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This document is an overview of the methods by which information can be registered in the GTR.  Detailed information is provided in specific pages, as summarized below.  The table of contents expedites navigation to the section of interest.

Table of Contents

1. What constitutes a test in the GTR?
2. What types of tests are currently accepted?
3. What data should be collected before submitting?
4. Submission scenarios
5. How do I get started?
6. Who is authorized to submit?
7. Overview of the steps to register labs and tests
8. List of the steps, with links to detailed information about each step
9. Conventions used in the interactive submission interface
10. Your submission home page
11. How to update your records in the GTR
12. Locate older versions of test and lab submissions

What constitutes a test in the GTR?

A test in the GTR is defined as the equivalent of an order code. The definition of a genetic test in the GTR may be found here.

What types of tests are currently accepted?

GTR is now accepting registration of clinical genetic tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests.

GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests. To receive notification when this status is changed, please consider subscribing to GTR News.

As noted, research tests are not yet in scope for GTR but submissions soon will be accepted. Laboratories offering research tests may participate in GTR now by newly registering their lab or migrating their lab information from GeneTests. Laboratories whose test menus include both clinical tests and research tests may migrate their clinical tests after registering their lab, but cannot yet migrate their research tests.

Laboratories that participate in the GeneTests Laboratory Directory have the option of registering their lab as a new record in GTR instead of migrating their laboratory information. Labs that wish to do so should notify GTR so that prior participation in GeneTests is recognized for processing purposes and to avoid duplicate display of lab records.

Some information in GeneTests that is represented as a Laboratory service is also represented as such in the GTR. Tests that are general and not specific to a particular condition, set of conditions or genes, or chromosomal structures are categorized by GTR as Laboratory services and will be entered in the laboratory record. One such example is Preimplantation Genetic Diagnosis (PGD). However, some entries processed as Laboratory services or miscellaneous testing by GeneTests but are truly tests or testing methods (e.g. Multi-Gene Panels) will not be migrated but can be registered as a fully-described test. Whole exome sequencing and whole genome sequencing are considered to be tests in GTR, but are not yet in scope as fully described tests. These may now be entered as Laboratory services, with the opportunity to provide information in a comment box, and at a later phase they will be registered as tests.

Tests which are performed entirely at an outside lab/facility (send-outs) should not be registered in GTR. 'Outside' means a lab/facility that is not covered by your lab's CLIA certification, even if both labs have the same parent organization.

What data should be collected before submitting?

The list of data elements that may be submitted is provided in GTR's Data Dictionary (pdf or Word). These elements are categorized as minimal, recommended, and optional. Minimal fields are required, and submission will fail if not supplied. Recommended elements are not required, and can be skipped in the submission process. The web interface will, however, report 'not provided' for blank recommended fields. Test records containing more completed recommended fields will be ranked higher in search results, as described here. Optional fields are not required, and can be skipped in the submission process. The web interface will not display optional fields left blank. A tabulation of field requirement types is located here.

For laboratories currently registered in GeneTests, most of the minimal data elements are already available electronically and can be copied from GeneTests to the GTR. While the GTR and GeneTests sites are both available, you may find it useful to consider timing the migration of your data to the GTR to follow immediately after you update your information in GeneTests. That way, the updates you wish to make public will be available in both resources, and will be transferred without duplicate data entry in the GTR.

Migration of lab and test data is not sufficient to achieve the minimal requirements of the GTR. Some supplementary data are required. In the Laboratory section, the minimal fields Facility phone number and email address may need to be entered depending on whether your lab previously submitted these data to GeneTests. The following fields must be completed to register a migrated test:

1. Laboratory test name (as you want it to be publicly displayed in the GTR)
2. Purpose of the test (indications selected from these choices: Diagnosis, Drug response, Mutation confirmation, Pre-implantation genetic diagnosis, Risk assessment, Screening)
3. Primary test methodology (name of the test method used in the assay, e.g. Oligonucleotide Ligation Assay (OLA), Enzymatic levels)
4. Target identified by and Name of target (Analyte, chromosomal region, gene, or protein; and specific name of the target such as a gene symbol or enzyme name)
5. Analytical validity (Quantitative information on the accuracy and reliability of the test for measuring the component of interest)

Submission scenarios

Registration in GTR is divided into two major categories:

1. Laboratory registration

• Laboratory and personnel data that are applicable to all tests are entered once.
• All laboratory registrations are performed through the interactive web-based submission user interface.
• The 'Default parameters' tab enables the entry of information that is shared by most tests offered by the lab. Information supplied in this tab will pre-populate test records for later review and editing, potentially saving keystrokes.

