PubMed identifiers preferred; otherwise, full citations or URLs. If multiple, separate by'|'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AS</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test-specific contact policy</em>
|
||
</td>
|
||
<td>
|
||
<p>Select the policy of the laboratory regarding who (patients or health care providers) and when (pre-test/post-test/anytime) can contact the lab for this test. If appropriate, select multiple options with each option on a separate line. Options include:</p>
|
||
<p>
|
||
<em>Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.</em>
|
||
<br />
|
||
<em>Post-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.</em>
|
||
<br />
|
||
<em>Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AT</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test-specific contact person</em>
|
||
</td>
|
||
<td>
|
||
<p>From the drop-down list, select the test-specific contact for thes test. This individual's name and contact information will be displayed on the test page for health care providers to view. If no test-specific contact is provided, the laboratory's general contact information will display. For multiple contacts, add each person on a separate line.</p>
|
||
<p>Note: If you do not see the staff member's name you want to select in the personnel list, you either have downloaded a generic full test submission template (and not a pre-loaded laboratory-specific template) or, you need to add the person to your laboratory registration. Either way, you will not be able to add the person on the spreadsheet you are currently working on. We recommend skipping this field on your current spreadsheet and then manually adding the test-specific contact using the GTR submission site. See <a href="https://www.ncbi.nlm.nih.gov/gtr/docs/submit/test_order/">http://www.ncbi.nlm.nih.gov/gtr/docs/submit/test_order/</a>for more information.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AU</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test performance location(s):</em>
|
||
</td>
|
||
<td>
|
||
<p>Select where the test is performed from the following options. Tests which are performed entirely at an outside lab/facility should not be registered in GTR. 'In-house' means within the lab/facility covered by the same CLIA certification number. 'Outside lab' means a different lab/facility than that dovered by your CLIA certification, even if both labs have the same parent organization. Multiple selections are allowed,<u>unless the entire test is performed in-house</u>. Select each option on a separate line.</p>
|
||
<p>
|
||
<em>Entire test performed in-house<br />Interpretation performed at an outside lab</em>
|
||
<br />
|
||
<em>Interpretation performed both in-house and at an outside lab</em>
|
||
<br />
|
||
<em>Interpretation performed in-house</em>
|
||
<br />
|
||
<em>Report generated at an outside lab</em>
|
||
<br />
|
||
<em>Report generated both in-house and at an outside lab</em>
|
||
<br />
|
||
<em>Report generated in-house</em>
|
||
<br />
|
||
<em>Specimen preparation performed at an outside lab</em>
|
||
<br />
|
||
<em>Specimen preparation performed both in-house and at an outside lab</em>
|
||
<br />
|
||
<em>Specimen preparation performed in-house</em>
|
||
<br />
|
||
<em>Wet lab work performed at an outside lab</em>
|
||
<br />
|
||
<em>Wet lab work performed both in-house and at an outside lab</em>
|
||
<br />
|
||
<em>Wet lab work performed in-house</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AV</td>
|
||
<td>
|
||
<p>Minimal* (if any part of the test is peformed outside the registering laboratory)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test performance location(s) comments</em>
|
||
</td>
|
||
<td>Briefly describe methods and location for components of test work done at an outside lab.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AW</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Method Category</em>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<p>Category of the method(s) being used in this test. If multiple methods are used in the test, add an additional line for each method. If your test uses more than one Test method per Method Category, you must select the category again in column AW to correspond to the value in column AX. To display the complete list of choices, please:</p>
|
||
<p>1. Click on the cell - an arrow displays to the right of the cell, then<br />2. Click on the gray arrow.</p>
|
||
<p>Options include:
|
||
<em>Analyte</em><br />
|
||
<em>Chromosome breakage studies</em><br />
|
||
<em>Deletion/duplication analysis</em><br />
|
||
<em>Detection of homozygosity</em><br />
|
||
<em>Detection of homozygosity</em><br />
|
||
<em>Enzyme assay</em><br />
|
||
<em>FISH-interphase</em><br />
|
||
<em>FISH-metaphase</em><br />
|
||
<em>Fluorescence in situ hybridization (FISH)</em><br />
|
||
<em>Immunohistochemistry</em><br />
|
||
<em>Karyotyping</em><br />
|
||
<em>Linkage analysis</em><br />
|
||
<em>Methylation analysis</em><br />
|
||
<em>Microsatellite instability testing (MSI)</em><br />
|
||
<em>Multicolor FISH (M-FISH)/Spectral Karyotyping™ (SKY™)</em><br />
|
||
<em>Mutation scanning of select exons</em><br />
|
||
<em>Mutation scanning of the entire coding region</em><br />
|
||
<em>Protein analysis</em><br />
|
||
<em>Protein expression</em><br />
|
||
<em>RNA analysis</em><br />
|
||
<em>Sequence analysis of select exons</em><br />
|
||
<em>Sequence analysis of the entire coding region</em><br />
|
||
<em>Sister chromatid exchange</em><br />
|
||
<em>Targeted variant analysis</em><br />
|
||
<em>Uniparental disomy study (UPD)</em></p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AX</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Test method</em>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<p>Select the test method that corresponds to the entry selected in column 'AW' for Method category. Each test must have an entry both in column 'AW' and column 'AX'. If the test has multiple test methods, add each test method on a new line, making certain the Test method value corresponds to the value in Method category. If the test method used in this test is not listed, please select 'Other' from the list in the spreadsheet and specify the test method in column 'AY'.</p>
