U.S. flag

An official website of the United States government

Submitting Clinical Microbe Tests Using the submission spreadsheet with All Clinical Test Fields

OMB NO: 0925-0651

EXPIRATION DATE: 01/31/2025

Burden Statement

This mode of submission is for clinical tests only.

Download the GTR Microbe Test Full Submission Template

There are two ways to download the submission template with all clinical tests fields:

  • From the GTR FTP site, download the microbe test full submission template
  • To download your lab-specific template, go to your home page in the GTR submission Portal.
  • For Microbe Tests: Under 'Submission of Tests', click to expand the section 'Microbe Tests', then click to expand 'Download spreadsheet submission templates and your previously submitted data for microbe clinical tests'. You will see the following option:
    • Download blank spreadsheet with all clinical test fields

Download your bulk submission spreadsheet

Download Previously Submitted Microbe Test Data

Go to your home page in the GTR submission Portal.

  • For Microbe Tests: Under 'Submission of Tests', click to expand the section 'Microbe Tests', then click to expand 'Download spreadsheet submission templates and your previously submitted data for microbe clinical tests'. You will see the following option:
    • Download/email a file with all your previously submitted data for microbe clinical tests

Download previously submitted data

Sample tests

A file with sample microbe tests in the full test submission template can be downloaded here.

Definitions and column values

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.

Four columns pertain to the spreadsheet submission process: (A) Test tracking ID, (B) GTR accession, (C) Action and (BT) Condition/phenotype: choose name or identifier source. All of the remaining columns correspond to fields that are part of overall GTR test submission.

Key for Status column

Private = field will not display to the public

Public = field will be viewable by GTR users

Minimal = field must be completed for this file to be processed successfully

Recommended = field will display as 'Not provided' if left blank

Optional = field will not display to the public if left blank (i.e. if not applicable for the test)

Lab Test Tab

All clinical fields submission spreadsheet: Submitting microbe tests
Column Status Description Hints
A

Minimal

Private

Test tracking ID 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 must 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 (e.g. 1,2,3,4,...)
B

Minimal* (if updating or deleting)

Private

GTR Accession 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.
C

Minimal

Private

Action

Field used to determine which action to perform on the row(s) corresponding to a single test. Only enter once per test. Selections include:

  • Update: Edit an existing GTR test
  • Delete: Permanently remove an existing GTR test
  • Add New: Create a new test registration
  • No Change: Do nothing to the existing test registration
D

Recommended

Public

Test order code 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.
E

Minimal

Public

Laboratory test name 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.
F

Optional

Public

Laboratory test short name 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. Complete this field only for the first line of data for each test.
G

Optional

Public

Manufacturer's test name 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.
H

Optional

Public

URL for the test Enter the URL for test-specific information on your laboratory's website. URLs should be entered with the appropriate prefix, i.e., http:// or https://. Complete this field only for the first line of data for each test.
I

Optional

Private

Search terms 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.
J

Minimal 

Public

Purpose of the test

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. In the spreadsheet, you can select from the following list:

Diagnosis
Drug Response
Microbe identification
Monitoring
Predictive
Recurrence
Screening
Therapeutic management
Viral load

K

Recommended

Public

Target population for this test Provide information on which population segment(s) the test is appropriate for and why. Complete this field once for each test. Example: Individuals presenting with clinical symptoms for Streptococcal sore throat.
L

Recommended

Public

Citations for target population 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.
M

Optional

Public

Has there been FDA review of this test? Select the option (Yes/No) 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.
N

Optional

Public

If no FDA review, FDA category designation

Select the appropriate option from the available choices:

EUA - Emergency Use Authorization
FDA exercises enforcement discretion
Not applicable

O

Optional

Public

If FDA review, item reviewed 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:

ASR - Analyte-specific reagents
Assay(s)
IVDMIA - In Vitro Diagnostic Multivariate Index Assay(s)
Instrument(s)
Test kit(s)
Other (specify in Column P)

P

Minimal* (if 'Other' selected in item reviewed)

Public

Item reviewed, 'Other' value Enter the text corresponding to the 'Other' value for Item reviewed.
Q

Optional

Public

If FDA review, FDA category designation 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:

IUO - Investigational Use Only -The performance characteristics of this product have not been established.
IVD - In Vitro Device
RUO - Research Use Only- Not for use in diagnostic procedures.

