GTR Test Accession:
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GTR000509909.3
CAP
Last updated in GTR: 2020-08-11
View version history
GTR000509909.3, last updated: 2020-08-11
GTR000509909.2, last updated: 2019-08-13
GTR000509909.1, last updated: 2018-08-20
Last annual review date for the lab: 2023-07-18
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At a Glance
Test purpose:
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Prognostic;
Monitoring;
Screening; ...
Conditions (1):
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Intellectual disability
Whole exome
Methods (1):
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Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)
Target population: Help
To confirm a genetic diagnosis in a patient who presents …
Clinical validity:
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Exome sequencing has been observed to identify the underlying genetic …
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Specimen Source:
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- Saliva
- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Physician Assistant
- Licensed Physician
- Nurse Practitioner
CPT codes:
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Contact Policy:
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Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.
How to Order:
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All samples should be shipped via overnight delivery at room temperature.
No weekend or holiday deliveries.
Label each specimen with the patient’s name, date of birth and date sample collected.
Send specimens with complete requisition and consent form, otherwise, specimen processing may be delayed.
Order URL
No weekend or holiday deliveries.
Label each specimen with the patient’s name, date of birth and date sample collected.
Send specimens with complete requisition and consent form, otherwise, specimen processing may be delayed.
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Confirmation of research findings
Test additional service:
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Custom mutation-specific/Carrier testing
Informed consent required:
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No
Pre-test genetic counseling required:
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No
Post-test genetic counseling required:
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No
Recommended fields not provided:
Test Order Code,
Lab contact for this test,
Test strategy,
Test development
Conditions
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Total conditions: 1
| Condition/Phenotype | Identifier |
|---|
Test Targets
Chromosomal regions/Mitochondria
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Total chromosomal regions/mitochondria: 1
| Chromosomal region/Mitochondrion | Associated condition |
|---|
Methodology
Total methods: 1
Method Category
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Test method
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Instrument *
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
* Instrument: Not provided
Clinical Information
Test purpose:
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Prognostic;
Monitoring;
Screening;
Recurrence;
Diagnosis
Clinical validity:
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Exome sequencing has been observed to identify the underlying genetic defect in approximately 25 – 35% of patients referred for evaluation of a possible genetic condition
View citations (1)
- Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369(16):1502-11. doi:10.1056/NEJMoa1306555. Epub 2013 Oct 02. PMID: 24088041.
Clinical utility:
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Establish or confirm diagnosis
View citations (1)
- Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, Bekheirnia MR, Leduc MS, Kirby A, Pham P, Scull J, Wang M, Ding Y, Plon SE, Lupski JR, Beaudet AL, Gibbs RA, Eng CM. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med. 2013;369(16):1502-11. doi:10.1056/NEJMoa1306555. Epub 2013 Oct 02. PMID: 24088041.
Target population:
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To confirm a genetic diagnosis in a patient who presents with features that could be applicable to a number of different conditions, or in which the differential diagnosis and sequential genetic testing would be cost prohibitive. To confirm a genetic diagnosis in a patient who presents with features of a …
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Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Variants are identified and evaluated using a custom collection of bioinformatic tools and comprehensively interpreted by our team of directors and genetic counselors.
Variants are identified and evaluated using a custom collection of bioinformatic tools and comprehensively interpreted by our team of directors and genetic counselors.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes.
Yes.
Research:
Is research allowed on the sample after clinical testing is complete?
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http://dnatesting.uchicago.edu/research-consent-form
http://dnatesting.uchicago.edu/research-consent-form
Recommended fields not provided:
Are family members with defined clinical status recruited to assess significance of VUS without charge?,
Sample negative report,
Sample positive report
Technical Information
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Approximately 90-95% of all exons are targeted at a minimum depth of 30X in the diagnostic Exome Sequencing test.
Assay limitations:
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Not all the exons in the genome are targeted and captured due to certain inherent characteristics of the genome. In addition, there is limited or no coverage in regions outside of the exome. Certain types of mutations are not detectable by this test. This methodology will not detect low level …
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Proficiency testing (PT):
Is proficiency testing performed for this test?
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Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
American College of Medical Genetics / College of American Pathologists, ACMG/CAP
VUS:
Software used to interpret novel variations
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A custom collection of bioinformatics tools.
Laboratory's policy on reporting novel variations Help
All novel and/or potentially pathogenic variants are confirmed by Sanger sequencing
A custom collection of bioinformatics tools.
Laboratory's policy on reporting novel variations Help
All novel and/or potentially pathogenic variants are confirmed by Sanger sequencing
Recommended fields not provided:
Test Confirmation,
Citations to support assay limitations,
Description of internal test validation method,
Citations for Analytical validity,
Description of PT method,
Major CAP category, CAP category, CAP test list
Regulatory Approval
FDA Review:
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Category:
Not Applicable
Additional Information
Reviews:
Clinical resources:
Consumer resources:
IMPORTANT NOTE:
NIH does not independently verify information submitted to GTR; it relies on submitters to provide information that is accurate and not misleading.
NIH makes no endorsements of tests or laboratories listed in GTR. GTR is not a substitute for medical advice.
Patients and consumers
with specific questions about a genetic test should contact a health care provider or a genetics professional.