|
||
<p>To display the complete list of choices, please:</p>
|
||
<p>1. Click on the cell - an arrow displays to the right of the cell, then<br />
|
||
2. Click on the gray arrow.</p>
|
||
<div>Options include:
|
||
<em>Allele-specific primer extension (ASPE)</em><br />
|
||
<em>Alternative splicing detection</em><br />
|
||
<em>Bi-directional Sanger Sequence Analysis</em><br />
|
||
<em>C-banding</em><br />
|
||
<em>Chemiluminescent Immunoassay (CIA)</em><br />
|
||
<em>Chromatin Immunoprecipitation on ChIP</em><br />
|
||
<em>Comparative Genomic Hybridization</em><br />
|
||
<em>DamID</em><br />
|
||
<em>Digital / Virtual karyotyping</em><br />
|
||
<em>Digital microfluidic microspheres</em><br />
|
||
<em>Enzymatic levels</em><br />
|
||
<em>Enzyme activity</em><br />
|
||
<em>Enzyme-Linked Immunosorbent Assays (ELISA)</em><br />
|
||
<em>Fluorescence in situ hybridization (FISH)</em><br />
|
||
<em>Fluorometry</em><br />
|
||
<em>Fusion genes microarrays</em><br />
|
||
<em>G-banding</em><br />
|
||
<em>Gas chromatography–mass spectrometry (GC-MS)</em><br />
|
||
<em>Gene expression profiling</em><br />
|
||
<em>GeneID</em><br />
|
||
<em>Gold nanoparticle probe technology</em><br />
|
||
<em>High-performance liquid chromatography (HPLC)</em><br />
|
||
<em>Liquid chromatography-tandem mass spectrometry (LC-MS/MS)</em><br />
|
||
<em>Liquid chromatography–mass spectrometry (LC-MS)</em><br />
|
||
<em>Metabolite levels</em><br />
|
||
<em>Methylation-specific PCR</em><br />
|
||
<em>Microarray</em><br />
|
||
<em>Multiplex Ligation-dependent Probe Amplification (MLPA)</em><br />
|
||
<em>Next-Generation (NGS)/Massively parallel sequencing (MPS)</em><br />
|
||
<em>Oligonucleotide Ligation Assay (OLA)</em><br />
|
||
<em>Oligonucleotide hybridization-based DNA sequencing</em><br />
|
||
<em>PCR</em><br />
|
||
<em>PCR with allele specific hybridization</em><br />
|
||
<em>PCR-RFLP with Southern hybridization</em><br />
|
||
<em>Protein truncation test</em><br />
|
||
<em>Pyrosequencing</em><br />
|
||
<em>Q-banding</em><br />
|
||
<em>Quantitative PCR (qPCR)</em><br />
|
||
<em>R-banding</em><br />
|
||
<em>RFLP</em><br />
|
||
<em>RT-LAMP</em><br />
|
||
<em>RT-PCR</em><br />
|
||
<em>RT-PCR with gel analysis</em><br />
|
||
<em>RT-qPCR</em><br />
|
||
<em>SNP Detection</em><br />
|
||
<em>Silver staining</em><br />
|
||
<em>Spectral karyotyping (SKY)</em><br />
|
||
<em>T-banding</em><br />
|
||
<em>Tandem mass spectrometry (MS/MS)</em><br />
|
||
<em>Tetra-nucleotide repeat by PCR or Southern Blot</em><br />
|
||
<em>Tiling Arrays</em><br />
|
||
<em>Trinucleotide repeat by PCR or Southern Blot</em><br />
|
||
<em>Uni-directional Sanger sequencing></em><br />
|
||
<em>Other</em>-please specify
|
||
</div>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AY</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected for test method)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test method, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for test method.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>AZ</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Instruments used for test method</em>
|
||
</td>
|
||
<td>
|
||
<p>Name the instrucment used for a specific methodology. Enter each instrument on a separate line, corresponding to the appropriate test method.</p>
|
||
<p>
|
||
<em>Affymetrix GeneChip Scanner 3000 7G Whole-Genome Association System<br />
|
||
Affymetrix GeneTitan® MC<br />
|
||
Affymetrix HotStart-IT Probe qPCR Master Mix with UDG (2X)<br />
|
||
Agilent 2100 Bioanalyzer<br />
|
||
Agilent SureSelect<br />
|
||
Applied Biosystems 3730 capillary sequencing instrument<br />
|
||
Applied Biosystems 7900HT Sequence Detection System<br />
|
||
Applied Biosystems SOLiD v4 System Sequencer<br />
|
||
BeadXpress® Reader<br />
|
||
BioRad CFX96<br />
|
||
Covaris S2 Sonicator<br />
|
||
GenMark Diagnostics eSensor XT-8 system<br />
|
||
Illumina Genome AnalyzerIIx and Genome AnalyzerIIe<br />
|
||
Illumina HiScan[TM] SQ system<br />
|
||
Illumina HiSeq[TM] 2000 system<br />
|
||
Other<br />
|
||
PerkinElmer Victor3 1420 Multilabel Plate Reader<br />
|
||
Qiagen AutoPure LS<br />
|
||
Qiagen QIAcube<br />
|
||
Roche LightCycler 480<br />
|
||
Tecan Genesis Robotic Workstation 150</em>
|
||
</p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BA</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected for instruments)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Instruments, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for instruments.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BB</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Platforms</em>
|
||
</td>
|
||
<td>
|
||
<p>Select the name of a platform used in your test, if appropriate. If you use a platform not on the list, choose 'Other' and then provide the name. A platform name typically corresponds to a unique catalogue number or a set of catalogue numbers which are bundled with other consumables. The format is usually manufacturer name, product name, and general specifications.</p>
|
||
<p>
|
||
<em>Affymetrix CytoScan HD Array<br />
|
||
Affymetrix Gene Profiling Array cGMP U133 P2<br />
|
||
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array<br />
|
||
Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0<br />
|
||
Affymetrix Genome-Wide Human SNP Array 6.0<br />
|
||
Affymetrix QuantiGene 2.0 Assay<br />
|
||
Agilent Human CpG Island Microarray Kit, 1x244K<br />
|
||
Agilent Human ENCODE ChIP-on-chip Microarray<br />
|
||
Agilent Human miRNA Microarray Kit Release 16.0, 8x60K<br />
|
||
Agilent SurePrint G3 Human CGH Microarray Kit, 2x400K<br />
|
||
Amersham CodeLink UniSet Human I Bioarray<br />
|
||
Illumina Infinium HD HumanCytoSNP-12<br />
|
||
Life Technologies TaqMan OpenArray MicroRNA Panels<br />
|
||
NimbleGen CGH 3-plex ISCA Plus Cytogenetic Array<br />
|
||
None/not applicable<br />
|
||
Other<br />
|
||
Oxford Gene Technology CytoSure DMD (4x44k)<br />
|
||
Oxford Gene Technology CytoSure ISCA UPD (4x180k)<br />
|
||
Oxford Gene Technology CytoSure ISCA v2 (4x180k)<br />
|
||
Oxford Gene Technology CytoSure ISCA v2 (4x44k)<br />
|
||
Oxford Gene Technology CytoSure ISCA v2 (8x60k)<br />
|
||
Oxford Gene Technology CytoSure Syndrome Plus v2 (2x105k)</em>