R

Optional

Public

If FDA review, FDA regulatory status 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:

FDA cleared/approved
FDA exempt
Pending
Not submitted
Other (specify in Column S)

S

Minimal* (if 'Other' selected in regulatory status)

Public

Regulatory status, 'Other' value Enter the corresponding 'Other' value for regulatory status.
T

Optional

Public

If FDA review, application number 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.
U

Optional

Public

NYS CLEP status This field is required if 'NYS CLEP' is a valid certification for the specific test. Enter the status of the NYS CLEP approval for the test. This field should only be completed once per test. Options include:

Approved
Not approved
Pending
Grandfathered
Exempt

V

Minimal* (if licensed by NYS)

Public

NYS CLEP license number This field is required if 'NYS CLEP' is a valid certification for the specific test. Enter the license number provided by NYS CLEP for the approved test. This field should only be completed once per test.
W

Recommended

Public

Test development 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:

FDA-reviewed (has FDA test name) -The test, test kit or reagents either have FDA approval or are currently in FDA review.
Manufactured (research use only; not FDA-reviewed) -The test or primary parts of the test are purchased from a commercial entity and have not gone through FDA review.
Modified FDA (has FDA-reviewed entry, but with lab modifications/field changes) -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.
Test developed by laboratory (no manufacturer test name) -This test is developed, produced and performed by the submitting laboratory. Also known as LDT.

X

Recommended

Public

How to order (text description) 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.
Y

Recommended

Public

How to order (URL) Enter the URL for information on how to order the test. URLs should be entered with the appropriate prefix,i.e., http:// or https://. Complete this field only for the first line of data for this test.
Z

Optional

Public

Sample collection and transportation requirements Enter any specific information regarding how the sample should be collected and transported
AA

Recommended

Public

Specimen source

Select the specimen type(s) allowed for the test. Multiple selections allowed. Each specimen type should be on a separate line. Choices include:

Amniotic fluid
Bone marrow
Bronchoalveolar lavage
Buccal swab
Buffy coat
Cell culture
Cerebrospinal fluid
Chorionic villi
Cord blood
Fetal blood
Fresh tissue
Frozen tissue
Nasal swab
Nasopharyngeal (NP) swab
Other (please specify in Column AB)
Paraffin block
Peripheral (whole) blood
Plasma
Product of conception (POC)
Saliva
Serum
Skin
Sputum
Throat swab
Urine
White blood cell prep

AB

Minimal* (if 'Other' is selected for specimen source)

Public

Specimen source, 'Other' value Enter the corresponding 'Other' value for specimen source.
AC

Recommended

Public

Specimen source URL 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,i.e., http:// or https://.
AD

Optional

Public

Z-code(s) Enter the Z-codes identifier for this test. The Z-code is a 5-character alpha-numeric code associated with certain molecular diagnostics (MDx) tests used in addition to the CPT code, to help payers and providers clearly understand which test is being ordered, performed, and billed.
AE

Optional

Public

Turnaround time Enter the usual number of hours or days between the time a specimen is received and a result is released. Specify the time unit (e.g., "2-3 days").
AF

Recommended

Public

Test codes (URL) 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,i.e., http:// or https://. Complete this field only for the first line of data for this test.
AG

Optional

Public

LOINC codes 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 '|'.
AH

Optional

Public

CPT codes 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.
AI

Optional

Public

Who can order this test? 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.

Choose from the following options:

Genetic counselor
Health care provider
In-state patients
Licensed dentist
Licensed physician
Nurse practitioner
Out-of-state patients
Physician assistant
Public health mandate
Registered nurse

AJ

Recommended

Public

Informed consent required?

Identify if the laboratory requires informed consent prior to performing the test. Select from the following choices:

Decline to answer
Required
Not required
Based on applicable state law

If not required but recommended, you can comment in the 'How to order' text field.

