GTR Test Accession:
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GTR000508734.3
CAP
Last updated in GTR: 2024-07-05
View version history
GTR000508734.3, last updated: 2024-07-05
GTR000508734.2, last updated: 2022-06-16
GTR000508734.1, last updated: 2021-06-23
Last annual review date for the lab: 2024-07-08
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At a Glance
Test purpose:
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Diagnosis;
Mutation Confirmation;
Risk Assessment; ...
Conditions (1):
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CHARGE syndrome
Genes (1):
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CHD7 (8q12.2)
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
Patients with a diagnosis of CHARGE syndrome or Hypogonadotropic hypogonadism-5 …
Clinical validity:
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Not provided
Clinical utility:
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Establish or confirm diagnosis
Ordering Information
Offered by:
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Test short name:
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CHD7
Specimen Source:
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- Peripheral (whole) blood
- View specimen requirements
Who can order: Help
- Genetic Counselor
- Health Care Provider
- Licensed Physician
Test Order Code:
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CHD7S
View other test codes
View other test codes
Lab contact:
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Chen Yang, PhD, ABMGG Board Certified, FACMG, Diplomate of the American Board of, Lab Director
chnyang@umich.edu
734-615-2429
chnyang@umich.edu
734-615-2429
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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Provide appropriate sample, relevant clinical information and a completed requisition form. Contact an MLabs client service representative, 800-862-7284, for any questions. 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 …
Order URL
Test service:
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Clinical Testing/Confirmation of Mutations Identified Previously
OrderCode: CHD7S
Confirmation of research findings
OrderCode: CLIFS
Custom Sequence Analysis
OrderCode: CLIFS
OrderCode: CHD7S
Confirmation of research findings
OrderCode: CLIFS
Custom Sequence Analysis
OrderCode: CLIFS
Test development:
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Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)
Informed consent required:
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Based on applicable state law
Test strategy:
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http://www.pathology.med.umich.edu/handbook/
Pre-test genetic counseling required:
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Decline to answer
Post-test genetic counseling required:
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Decline to answer
Conditions
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Total conditions: 1
Condition/Phenotype | Identifier |
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Test Targets
Genes
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Total genes: 1
Gene | Associated Condition | Germline or Somatic | Allele (Lab-provided) | Variant in NCBI |
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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)
Illumina NextSeq 550
Clinical Information
Test purpose:
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Diagnosis;
Mutation Confirmation;
Risk Assessment;
Screening
Clinical utility:
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Establish or confirm diagnosis
Target population:
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Patients with a diagnosis of CHARGE syndrome or Hypogonadotropic hypogonadism-5 with or without anosmia.
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS?
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Follow ACMG guidelines, suggest family study
Follow ACMG guidelines, suggest family study
Are family members with defined clinical status recruited to assess significance of VUS without charge?
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No.
No.
Will the lab re-contact the ordering physician if variant interpretation changes?
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Yes. by Phone or secure email
Yes. by Phone or secure email
Recommended fields not provided:
Clinical validity,
Is research allowed on the sample after clinical testing is complete?,
Sample negative report,
Sample positive report
Technical Information
Test Procedure:
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All coding exons (plus 15 bp upstream and downstream of each coding exon) of the targeted gene(s) are captured, sequenced using NGS and aligned to the human reference genome. A minimum NGS coverage of 20X is achieved for all coding exons +/- 5 bp, and a minimum coverage of 10X …
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Test Confirmation:
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All reported variants of potential clinical significance not meeting the sequencing quality criteria will be confirmed by a different technology.
Availability:
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Tests performed
Entire test performed in-house
Entire test performed in-house
Analytical Validity:
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Analytical Sensitivity 99-100% Accuracy 100% Precision 100%
Assay limitations:
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This analysis will not identify variants in the regulatory elements or deep intronic regions of the targeted gene(s) or other regions of the genome that are not included in this test. This assay may not detect large insertion/deletion, small copy number loss/gain, or balanced inversion/translocations involving the targeted gene(s).
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
College of American Pathologists, CAP
CAP Testing Information Help
Next-Generation Sequencing-Germline; Next-generation sequencing; NGS
Yes
Method used for proficiency testing: Help
Formal PT program
PT Provider: Help
College of American Pathologists, CAP
CAP Testing Information Help
Next-Generation Sequencing-Germline; Next-generation sequencing; NGS
VUS:
Software used to interpret novel variations
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REVEL, BayesDel_noAF, SpliceAI, Varsome, varSEAK
Laboratory's policy on reporting novel variations Help
Contact ordering physician by phone and by routine report; recommend clinical genetics follow up and/or genetic counseling and parental testing
REVEL, BayesDel_noAF, SpliceAI, Varsome, varSEAK
Laboratory's policy on reporting novel variations Help
Contact ordering physician by phone and by routine report; recommend clinical genetics follow up and/or genetic counseling and parental testing
Recommended fields not provided:
Citations to support assay limitations,
Description of internal test validation method,
Citations for Analytical validity,
Description of PT method
Regulatory Approval
FDA Review:
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Category:
FDA exercises enforcement discretion
Additional Information
Clinical resources:
Molecular resources:
Practice guidelines:
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.