Invitae Nephrolithiasis Panel - Clinical Genetic Test - GTR

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Invitae Nephrolithiasis Panel

Clinical Genetic Test

offered by

Labcorp Genetics (formerly Invitae)

View lab's test page

GTR Test Accession: GTR000591261.3

NYS CLEP

INHERITED DISEASEMETABOLIC DISEASEURINARY SYSTEM DISEASE ... View more

Last updated in GTR: 2021-07-16

Last annual review date for the lab: 2023-10-10 Past due

At a Glance

Test purpose:

Diagnosis; Pre-symptomatic; Therapeutic management

Conditions (66):

Dent disease type 1; Adenine phosphoribosyltransferase deficiency; Adult hypophosphatasia more...

Genes (40):

ADCY10 (1q24.2); AGXT (2q37.3); ALPL (1p36.12); APRT (16q24.3); ATP6V0A4 (7q34) more...

Methods (2):

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

Target population:

The Invitae Nephrolithiasis Panel analyzes genes that are associated with …

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Labcorp Genetics (formerly Invitae)
View lab's website
View lab's test page

Specimen Source:

Buccal swab
Isolated DNA
Peripheral (whole) blood
Saliva
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Physician
Nurse Practitioner
Physician Assistant
Registered Nurse

Test Order Code:

72037

How to Order:

Tests can be ordered online or by submitting a paper requisition form.
Order URL

Test service:

Clinical Testing/Confirmation of Mutations Identified Previously
Genetic counseling

Test development:

Test developed by laboratory (no manufacturer test name)

Informed consent required:

Based on applicable state law

Test strategy:

Full gene sequencing and deletion/duplication analysis of targeted gene

Pre-test genetic counseling required:

Post-test genetic counseling required:

Recommended fields not provided:

Lab contact for this test, Contact policy

Conditions

Total conditions: 66

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 40

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

Methodology

Total methods: 2

Method Category

Test method

Instrument *

Deletion/duplication analysis

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

Sequence analysis of the entire coding region

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

* Instrument: Not provided

Clinical Information

Test purpose:

Diagnosis; Pre-symptomatic; Therapeutic management

Target population:

The Invitae Nephrolithiasis Panel analyzes genes that are associated with nephrolithiasis.

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
Invitae's variant interpretation methodology adheres closely to ACMG guidelines. Observed variants are interpreted according to the framework of evidence recommended by these guidelines, based on evidence in peer-reviewed literature and Invitae's database. Our clinical report documents the evidence and logic supporting each variant interpretation to make it easy for the … View more

Are family members with defined clinical status recruited to assess significance of VUS without charge?
Yes.

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

Recommended fields not provided:

Clinical validity, Clinical utility, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report

Technical Information

Test Procedure:

Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Our analytic validation study has demonstrated >99.9% sensitivity and specificity for tested mutations.

Assay limitations:

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS). Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic … Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS). Our sequence analysis covers clinically important regions of each gene, including coding exons and 10 to 20 base pairs of adjacent intronic sequence on either side of the coding exons in the transcript listed below. In addition, the analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any limitations in the analysis of these genes will be listed on the report. Contact client services with any questions. Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome. View more

Proficiency testing (PT):

Is proficiency testing performed for this test?
No

Recommended fields not provided:

Test Confirmation, 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:

Category: FDA exercises enforcement discretion

NYS CLEP Approval:

Number: 8884
Status: Approved

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Clinical resources:

Molecular resources:

View CLCN5 variations in ClinVar

RefSeqGene

Coriell Institute for Medical Research

Consumer resources:

Genetic Alliance

MalaCards

MedlinePlusGenetics (GHR)

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.