AK

Optional

Public

Test service

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:

Data Storage and Backup
Other (please specify in Column AL)
Result interpretation

AL

Minimal* (if 'Other' is selected in test service)

Public

Test service, 'Other' value Enter the corresponding 'Other' value for test-specific services.
AM

Optional

Public

Test service order code 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.
AN

Optional

Public

Test service comment Enter further information to assist health care providers in ordering the test-specific services. If multiple services are entered, enter the associated test-specific comment on separate corresponding lines.
AO

Recommended

Public

Testing strategy 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.
AP

Recommended

Public

Citations to support testing strategy 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'|'.
AQ

Recommended

Public

Test-specific contact policy

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:

Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
Post-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.
Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.

AR

Recommended

Public

Test-specific contact person

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.

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 Portal site.

AS

Minimal

Public

Test performance location(s):

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,unless the entire test is performed in-house. Select each option on a separate line.

Entire test performed in-house
Interpretation performed at an outside lab
Interpretation performed both in-house and at an outside lab
Interpretation performed in-house
Report generated at an outside lab
Report generated both in-house and at an outside lab
Report generated in-house
Specimen preparation performed at an outside lab
Specimen preparation performed both in-house and at an outside lab
Specimen preparation performed in-house
Wet lab work performed at an outside lab
Wet lab work performed both in-house and at an outside lab
Wet lab work performed in-house

AT

Minimal* (if any part of the test is performed outside the registering laboratory)

Public

Test performance location(s) comments Briefly describe methods and location for components of test work done at an outside lab.
AU

Minimal

Public

Method Category

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 AU to correspond to the value in column AV. To display the complete list of choices, please:

1. Click on the cell - an arrow displays to the right of the cell, then
2. Click on the gray arrow.

Options include:

Antibody assay
Antigen assay
Combination antibody and antigen assay
Mutation scanning of select exons
Mutation scanning of the entire coding region
RNA analysis
Sequence analysis of select exons
Sequence analysis of the entire coding region
Targeted variant analysis

AV

Minimal

Public

Test method

Select the test method that corresponds to the entry selected in column 'AU' for Method category. Each test must have an entry both in column 'AU' and column 'AV'. 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 'AW'.

To display the complete list of choices, please:

1. Click on the cell - an arrow displays to the right of the cell, then
2. Click on the gray arrow.

Options include:

Allele-specific primer extension (ASPE)
Alternative splicing detection
Antibody detection
Antigen detection
Bi-directional Sanger Sequence Analysis
Chemiluminescent Immunoassay (CIA)
Combination antibody and antigen detection
Comparative Genomic Hybridization
Digital microfluidic microspheres
Enzymatic levels
Enzyme activity
Enzyme-Linked Immunosorbent Assays (ELISA)
Fluorescence in situ hybridization (FISH)
Fluorometry
Gas chromatography–mass spectrometry (GC-MS)
GeneID
Gold nanoparticle probe technology
High-performance liquid chromatography (HPLC)
Liquid chromatography-tandem mass spectrometry (LC-MS/MS)
Liquid chromatography–mass spectrometry (LC-MS)
Metabolite levels
Methylation-specific PCR
Microarray
Multiplex Ligation-dependent Probe Amplification (MLPA)
Multiplex PCR
Multiplex real-time PCR
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Nucleic acid amplification test (NAAT)
Oligonucleotide Ligation Assay (OLA)
Oligonucleotide hybridization-based DNA sequencing
PCR
PCR with allele specific hybridization
PCR-RFLP with Southern hybridization
Pyrosequencing
Quantitative PCR (qPCR)
RFLP
RT-LAMP
RT-PCR
RT-PCR with gel analysis
RT-qPCR
SNP Detection
Tandem mass spectrometry (MS/MS)
Tiling Arrays
Uni-directional Sanger sequencing
Viral load

AW

Minimal* (if 'Other' is selected for test method)

Public

Test method, 'Other' value Enter the corresponding 'Other' value for test method.
AX

Recommended

Public

Instruments used for test method

Name the instrucment used for a specific methodology. Enter each instrument on a separate line, corresponding to the appropriate test method.