2. Test registration

• Submission of test-specific information, where a test is defined as the equivalent of an order code.

Scenarios for test submissions

1. Completely interactive:
   The submitter enters and reviews information via web-based forms.
   Labs that participate in the GeneTests Laboratory Directory can migrate test information after registering their laboratory information in the GTR.  New tests can be created by any lab registered in GTR.

2. Semi-automatic submission using the GTR test submission template:
   The submitter downloads a test submission template file (gtr_test_submission_template.xlsx) which supports entry of all required test fields and certain recommended fields.
   The submitter completes the spreadsheet for each test the lab wishes to register. This submission scenario is mutually exclusive from migration of test data from GeneTests to the GTR. The submitter uses the interactive submission interface to review each record seeded by the spreadsheet, enters information as desired for any recommended and optional fields not supported by the spreadsheet, and submits each test. Read more about this mode of submission here.

3. Bulk submission of test targets and corresponding test indications (pending):
   This mode of submission is intended for tests that assay multiple markers or test targets (e.g. genes, variations, proteins) for multiple indications (i.e. conditions/phenotypes).
   Test submission will be through the interactive submission interface (but could be seeded by the semi-automatic test submission mode).  The submitter will download a spreadsheet template from the methodology tab of the submission interface, complete a spreadsheet for each pertinent test, upload the result, and use interactive submission site to review and submit the information for processing.

4. Completely automatic (pending):
   The submitter uploads an XML file containing comprehensive information for each test the lab wishes to register.
   We encourage laboratories that are potentially interested in this mode of submission to examine the xml and xsd files on our ftp site and to contact GTR staff to discuss this option.

How do I get started?

The GTR help site includes multiple documents about registering laboratories and tests, with some specific and distinctive aspects of the submission/update process. The tabs at the top of the page provide menus from which to select the page specific to your topic of choice.  Details about each tab are provided in the table below.

The submitter needs a MyNCBI account to access the GTR submission user interface.

Laboratory information must be entered first. New laboratories have a wait period of 2-3 business days for GTR staff to review the laboratory record. Test information laboratory can be entered only after the laboratory has been registered in the GTR.

Who is authorized to submit?

At the moment, only one person per lab can submit lab and test data to GTR. You may choose whom to designate in your lab to submit to GTR, and that person will need a MyNCBI account.

If your lab will be migrating data from GeneTests, the same individual will need to be authorized to login to GeneTests. The GeneTests login is distinct from the MyNCBI account and they are not linked to each other.

Overview of the steps to register labs and tests

1. Go to the GTR Submission user interface
2. Login with your MyNCBI credentials
3. If your laboratory participates in the GeneTests Laboratory Directory, you can copy information from GeneTests to GTR about both your laboratory and each of the tests you offer by a process termed migration.  You can then review the content, add more details about your laboratory interactively, and submit your lab data.
4. If your lab is not registered in GeneTests, you can create a new record about your laboratory. Log in to the submission interface and proceed through the steps below, then click the Add a new lab button. Once you submit your lab, you will receive an email informing you your information was submitted. GTR staff will review the information and must approve your lab before you can register your tests. This process may take 2-3 business days. We may contact the lab if more information is needed. When your lab is approved, you will receive a notification email informing you that you can register your tests.
5. Once you have an active laboratory record, you may migrate (copy) test information from GeneTests or create new test records, review the information and submit the records interactively.
6. If you have many tests to register, you can consider submitting data to GTR in bulk. For tests in GeneTests you must choose whether you want to migrate their data or create new records using the bulk process. Currently in scope is a mechanism to provide a file containing details about each test, to be reviewed and submitted via the interactive submission interface. 

List of the steps, with links to detailed information about each step