|
||
</p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BC</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected for platform)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Platform, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for platforms.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BD</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test procedure or protocol</em>
|
||
</td>
|
||
<td>Summarize the methodology and descrie the specific steps for each method of the assay.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BE</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support test procedure or protocol</em>
|
||
</td>
|
||
<td>Provide citations or URL for the protocol. PubMed identifiers preferred; otherwise, full citations or URLs. If multiple, separate by'|'. URLs should be entered with the appropriate prefix,<em>i.e.,</em>http:// or https://<em>.</em></td>
|
||
</tr>
|
||
<tr>
|
||
<td>BF</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Confirmation of test results</em>
|
||
</td>
|
||
<td>Describe whether and how test results are confirmed (beyond initial validation of the assay). For example, 'Positive results are confirmed on a new DNA preparation using sequence analysis'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BG</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Test comment</em>
|
||
</td>
|
||
<td>Provide textual description of the test methods or any other information about your test not described elsewhere that may be useful to clinicians ordering your test, e.g. 'Bi-directional sequencing of exons 1-5 with concurrent analysis of NP_000000.0:p.Glu234Gly'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BH</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Analytical Validity</em>
|
||
</td>
|
||
<td>
|
||
<p>The Analytical validity field needs a statement that includes quantitative information for analytical sensitivity, analytical specificity, accuracy, and/or precision of this test. General statements about methodologies that do not contain specific information about the test do not satisfy the specifications for this field. Nor do statements such as "N/A", "not applicable", "Yes" or "unknown". Example: 'The OtoChip is greater than 99% sensitive for detecting substitution variants in the sequence analyzed. In addition, this assay is 95% sensitive for detecting small insertions or deletions (inDels), and 100% for 1-2bp indels, 92.3% for 3-5bp indels and 87.5% for >10bp indels.'</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BI</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support analytical validity</em>
|
||
</td>
|
||
<td>Provide PubMed ID when available, otherwise full citations or URLs. If multiple, separate by'|'. URLs should be entered with the appropriate prefix, i.e., http:// or https://. This will allow GTR to provide a link for users to have easy access to the citation. If no publications are available, provide non-proprietary internal lab data in analytical validity statement, if available. You can also provide a link to your lab's webpage with information about analytical validity for this test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BJ</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Clinical validity</em>
|
||
</td>
|
||
<td>Clinical validity is how consistently and accurately the test detects or predicts the intermediate or final outcomes of interest. This information will display in the Overview and Indication tabs of the test record. Describe clinical sensitivity and specificity, positive and negative predictive values, the population(s) assessed, adn the number of specimens used to calculate clinical validity. Clinical sensitivity is the proportion of positive test results among patients with the defined clinical presentation. Clincal specificity is the proportion of negative test results among patients witout the defined clinical presentation. Positive predictive value is the chance of having the marker among those that test positive. Negative predictive value is the chance of not having the marker among those that test negative.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BK</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support clinical validity</em>
|
||
</td>
|
||
<td>Provide citations to support clinical validity statment. Provide PubMed ID when available, otherwise full citations or URLs. If multiple, separate by '|'. URLs should be entered with the appropriate prefix, i.e., http:// or https://.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BL</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Assay limitations</em>
|
||
</td>
|
||
<td>Describe any factors that affect the value of the test for its intended use. Includes limits of detection and validation of test for only specific subpopulations or particular uses.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BM</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support assay limitations</em>
|
||
</td>
|
||
<td>Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BN</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Clinical utility category</em>
|
||
</td>
|
||
<td>
|
||
<p>Select a category from the list and support it with an URL and/or citations. Enter multiple clinical utitity statements on separate lines. Choose from the following options:</p>
|
||
<p>
|
||
<em>Avoidance of invasive testing</em>
|
||
<br />
|
||
<em>Establish or confirm diagnosis</em>
|
||
<br />
|
||
<em>Guidance for management</em>
|
||
<br />
|
||
<em>Guidance for selecting a drug therapy and/or dose</em>
|
||
<br />
|
||
<em>Lifestyle planning</em>
|
||
<br />
|
||
<em>Predictive risk information for patient and/or family members</em>
|
||
<br />
|
||
<em>Reproductive decision-making</em>
|
||
<br />
|
||
<em>Sufficient research has not been conducted to establish utility of the test</em>
|
||
<br />
|
||
<em>Other (please specify)</em>
|
||
</p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BO</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected for Clinical utility category)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>
|
||
<em>Clinical utility category other value</em>
|
||
</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for Clinical utility category.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BP</td>