Instruments used for test methodInstruments used for test method:pulldown_list
Abbott ID NOW™
Affymetrix GeneChip Scanner 3000 7G Whole-Genome Association System
Affymetrix GeneTitan® MC
Affymetrix HotStart-IT Probe qPCR Master Mix with UDG (2X)
Agilent 2100 Bioanalyzer
Agilent SureSelect
Applied Biosystems 3730 capillary sequencing instrument
Applied Biosystems 7900HT Sequence Detection System
Applied Biosystems SOLiD v4 System Sequencer
BeadXpress® Reader
BioFireDx FilmArray
BioRad CFX96
Cobas® 6800 / 8800 System
Covaris S2 Sonicator
GenMark Diagnostics eSensor XT-8 system
Illumina Genome AnalyzerIIx and Genome AnalyzerIIe
Illumina HiScan™SQ system
Illumina HiSeq™2000 system
Other (please specify in Column AY)
PerkinElmer Victor3 1420 Multilabel Plate Reader
Qiagen AutoPure LS
Qiagen QIAcube
Roche LightCycler 480
Tecan Genesis Robotic Workstation 150

AY

Minimal* (if 'Other' is selected for instruments)

Public

Instruments, 'Other' value Enter the corresponding 'Other' value for instruments.
AZ

Optional

Public

Platforms

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 in Column BA.  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.


PlatformsPlatforms:pulldown_list
Abbott ID NOW™ COVID-19
Affymetrix CytoScan HD Array
Affymetrix Gene Profiling Array cGMP U133 P2
Affymetrix GeneChip Human Genome U133 Plus 2.0 Array
Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0
Affymetrix Genome-Wide Human SNP Array 6.0
Affymetrix QuantiGene 2.0 Assay
Agilent Human CpG Island Microarray Kit, 1x244K
Agilent Human ENCODE ChIP-on-chip Microarray
Agilent Human miRNA Microarray Kit Release 16.0, 8x60K
Agilent SurePrint G3 Human CGH Microarray Kit, 2x400K
Amersham CodeLink UniSet Human I Bioarray
BioFireDx FilmArray Pneumonia Panel plus
Cobas® SARS-CoV-2 Test
Illumina Infinium HD HumanCytoSNP-12
Life Technologies TaqMan OpenArray MicroRNA Panels
LightMix® Modular Assays
NimbleGen CGH 3-plex ISCA Plus Cytogenetic Array
None/not applicable
Other
Oxford Gene Technology CytoSure DMD (4x44k)
Oxford Gene Technology CytoSure ISCA UPD (4x180k)
Oxford Gene Technology CytoSure ISCA v2 (4x180k)
Oxford Gene Technology CytoSure ISCA v2 (4x44k)
Oxford Gene Technology CytoSure ISCA v2 (8x60k)
Oxford Gene Technology CytoSure Syndrome Plus v2 (2x105k)
RIDA®GENE Bacterial Stool Panel
RIDA®GENE Viral Stool Panel III
ZEUS Borrelia Modified Two-Tiered Testing™ (MTTT) for Lyme Disease

BA

Minimal* (if 'Other' is selected for platform)

Public

Platform, 'Other' value Enter the corresponding 'Other' value for platforms.
BB

Optional

Public

Test procedure or protocol Summarize the methodology and describe the specific steps for each method of the assay.
BC

Optional

Public

Citations to support test procedure or protocol 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,i.e.,http:// or https://.
BD

Recommended

Public

Confirmation of test results 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'.
BE

Optional

Public

Test comment 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.
BF

Minimal

Public

Analytical Validity

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".

BG

Recommended

Public

Citations to support analytical validity 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.
BH

Optional

Public

Positive and negative predictive value (PPV and NPV) Provide quantitative information about this test's positive and negative predictive values (e.g. PPV at prevalence = 5% is 100%; NPV at prevalence = 5% is 99.5%).
BI

Optional

Public

Citations to support PPV and NPV 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.
BJ

Recommended

Public

Clinical validity 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, the population(s) assessed, and 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. Clinical specificity is the proportion of negative test results among patients without the defined clinical presentation.
BK

Recommended

Public

Citations to support clinical validity 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://.
BL

Recommended

Public

Assay limitations 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.
BM

Recommended

Public

Citations to support assay limitations 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 '|'.
BN

