CHD7 Gene Sequencing - Clinical Genetic Test - GTR

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CHD7 Gene Sequencing

Clinical Genetic Test

offered by

Michigan Medical Genetics Laboratories

View lab's test page

GTR Test Accession: GTR000508734.3

CAP

INHERITED DISEASECARDIOVASCULARDYSMORPHOLOGY ... View more

Last updated in GTR: 2024-07-05

Last annual review date for the lab: 2024-07-08

At a Glance

Test purpose:

Diagnosis; Mutation Confirmation; Risk Assessment; ...

Conditions (1):

CHARGE syndrome

Genes (1):

CHD7 (8q12.2)

Methods (1):

Molecular Genetics - Sequence analysis of the entire coding region: Next-Generation (NGS)/Massively parallel sequencing (MPS)

Target population:

Patients with a diagnosis of CHARGE syndrome or Hypogonadotropic hypogonadism-5 …

Clinical validity:

Not provided

Clinical utility:

Establish or confirm diagnosis

Ordering Information

Offered by:

Michigan Medical Genetics Laboratories
View lab's website
View lab's test page

Test short name:

CHD7

Specimen Source:

Peripheral (whole) blood
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Physician

Test Order Code:

CHD7S
View other test codes

Lab contact:

Chen Yang, PhD, ABMGG Board Certified, FACMG, Diplomate of the American Board of, Lab Director
chnyang@umich.edu
734-615-2429

Contact Policy:

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:

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 …

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Order URL

Test service:

Clinical Testing/Confirmation of Mutations Identified Previously
    OrderCode: CHD7S
Confirmation of research findings
    OrderCode: CLIFS
Custom Sequence Analysis
    OrderCode: CLIFS

Test development:

Test developed by laboratory but exempt from FDA oversight (eg. NYS CLEP approved, offered within a hospital or clinic)

Informed consent required:

Based on applicable state law

Test strategy:

http://www.pathology.med.umich.edu/handbook/

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 1

Gene	Associated Condition	Germline or Somatic	Allele (Lab-provided)	Variant in NCBI

Methodology

Total methods: 1

Method Category

Test method

Instrument

Sequence analysis of the entire coding region

Next-Generation (NGS)/Massively parallel sequencing (MPS)

Illumina NextSeq 550

Clinical Information

Test purpose:

Diagnosis; Mutation Confirmation; Risk Assessment; Screening

Clinical utility:

Establish or confirm diagnosis

View citations (1)

http://omim.org/entry/214800?search=chd7&highlight=chd7

Target population:

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?
Follow ACMG guidelines, suggest family study

Are family members with defined clinical status recruited to assess significance of VUS without charge?
No.

Will the lab re-contact the ordering physician if variant interpretation changes?
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:

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 … View more

Test Confirmation:

All reported variants of potential clinical significance not meeting the sequencing quality criteria will be confirmed by a different technology.

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Analytical Sensitivity 99-100% Accuracy 100% Precision 100%

Assay limitations:

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?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
College of American Pathologists, CAP

CAP Testing Information
Next-Generation Sequencing-Germline; Next-generation sequencing; NGS

VUS:

Software used to interpret novel variations
REVEL, BayesDel_noAF, SpliceAI, Varsome, varSEAK

Laboratory's policy on reporting novel variations
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:

Category: FDA exercises enforcement discretion

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View CHD7 variations in ClinVar

RefSeqGene

Coriell Institute for Medical Research

Practice guidelines:

EuroGentest, 2011

Consumer resources:

MalaCards

NCATS Office of Rare Diseases Research (GARD)

MedlinePlus

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.