|
||
<td>
|
||
<p>Minimal* (if a clinical utility category is chosen, a citation or URL is required)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>URL to explain clinical utility</em>
|
||
</td>
|
||
<td>Cite recommendations or practice guidelines for the test that have been issued by authoritative groups. Some practice guidelines may be available via URL but not a citation. URL to the laboratory web page may be used. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple clinical utility statements, enter on separate lines, with each corresponding to the appropriate entry in column BN.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BQ</td>
|
||
<td>
|
||
<p>Minimal* (if a clinical utility category is chosen, a citation or URL is required)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support clinical utility</em>
|
||
</td>
|
||
<td>Provide citations to support clinical utility statements. Provide PubMed ID when available, otherwise full ciations. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple clinical utility statements, enter on separate lines, with each corresponding to the appropriate entry in column BN. If multiple citations for a single clinical utility statement, enter on the same row, but separate by '|'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BR</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Condition/phenotype: choose name or identifier source</em>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<p>Select whether the condition/phenotype will be provided by condition name or identifier (OMIM, CUI, HPO, Orphanet, MeSH, or MONDO). You can find the GTR preferred name by searching the public web site at <a href="https://www.ncbi.nlm.nih.gov/gtr">http://www.ncbi.nlm.nih.gov/gtr</a>. In the spreadsheet, you can select from the following list:</p>
|
||
<p>
|
||
<em>condition name<br />
|
||
CUI<br />
|
||
HPO identifier<br />
|
||
MeSH ID<br />
|
||
MIM number<br />
|
||
MONDO ID<br />
|
||
Orphanet identifier</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BS</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Conditions/Phenotypes</em>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<p>If you selected MIM number in previous column (BR), enter the valid MIM condition number (<u>please do not enter MIM number for gene records</u>). If you enter a MIM number for the condition being tested, GTR will use this to match your submission to disorders already represented in GTR's database. Similarly, if you selected one of the other identifier sources in Column BR, enter the valid identifier here.</p>
|
||
<p>The list of names GTR uses per MIM number is provided from the <a href="https://ftp.ncbi.nlm.nih.gov/pub/clinvar/gene_condition_source_id">ClinVar's FTP site.</a></p>
|
||
<p>If you selected condition name in column BR, write the preferred name of the condition/phenotype. You can <a href="/gtr/">search GTR</a> to find the condition name in the database. Linking to an existing condition name ensures that this test will be connected to available resources such as clinical and molecular resources. <a href="https://ftp.ncbi.nlm.nih.gov/pub/medgen/presentations/Conditions_Phenotypes.pptx">Learn how to use MedGen to select condition and phenotype terms</a>.</p>
|
||
<p>If multiple conditions/phenotypes exist for a single target (columns BT through BV), enter values separated by a vertical bar (|). If same condition/phenotype exists for multiple targets, the conditon/phenotype must be repeated on each target line.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BT</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Germline or Somatic</em>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<p>Select the type of target from the following options:</p>
|
||
<p>
|
||
<em>Germline</em>
|
||
<br />
|
||
<em>Somatic</em>
|
||
<br />
|
||
<em>Both</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BU</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Target category</em>
|
||
</p>
|
||
<div> </div>
|
||
</td>
|
||
<td>
|
||
<p>Select the category describing the test target measures in the test. If multiple targets are being tested, add each target on a separate line. In the spreadsheet, you can select from the following list:</p>
|
||
<p>
|
||
<em>analyte<br />
|
||
chromosomal region/mitochondrion<br />
|
||
gene<br />
|
||
protein</em>
|
||
</p>
|
||
<p>Note that <strong>gene</strong> is used to represent molecular assays that detect variations in a gene or set of genes.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BV</td>
|
||
<td>
|
||
<p>Minimal</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Name of what is tested</em>
|
||
</td>
|
||
<td>
|
||
<p>If gene in column BU, enter HGNC official gene symbol. If chromosomal region/mitochondrion in column BU, enter region. If protein, please use Swiss-Prot protein name. If an analyte, enter its name. If multiple targets are being tested, each target must be stored on a separate line.</p>
|
||
<p>Examples:</p>
|
||
<p>Analyte: 'Branched-chain amino acids' or the enzyme 'Branched-chain ketoacid dehydrogenase'</p>
|
||
<p>Chromosomal region/mitochondrion: '11q15' or 'm.7446-m.7514'</p>
|
||
<p>Gene: 'CDKN2A' or 'CFTR'</p>
|
||
<p>Protein: 'Hemoglobin subunit beta' or 'Adenomatous polyposis coli protein'</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BW</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Variants(s)</em>
|
||
</td>
|
||
<td>
|
||
<p>Describe variation using fully qualified HGVS expression,<em>e.g.</em>NM_000258.2:c.427G>A. If multiple variants for Conditions/phenotypes named in Column BS, separate with '|'. Fill this column only if gene is provided in column BV.</p>
|
||
<p>Example: for a test that interrogates the 1477_1478del and 1477C>T of the CFTR gene for Cystic fibrosis, you would enter:</p>
|
||
<div>Column BR: MIM number</div>
|
||
<div>Column BS: 219700</div>
|
||
<div>Column BT: Germline</div>
|
||
<div>Column BU: gene</div>
|
||
<div>Column BV: CFTR</div>
|
||
<div>Column BW: NM_000492.4:c.1477_1478del|NM_000492.4:c.1477C>T
|
||
</div></td>
|
||
</tr>
|
||
<tr>
|
||