Optional

Public

Minimal microbe load your test can detect Limit of detection for the microbe load below which the test cannot reliably detect the microbe (e.g., Viral loads < 20 copies/ml cannot be reliable detected and will be reported as “below the limit of detection”).
BO

Optional

Public

Citations to minimal microbe load your test can detect 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 '|'.
BP

Recommended

Public

Clinical utility category

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:

Avoidance of invasive testing
Establish or confirm diagnosis
Guidance for management
Guidance for selecting a drug therapy and/or dose
Lifestyle planning
Other (please specify in Column BQ)
Sufficient research has not been conducted to demonstrate the utility of the test

BQ

Minimal* (if 'Other' is selected for Clinical utility category)

Public

Clinical utility category other value Enter the corresponding 'Other' value for Clinical utility category.
BR

Minimal* (if a clinical utility category is chosen, a citation or URL is required)

Public

URL to explain clinical utility 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 BP.
BS

Minimal* (if a clinical utility category is chosen, a citation or URL is required)

Public

Citations to support clinical utility Provide citations to support clinical utility statements. Provide PubMed ID when available, otherwise full citations. 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 BP. If multiple citations for a single clinical utility statement, enter on the same row, but separate by '|'.
BT

Minimal

Private

Condition/phenotype: choose name or identifier source

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 http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/gtr. In the spreadsheet, you can select from the following list:

condition name
CUI
HPO identifier
MeSH ID
MIM number
MONDO ID
Orphanet identifier

BU

Minimal

Public

Conditions/Phenotypes

If you selected condition name in column BT, write the preferred name of the condition/phenotype. You can search GTR 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. Learn how to use MedGen to select condition and phenotype terms.

If you selected another identifier source in Column BT, enter the corresponding identifier here.

If multiple conditions/phenotypes exist for a single target (columns BT through BY), enter values separated by a vertical bar (|). If same condition/phenotype exists for multiple targets, the condition/phenotype must be repeated on each target line.

BV

Minimal

Public

Target is identified by

Select the type of target from the following options:

bacterium
fungus
microbe
protozoan
virus

BW

Minimal

Public

Organism

Enter the name of the microbe.

BX

Minimal (for Serology test)

Public

Target category

 

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:

gene
protein
analyte
variant
chromosomal region/mitochondrion

Note that gene is used to represent molecular assays that detect variations in a gene or set of genes. Multiple genes for the same microorganism can be separated by a vertical bar (|)

BY

Minimal (for Serology test)

Public

Name of what is tested

If gene in column BX, enter official gene symbol. If chromosomal region/mitochondrion in BX, 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.

BZ

Optional

Public

How long can the microbe be present after therapy (rendering consequent tests meaningless)

Describe the usual or average timeframe the microbe may be present after therapy in which case testing is not recommended.

CA

Optional

Public

Comments about the test interpretation (e.g. clinical implication of test results)

Explain how the lab addresses findings from test results.

CB

Optional

Public

Research performed after clinical testing is complete

Describe whether the submitted sample is used for research after clinical analysis is complete (quality control is not considered research in this question).

CC

Recommended

Public

Is proficiency testing performed for this test? Select Yes or No to indicate whether the test is subject to periodic internal or external evaluation of the accuracy of test results.
CD

Minimal* (if 'Yes' is selected for PT performed)

Public

Proficiency testing method

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:

Alternative Assessment
Formal PT program
Inter-Laboratory
Intra-Laboratory
Other

CE

Minimal* (if 'Other' is selected for PT method)

Public

Proficiency testing method, 'Other' value Enter the corresponding 'Other' value for proficiency testing method.
CF

Recommended

Public

Provider for proficiency testing

Specify the agency or society that administers the proficiency testing program for the test. Options include:

American College of Medical Genetics / College of American Pathologists, ACMG/CAP
American College of Physicians - Medical Laboratory Evaluation, ACP MLE
Association for Molecular Pathology, AMP
Belgian Official EKE Schemes, GLP Monitoring Programme
Canadian External Quality Assessment Laboratory, CEQAL
Centers for Disease Control and Prevention Newborn Screening Quality Assurance Program, CDC DLS
Clinical Pathology Accreditation (UK) Ltd., CPA
College of American Pathologists, CAP
European Concerted Action on Thrombosis External Quality Assessment Program, ECAT EQAP
European Molecular Genetics Quality Network, EMQN
European Research Network for the Evaluation and Improvement of Screening Diagnosis and Treatment of Inherited Metabolic Disorders - External Quality Assessment Schemes, ERNDIM EQAS
External Quality Assessment for Molecular Genetic Testing for Phenylketonuria, EQA-PKU
Human Genetic Society of Australasia, HGSA
Institute for Standardization and Documentation in the Medical Laboratory, INSTAND
Other
Pacific Northwest Regional Genetics Group, PacNoRGG
Society for Inherited Metabolic Disorders, SIMD

CG

Minimal* (if 'Other' is selected for Provider for proficiency testing)

Public

Provider for proficiency testing other value Enter the corresponding 'Other' value for provider for proficiency testing.
CH

Recommended

Public

Description of proficiency testing method 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.
CI

Recommended

Public

Citations to support proficiency testing description 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 '|'.
CJ

Recommended

Public

Description of internal test validation method Explain how the laboratory validates the test.
CK

Recommended

Public

Citations to support internal test validation description 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 '|'.
CL

Recommended

Public

Major CAP category

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:

For the complete, current list of choices for this field, see https://ftp.ncbi.nlm.nih.gov/pub/GTR/standard_terms/CAP_test_categories.txt.

CM

Recommended

Public

CAP category

If Major CAP category is selected, specify relevant sub-category. Add multiple as needed by entering on separate lines, corresponding to entry in column CQ. Choices are available in the dropdown menu.

CN

Optional

Public

CAP test list

Choose the appropriate test code corresponding to the CAP category if provided. Choices are available in the dropdown menu.

Novel Condition Tab

Microbe tests full submission spreadsheet: Novel conditions tab
Column Status Description Hints
A

Minimal* (if providing novel condition)

Public

#Conditions/Phenotypes Enter your novel condition/phenotype name. To be sure the condition is novel, please search the GTR public web site (www.ncbi.nlm.nih.gov/gtr) 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.
B

Minimal* (if providing novel condition)

Private

Indication type

Choose the category most appropriate for your novel condition/phenotype term. Options include:

Infectious disease
disease
pharmacological response

C

Optional

Public

Lab displayed condition preferred name 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.
D

Optional

Public

Suggest synonyms for condition Enter synonyms for the novel condition.
E

Optional

Public

Lab displayed acronym for the condition Enter your preferred acronym for the novel condition. This should be a single term.
F

Optional

Private

Suggest acronyms for condition Enter acronyms for the novel condition.
G

Optional

Private

Prevalence (text description) Enter the prevalence, or the most current estimated number of cases of the disease in the population.
H

Optional

Private

Prevalence URL 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://.
I

Optional

Private

Citations to support Prevalence 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.
J

Optional

Private

Private comment to GTR staff about condition 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.

Upload your completed spreadsheet

  • On the home page for your lab in the GTR submission Portal.
  • For Microbe Tests: Under 'Submission of Tests', click to expand the section 'Microbe Tests'
  • Click to expand 'Bulk submit microbe tests using a spreadsheet'.
  • Click 'Choose file'
  • Browse your computer to select your file
  • Click 'Upload your bulk submission file'

Upload microbe test bulk submission spreadsheet

File upload history

The file you uploaded will display in the history table ('History of bulk microbe test uploads') and is accessible to you. You can download that file if you need to address errors or edit data. Please consider versioning your spreadsheet if you need to make corrections so that you can later distinguish which version you uploaded to GTR.

You will also notice the date and time of upload. A status box on the table shows the file's processing status: 'success', 'warnings' or 'error'.

Submission notifications

You will receive a notification via email within a few minutes of uploading your file.

  • Success. If your spreadsheet is successfully uploaded, you will receive an email entitled 'Your tests submitted in bulk have been successfully registered in GTR'.
  • Warnings. 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.
  • Errors. 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.

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.

Last updated: 2022-05-13T22:57:52Z