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Exome Sequencing
Clinical Genetic Test
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offered by
Genetic Services Laboratory
View lab's test page
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GTR Test Accession: Help GTR000509909.3
CAP
NERVOUS SYSTEMPSYCHIATRIC
Last updated in GTR: 2020-08-11
View version history
Last annual review date for the lab: 2024-07-22 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Monitoring; Prognostic; ...
Conditions (1): Help
Intellectual disability
Chromosomal regions/ Mitochondria (1): Help
Whole exome
Methods (1): Help
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: Help
Exome sequencing has been observed to identify the underlying genetic …
Clinical utility: Help
Establish or confirm diagnosis
Ordering Information
Offered by: Help
Genetic Services Laboratory
View lab's website
View lab's test page
Specimen Source: Help
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
CPT codes: Help
**AMA CPT codes notice

Copyright: 2023 American Medical Association. All rights reserved.

Contact Policy: Help
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: Help
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
Test service: Help
Clinical Testing/Confirmation of Mutations Identified Previously
Confirmation of research findings
Test additional service: Help
Custom mutation-specific/Carrier testing
Informed consent required: Help
No
Pre-test genetic counseling required: Help
No
Post-test genetic counseling required: Help
No
Recommended fields not provided:
Test Order Code, Lab contact for this test, Test strategy, Test development
Conditions Help
Total conditions: 1
Condition/Phenotype Identifier
Test Targets
Chromosomal regions/Mitochondria Help
Total chromosomal regions/mitochondria: 1
Chromosomal region/Mitochondrion Associated condition
Methodology
Total methods: 1
Method Category Help
Test method Help
Instrument *
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
* Instrument: Not provided
Clinical Information
Test purpose: Help
Diagnosis; Monitoring; Prognostic; Recurrence; Screening
Clinical validity: Help
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: Help
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: Help
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 … View more
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
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? Help
Yes.
Research:
Is research allowed on the sample after clinical testing is complete? Help
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: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
Approximately 90-95% of all exons are targeted at a minimum depth of 30X in the diagnostic Exome Sequencing test.
Assay limitations: Help
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 … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
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 Help
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: Help
Category: Not Applicable
Additional Information

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.