<td>BX</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Clinical significance of variant</em>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<p>Assign the clinical significance of the variant(s) entered in column BW. Options include:</p>
|
||
<p>
|
||
<em>Affects<br />
|
||
association<br />
|
||
association not found<br />
|
||
Benign<br />
|
||
confers sensitivity<br />
|
||
conflicting data from submitters<br />
|
||
drug response<br />
|
||
Likely benign<br />
|
||
Likely pathogenic<br />
|
||
not provided<br />
|
||
other<br />
|
||
Pathogenic<br />
|
||
protective<br />
|
||
risk factor<br />
|
||
Uncertain significance</em>
|
||
</p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BY</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>Citations to support the clinical significance</em>
|
||
</p>
|
||
</td>
|
||
<td>
|
||
<p>Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'. Citations should be entered on lines corresponding to associated clinical significance statment, entered in column BX.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BZ</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<p>
|
||
<em>RefSeq:relevant exons</em>
|
||
</p>
|
||
</td>
|
||
<td><p>Provide details about the exons analyzed and specify the associated reference sequences. Format by first specifying reference sequence, include assession number and version, then using ':', and then listing exons. If multiple reference sequences per gene, separate these by '|'.</p>Valid only if gene is provided in column BV. The RefSeq defining the exon numbering system must be supplied in this column.<p>Example: NM_4433221.1:1-5(all)|NM_123456.1:1,3,4-5 including 5 bp in intron-exon boundaries.</p><p>If a continuous range is tested: provide the exon numbers as a range,<em>e.g</em>. 2-5. If the range includes all exons, add (All),<em>e.g</em>. 1-5 (All)</p><p>If a subset is tested: enumerate the exons tested. Ranges are allowed,<em>e.g.</em>3,5,9-12</p><p>NOTE: If gene name is provided, the chromosomal location (RefSeq) will be automatically provided and does not need to be entered UNLESS you are providing exons.</p></td>
|
||
</tr>
|
||
<tr>
|
||
<td>CA</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>VUS: What is the protocol for interpreting a variation as a VUS?</em>
|
||
</td>
|
||
<td>Describe how your lab interprets a variation as a VUS.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CB</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>VUS: What software is used to interpret novel variations?</em>
|
||
</td>
|
||
<td>Describe the software your lab uses to interpret novel variations. You can include lab-developed software.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CC</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>VUS: What is the laboratory's policy on reporting novel variations?</em>
|
||
</td>
|
||
<td>Describe how your lab reports novel variations.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CD</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>VUS: Are family members recruited without charge?</em>
|
||
</td>
|
||
<td>
|
||
<p>Select from the provided options:</p>
|
||
<p>
|
||
<em>Not provided</em>
|
||
<br />
|
||
<em>Yes</em>
|
||
<br />
|
||
<em>No</em>
|
||
<br />
|
||
<em>Decline to answer</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CE</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>VUS: Comments about recruiting family members.</em>
|
||
</td>
|
||
<td>Describe if your lab offers testing for a variant of unknown significance to family members free of charge; for example, to affected individuals and/or presumed obligate carriers to help determine clinical significance of a VUS. Write an explanation or give information about who would be eligible to testing free of charge and how the lab does it.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CF</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>VUS: Will the lab re-contact the ordering physician if variant interpretation changes?</em>
|
||
</td>
|
||
<td>
|
||
<p>Select from the provided options:</p>
|
||
<p>
|
||
<em>Not provided</em>
|
||
<br />
|
||
<em>Yes</em>
|
||
<br />
|
||
<em>No</em>
|
||
<br />
|
||
<em>Decline to answer</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CG</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>VUS: Comments about re-contacting the ordering physician</em>
|
||
</td>
|
||
<td>Type a description or explanation about how the lab monitors and addresses reinterpretation of genetic test results over time, after issuing the report. For example, is there a time limit, do you systematically re-evaluate prior interpretations and generate new reports, or does the person ordering the test need to peridically recontact the laboratry to inquire about changes in test interpretation?</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CH</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Research performed after clinical testing is complete</em>
|
||
</td>
|
||
<td>Describe any research testing being performed using the submitted sample after clinical testing is complete. For example, research testing is allowed under IRB approved protocols or the patient would have to sign an informed consent for the research protocol. If the protocol is registered in clincaltrials.gov, you can enter that information here. Please note, Quality Control is not considered as research for this question.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CI</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Is proficiency testing performed for this test?</em>
|
||
</td>
|
||
<td>Select Yes or No to indicate whether the test is subject to periodic internal or external evaluation of the accuracy of test results.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CJ</td>
|
||
<td>
|
||
<p>Minimal* (if 'Yes' is selected for PT performed)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Proficiency testing method</em>
|
||
</td>
|
||
<td>
|
||
<p>Specify which type of proficiency testing is performed. Proficiency testing is a determination of laboratory testing performance by means of interlaboratory comparisons wherby a group of laboratories receive multiple specimens for analysis and/or identification and the program compares the results among laboratories and/or with an assigned valude. Alternative assessment is the determination of laboratory testing performance by means other than PT such as split-sample testing or testing by a different method. Choices include:</p>
