Genomic Unity Exome Plus Analysis (includes STR analysis of 36 loci) - Proband - Clinical Genetic Test - GTR

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Clinical Genetic Test

offered by

Variantyx, Inc.

View lab's test page

GTR Test Accession: GTR000559624.10

INHERITED DISEASE

Last updated in GTR: 2023-12-05

Last annual review date for the lab: 2024-01-30

At a Glance

Test purpose:

Diagnosis

Conditions (1):

Hereditary disease

Chromosomal regions/ Mitochondria (2):

Human genome; Mitochondrion

Methods (3):

Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...

Target population:

Patients with a suspected genetic etiology when: the patient exhibits …

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Variantyx, Inc.
View lab's website
View lab's test page

Specimen Source:

Isolated DNA
Peripheral (whole) blood
Saliva
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Physician

Test Order Code:

CP010
View other test codes

CPT codes:

0214U

**AMA CPT codes notice

Lab contact:

Christine Stanley, PhD, FACMG, Medical Director
christine.stanley@variantyx.com
+1 617-209-2090

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:

Genomic Unity Exome Plus Analysis can be ordered for the proband alone, or with additional family members. Test orders are initiated at https://www.variantyx.com/resources/provider-resources/order-forms/. Following submission, a clinical coordinator will get in touch to send a blood or saliva sample collection kit if required and facilitate collection of the test requisition …

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Order URL

Informed consent required:

Yes

Test strategy:

When results are not positive, there is an option to reflex up to Genomic Unity Whole Genome Analysis.

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Test development

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Chromosomal regions/Mitochondria

Total chromosomal regions/mitochondria: 2

Chromosomal region/Mitochondrion	Associated condition

Methodology

Total methods: 3

Method Category

Test method

Instrument *

Deletion/duplication analysis

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

Mutation scanning of select exons

Tandem repeat expansion analysis

Sequence analysis of the entire coding region

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

* Instrument: Not provided

Clinical Information

Test purpose:

Diagnosis

Target population:

Patients with a suspected genetic etiology when: the patient exhibits a phenotype with significant genetic heterogeneity, or that is suggestive of multiple conditions; the patient exhibits symptoms with an unclear or atypical phenotype; no or multiple targeted testing options are available for the suspected disease, or there are a large … View more

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
Variants are categorized as pathogenic, likely pathogenic or a variant of uncertain significance (VUS) utilizing the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines as published by Richards et al 2015.

Will the lab re-contact the ordering physician if variant interpretation changes?
Not provided.

Recommended fields not provided:

Clinical validity, Clinical utility, Are family members with defined clinical status recruited to assess significance of VUS without charge?, Will the lab re-contact the ordering physician if variant interpretation changes?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report

Technical Information

Test Procedure:

The patient's DNA is sequenced using whole genome sequencing conducted on an Illumina platform at 30X mean mappable coverage. The relevant region(s) of DNA are subsequently isolated in-silico for analysis.

Test Confirmation:

Tandem repeat expansions are sent out to a third party CLIA/CAP lab for orthogonal confirmation.

Test Comments:

This test includes repeat expansion analysis of 36 loci: AFF2, AR, ARX, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, ATXN8OS, ATXN10, C9ORF72, CACNA1A, CNBP, CSTB, DIP2B, DMPK, FGF14, FMR1, FOXL2, FXN, GIPC1, GLS, HTT, JPH3, LRP12, NOP56, NOTCH2NLC, PABPN1, PHOX2B, PPP2R2B, RFC1, SOX3, TBP, TCF4, VWA1 and ZIC2 genes.

Availability:

Tests performed
Entire test performed in-house

Test performance comments
Specimen preparation and clinical grade sequencing is performed by outside CLIA labs. All data processing, analysis, interpretation, diagnosis and report generation is performed in-house.

Analytical Validity:

The Genomic Unity® Exome Plus Analysis is a whole genome sequence based test designed to identify genetic variants that correlate with the patient's clinical symptoms. This test includes sequence analysis (single nucleotide variants, deletions/insertions, characterized intronic and regulatory variants); analysis of copy number variants, duplications/deletions, regions of homozygosity, mobile element … View more

Assay limitations:

The false negative rate for repeat expansions has not been determined.

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Intra-Laboratory

VUS:

Software used to interpret novel variations
Proprietary Variantyx Genomic Intelligence platform

Laboratory's policy on reporting novel variations
Test results will only be released to the ordering healthcare provider and additional healthcare provider(s) indicated on the test requisition form.

Recommended fields not provided:

Citations to support assay limitations, Description of internal test validation method, Citations for Analytical validity, PT Provider, Description of PT method, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Not provided

Additional Information

Reviews:

PubMed Clinical Queries

Clinical 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.