|
||
<p>
|
||
<em>Alternative Assessment<br />Formal PT program<br />Inter-Laboratory<br />Intra-Laboratory<br />Other</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CK</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected for PT method)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Proficiency testing method, 'Other' value</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for proficiency testing method.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CL</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Provider for proficiency testing</em>
|
||
</td>
|
||
<td>
|
||
<p>Specify the agency or society that administers the proficiency testing program for the test. Options include:</p>
|
||
<p>
|
||
<em>American College of Medical Genetics / College of American Pathologists, ACMG/CAP<br />
|
||
American College of Physicians - Medical Laboratory Evaluation, ACP MLE<br />
|
||
Association for Molecular Pathology, AMP<br />
|
||
Belgian Official EKE Schemes, GLP Monitoring Programme<br />
|
||
Canadian External Quality Assessment Laboratory, CEQAL<br />
|
||
Centers for Disease Control and Prevention Newborn Screening Quality Assurance Program, CDC DLS<br />
|
||
Clinical Pathology Accreditation (UK) Ltd., CPA<br />
|
||
College of American Pathologists, CAP<br />
|
||
European Concerted Action on Thrombosis External Quality Assessment Program, ECAT EQAP<br />
|
||
European Molecular Genetics Quality Network, EMQN<br />
|
||
European Research Network for the Evaluation and Improvement of Screening Diagnosis and Treatment of Inherited Metabolic Disorders - External Quality Assessment Schemes, ERNDIM EQAS<br />
|
||
External Quality Assessment for Molecular Genetic Testing for Phenylketonuria, EQA-PKU<br />
|
||
Human Genetic Society of Australasia, HGSA<br />
|
||
Institute for Standardization and Documentation in the Medical Laboratory, INSTAND<br />
|
||
Other<br />
|
||
Pacific Northwest Regional Genetics Group, PacNoRGG<br />
|
||
Society for Inherited Metabolic Disorders, SIMD</em>
|
||
</p>
|
||
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CM</td>
|
||
<td>
|
||
<p>Minimal* (if 'Other' is selected for Provider for proficiency testing)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>
|
||
<em>Provider for proficiency testing other value</em>
|
||
</em>
|
||
</td>
|
||
<td>Enter the corresponding 'Other' value for provider for proficiency testing.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CN</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Description of proficiency testing method</em>
|
||
</td>
|
||
<td>Explain proficiency testing (PT) method and provide PT scores and/or results, the PT reportable range, the PT interval and the number of specimens tested.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CO</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support proficiency testing description</em>
|
||
</td>
|
||
<td>Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CP</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Description of internal test validation method</em>
|
||
</td>
|
||
<td>Explain how the laboratory validates the test.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CQ</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support internal test validation description</em>
|
||
</td>
|
||
<td>Provide citations to support assay limitation statements. Provide PubMed ID when available, otherwise full citations or URLs. URLs should be entered with the appropriate prefix, i.e., http:// or https://. If multiple, separate by '|'.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CR</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Major CAP category</em>
|
||
</td>
|
||
<td>
|
||
<p>If College of American Pathologists (CAP) is chosen as Provider for proficiency testing, select Major CAP category from list. Add multiple as needed by entering on a separate line. Choices include:</p>
|
||
<p>
|
||
<em>ABO Subgroup Typing<br />
|
||
Alpha-1 Antitrypsin (SERPINA1) Genotyping<br />
|
||
Anti-HCV, Rapid Methods, Waived<br />...
|
||
</em></p>
|
||
<p>For the complete, current list of choices for this field, see <a href="https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_categories.txt">https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_categories.txt</a>.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CS</td>
|
||
<td>
|
||
<p>Recommended</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>CAP category</em>
|
||
</td>
|
||
<td>
|
||
<p>If Major CAP category is selected, specify relevant sub-category. Add multiple as needed by entering on separate lines, corresponding to entry in column CR. Choices include: </p>
|
||
<p><em>10q (PTEN) deletion<br />ABO grouping<br />ABO grouping (includes A subtyping)...</em></p>
|
||
<p>For the complete, current list of choices for this field, see <a href="https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_list.txt">https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_list.txt</a>.</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>CT</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>CAP test list</em>
|
||
</td>
|
||
<td>
|
||
<p>Choose the appropriate test code corresponding to the CAP category if provided. Choices include:</p>
|
||
<p><em>AAT<br />ABO<br />ABOSG<br />...</em></p>
|
||
<p>For the complete, current list of choices for this field, see <a href="https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_codes.txt">https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_codes.txt</a>.</p>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table></p>
|
||
|
||
|
||
<h3 id="novel-condition-tab"><em>Novel Condition Tab</em></h3>
|
||
|
||
|
||
<p><table border="1" cellpadding="1" cellspacing="1" height="463" width="934">
|
||
<thead>
|
||
<tr>
|
||
<th scope="col">
|
||
<strong>Column</strong>
|
||
</th>
|
||
<th scope="col">
|
||
<strong>Status</strong>
|
||
</th>
|
||
<th scope="col">
|
||
<strong>Description</strong>
|
||
</th>
|
||
<th scope="col">
|
||
<strong>Hints</strong>
|
||
</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>A</td>
|
||
<td>
|
||
<p>Minimal* (if providing novel condition)</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>#Conditions/Phenotypes</em>
|
||
</td>
|
||
<td>Enter your novel condition/phenotype name. To be sure the condition is novel, please search the GTR public web site (<a href="https://www.ncbi.nlm.nih.gov/gtr">www.ncbi.nlm.nih.gov/gtr</a>) for condition names. Note, your term may be an alternate term for a GTR condition name. Searching GTR will help prevent duplicate entries and ease test discovery for health care providers. If known, provide the term as the SNOMED CT preferred terminology.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>B</td>
|
||
<td>
|
||
<p>Minimal* (if providing novel condition)</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Indication type</em>
|
||
</td>
|
||
<td>
|
||
<p>Choose the category most appropriate for your novel condition/phenotype term. Options include:</p>
|
||
<p>
|
||
<em>Disease<br />Pharmacological response<br />Named protein variant<br />Blood group<br />Finding<br />Quantitative trait</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>C</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Lab displayed condition preferred name</em>
|
||
</td>
|
||
<td>If the term submitted in column A is the SNOMED CT preferred term, but you would like a different term displayed for your test, enter the alternate term here. This should be a single term.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>D</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Suggest synonyms for condition</em>
|
||
</td>
|
||
<td>Enter synonyms for the novel condition.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>E</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Public</p>
|
||
</td>
|
||
<td>
|
||
<em>Lab displayed acronym for the condition</em>
|
||
</td>
|
||
<td>Enter your preferred acronym for the novel condition. This should be a single term.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>F</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Suggest acronyms for condition</em>
|
||
</td>
|
||
<td>Enter acronyms for the novel condition.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>G</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Mode of inheritance for the condition</em>
|
||
</td>
|
||
<td>
|
||
<p>Select the mode of inheritance for the novel condition. Options include:</p>
|
||
<p>
|
||
<em>Autosomal dominant inheritance<br />Autosomal recessive inheritance<br />Autosomal unknown<br />Codominant<br />Genetic anticipation<br />Mitochondrial inheritance<br />Other<br />Sex-limited autosomal dominant<br />Somatic mutation<br />Sporadic<br />X-linked dominant inheritance<br />X-linked inheritance<br />X-linked recessive inheritance<br />Y-linked inheritance</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>H</td>
|
||
<td>Minimal* (if 'Other' selected in column 'G')</td>
|
||
<td>
|
||
<em>Mode of inheritance, 'Other' value</em>
|
||
</td>
|
||
<td>If 'Other' was selected in column G, please specify the new term.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>I</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Disease mechanism for the condition</em>
|
||
</td>
|
||
<td>
|
||
<p>Describe the disease mechanism for the relationship of condition to test target. Options include:</p>
|
||
<p>
|
||
<em>Other<br />Gain of function<br />Loss of function</em>
|
||
</p>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>J</td>
|
||
<td>Minimal* (if 'Other' selected in column 'I')</td>
|
||
<td>
|
||
<em>Disease mechanism, 'Other' value</em>
|
||
</td>
|
||
<td>If 'Other' was selected in column I, please specify the new term.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>K</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Prevalence (text description)</em>
|
||
</td>
|
||
<td>Enter the prevalence, or the most current estimated number of cases of the disease in the population.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>L</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Prevalence (URL)</em>
|
||
</td>
|
||
<td>If 'Prevalence' is provided, either an URL or a citation is recommened to support the prevalence claim. URLs should be entered with the appropriate prefix, i.e., http:// or https://.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>M</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Citations to support prevalence</em>
|
||
</td>
|
||
<td>If 'Prevalence' is provided, either an URL or a citation is recommended to support the prevalence claim. Please enter PubMed ID if known, otherwise full citation.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>N</td>
|
||
<td>
|
||
<p>Optional</p>
|
||
<p>Private</p>
|
||
</td>
|
||
<td>
|
||
<em>Comments to GTR staff about condition</em>
|
||
</td>
|
||
<td>Enter information for GTR staff regarding the addition of a novel condition/phenotype name to the GTR database. Please include reasoning and if you searched for the term on the GTR public site. Citations are useful when GTR staff evaluates the novel condition.</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
|
||
|
||
<h2 id="bulk-submit">Upload your completed spreadsheet.</h2>
|
||
|
||
|
||
<p>From your home page in Submission Portal, go to the section 'Tests in this lab'. Then click on 'Submit tests' to go to the test submission page. See <a href="/gtr/docs/submit_tests/#multiple_tests">Submit multiple tests</a>.</p>
|
||
|
||
|
||
<h3 id="submission-notifications">Submission notifications</h3>
|
||
|
||
|
||
<p>You will receive a notification via email within a few minutes of uploading your file. </p>
|
||
|
||
|
||
<ul>
|
||
<li><em>Success</em>. If your spreadsheet is successfully uploaded, you will receive an email entitled '<em>Your tests submitted in bulk have been successfully registered in GTR</em>'.</li>
|
||
<li><em>Warnings</em>. If your speadsheet is successfully uploaded but has tests with order codes that match tests you already submitted to GTR, you will receive an email with warnings for the list of tests that have the same order codes as tests already in the GTR. You can review these tests in the submission user interface, in case they were submitted in error as duplicates or the order codes need to be edited. Distinct tests can have the same order code, so you are not required to make edits. This validation step is performed to help you detect possible duplications in your submissions.</li>
|
||
<li><em>Errors</em>. If your spreadsheet contains errors and cannot be processed, , you will receive an email with the list of errors. You will need to correct these errors and resubmit your spreadsheet. See the <a href="#errors">list of errors</a> and how to address them.</li>
|
||
</ul>
|
||
|
||
|
||
<p>Once the spreadsheet has been successfully processed, the tests uploaded will display in your GTR Submission Portal homepage, under 'Tests in this lab'. If successful, your tests will display on the GTR public web site following indexing, within 24-48 hours.</p>
|
||
|
||
|
||
<h2 id="submission_tips">Submission tips</h2>
|
||
|
||
|
||
<h3 full_submission_variant="full_submission_variant" id="variants">Variants</h3>
|
||
|
||
|
||
<p><strong>HGVS expressions:</strong> </p>
|
||
|
||
|
||
<p>When submitting variants use the fully qualified <a href="https://varnomen.hgvs.org/">HGVS</a> expression. Use the Refseq assession with version (Accession.version) for a complete expression, preferably only including the nucleotide change.</p>
|
||
|
||
|
||
<p>Examples:<br />
|
||
Gene: FBN1<br />
|
||
Variant: NM_000138.5:c.8512A>T </p>
|
||
|
||
|
||
<p>Gene: DHCR7<br />
|
||
Variant: NM_001360.3:c.964-1G>C </p>
|
||
|
||
|
||
<p>You may use the following tools to validate HGVS expressions prior to submission: </p>
|
||
|
||
|
||
<p><a href="https://mutalyzer.nl/">Mutalyzer</a><br />
|
||
<a href="https://variantvalidator.org/">Variant Validatator</a> </p>
|
||
|
||
|
||
<p><strong>Submitting variant data in the spreadsheet</strong> </p>
|
||
|
||
|
||
<p>For the full template spreadsheet submission, if there are multiple variants for a Condition or phenotype, use the pipe delimiter ("|") to separate them. </p>
|
||
|
||
|
||
<p>Example: for a test that interrogates the 1477_1478del and 1477C>T of the CFTR gene for Cystic fibrosis, you would enter: </p>
|
||
|
||
|
||
<p>Column BR: MIM number<br />
|
||
Column BS: 219700<br />
|
||
Column BT: Germline<br />
|
||
Column BU: gene<br />
|
||
Column BV: CFTR<br />
|
||
Column BW: NM_000492.4:c.1477_1478del|NM_000492.4:c.1477C>T </p>
|
||
|
||
|
||
<p><strong>Clinical significance of the variant</strong> </p>
|
||
|
||
|
||
<p>When multiple variants are separated by a pipe delimiter ("|"), if provided, the clinical significance and citation are associated with each variant. For a variant to have a distinct clinical significance and citation, enter the variant in a new row, with its own clinical significance.</p>
|
||
|
||
|
||
<h2 id="errors">Validation error messages</h2>
|
||
|
||
|
||
<p>Once your file is uploaded, the submission processing software performs validation checks on the data. Errors will be flagged in the email notification. You will need to make the apppropriate edits to the data to address these errors and then upload the file again. </p>
|
||
|
||
|
||
<ol>
|
||
<li>
|
||
<p>Cell with missing values (required fields only, for a list of required fields, please see the table <a href="#definitions">'Definitions and column values'</a>).</p>
|
||
</li>
|
||
<li>
|
||
<p>Cell contains multiple values whereas only a single value is allowed.</p>
|
||
</li>
|
||
<li>
|
||
<p>The number of values between certain cells is required to match. Some cells are interdependent; for example, each test target needs to be linked to at least one indication.</p>
|
||
</li>
|
||
<li>
|
||
<p>The condition/phenotype name is not recognized by GTR. Please check the syntax or spelling of the terms you enter. You can find recognized terms by <a href="/gtr/conditions/">searching GTR</a>.</p>
|
||
</li>
|
||
<li>
|
||
<p>The MIM number is not recognized as a condition record. Please make sure that all MIM numbers correspond to a condition/phenotype record in OMIM (i.e., MIM numbers for gene records are not accepted as condition identifiers).</p>
|
||
</li>
|
||
<li>
|
||
<p>The entry for 'Name of what is tested' does not match a gene symbol in the GTR database, which uses symbols from the HUGO Gene Nomenclature Committee (HGNC). Please review entries for misspellings and/or <a href="/gtr/genes/">search GTR for recognized gene symbols</a>.</p>
|
||
</li>
|
||
<li>
|
||
<p>Value entered does not match any of the allowed values, e.g., in a controlled field list such as 'Purpose of the test'. Check the options available in the column.</p>
|
||
</li>
|
||
<li>
|
||
<p>Test performance location(s): Either entire test in-house, or all test work location must be specified (Specimen preparation; Wet lab work; Interpretation; Generate report).</p>
|
||
</li>
|
||
<li>
|
||
<p>Permission error. If the current login account is not associated with the lab.</p>
|
||
</li>
|
||
<li>
|
||
<p>AMA license agreement is required if CPT code is provided in Excel file. The submitter must read and agree to the AMA license agreement prior to uploading a full test submission file with CPT codes entered. Please log into the submission site and review the AMA license agreement.</p>
|
||
</li>
|
||
<li>
|
||
<p>Un-recognized column header or empty header in the Excel fiel, e.g., column has been renamed by user.</p>
|
||
</li>
|
||
<li>
|
||
<p>Excel file error, such as the file is not an Excel file, or the file does not have a 'lab test' worksheet, or we cannot read data from the file.</p>
|
||
</li>
|
||
<li>
|
||
<p>Database error during validation. This is the rare case when the database connection is broken during validation. Please try uploading again.</p>
|
||
</li>
|
||
</ol>
|
||
|
||
|
||
<p>Processing also checks for order codes that match tests already registered by your lab in GTR and if found, will generate a warning message. This is not considered to be an error. Laboratories may use the same order code for different tests, so this check is meant to alert you to the possibility of duplication or a typographical error in entering a code. This message is information for your consideration and will not halt processing of your file.</p></div>
|
||
|
||
</div>
|
||
<!--/.col1-->
|
||
<div class="col2">
|
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|
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|
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|
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