qPCR - Clinical Genetic Test - GTR

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qPCR

Clinical Genetic Test

offered by

Clinical Cytogenetics Laboratory

GTR Test Accession: GTR000576385.3

NYS CLEP

Last updated in GTR: 2024-01-17

Last annual review date for the lab: 2024-01-08

At a Glance

Test purpose:

Diagnosis; Mutation Confirmation; Recurrence; ...

Conditions (1):

Congenital chromosomal disease

Chromosomal regions/ Mitochondria (1):

Human genome

Methods (1):

Molecular Genetics - Targeted variant analysis: Quantitative PCR (qPCR)

Target population:

Relatives of patients found to have specific deletions or duplications …

Clinical validity:

Not provided

Clinical utility:

Predictive risk information for patient and/or family members

Ordering Information

Offered by:

Clinical Cytogenetics Laboratory
View lab's website

Test short name:

qPCR

Specimen Source:

Buccal swab
Isolated DNA
Peripheral (whole) blood
Skin

Who can order:

Health Care Provider

CPT codes:

81479

**AMA CPT codes notice

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:

Health care providers should submit an order (electronically or hard copy requisition) under LabCorp account number. This is not a published test code.

Test service:

qPCR
Comment: requires proband control to run familial testing

Test development:

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

Informed consent required:

Decline to answer

Test strategy:

Previous SNP microarray must've been run on the proband previously, and there must be usable DNA remaining from proband testing to order qPCR on the relative. Please check with the lab to confirm the correct test code to order

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Test Order Code, Lab contact for this test

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Chromosomal regions/Mitochondria

Total chromosomal regions/mitochondria: 1

Chromosomal region/Mitochondrion	Associated condition

Methodology

Total methods: 1

Method Category

Test method

Instrument

Targeted variant analysis

Quantitative PCR (qPCR)

QuantStudio(TM) 7 Flex Real-Time PCR system

Clinical Information

Test purpose:

Diagnosis; Mutation Confirmation; Recurrence; Risk Assessment

Clinical utility:

Predictive risk information for patient and/or family members

View citations (1)

Oikonomakis V, Kosma K, Mitrakos A, Sofocleous C, Pervanidou P, Syrmou A, Pampanos A, Psoni S, Fryssira H, Kanavakis E, Kitsiou-Tzeli S, Tzetis M. Recurrent copy number variations as risk factors for autism spectrum disorders: analysis of the clinical implications. Clin Genet. 2016;89(6):708-18. doi:10.1111/cge.12740. Epub 2016 Feb 09. PMID: 26777411.

Target population:

Relatives of patients found to have specific deletions or duplications detected on SNP Microarray performed at Integrated Genetics/Labcorp, wherein qPCR is listed as the designated follow-up on that patient's report. Testing can only be performed if there is DNA from the proband that can be used as a control sample.

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
This test is only used for follow-up of either pathogenic, likely pathogenic, or benign variants detected on SNP microarray.

Are family members with defined clinical status recruited to assess significance of VUS without charge?
This follow-up test is charged testing only.

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

Research:

Is research allowed on the sample after clinical testing is complete?
no

Recommended fields not provided:

Clinical validity, 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?, Sample negative report, Sample positive report

Technical Information

Test Procedure:

Real-time PCR monitors the amount of amplicon generated as the reaction occurs. Usually, the amount of product is directly related to the fluorescence of a reporter dye. Because it detects the amount of product as the reaction progresses, real-time PCR provides a wide linear dynamic range, demonstrates high sensitivity, and … View more

Test Platform:

Life Technologies

Test Confirmation:

This is a familial follow-up test used to confirm abnormal SNP microarray results and establish inheritance of a known variant detected in a proband.

Test Comments:

This is a charged follow-up test for abnormal SNP micorarrays that were reported only by Labcorp/Integrated Genetics.

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Validity was tested for accuracy, sensitivity, specificity and reproducibility. Overall - There was 100% accuracy - For clinical sensitivity and specificity o False positive rate is 0% o False negative rate is 0% - For reproducibility o There was greater than 95% reproducibility in detected allele/quantitation variation

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Intra-Laboratory

Description of internal test validation method: Help
Semi-Annual internal proficiency testing is done and the laboratory must demonstrate that tests performed in the laboratory obtain equivalent results for the same analyte. In this case, an analyte is the material that an assay measures; i.e. patient DNA for qPCR. Proficiency samples from a previous analyzed retained specimen is … View more

VUS:

Laboratory's policy on reporting novel variations
This test is not intended to detect or report novel variants. It is a follow-up test to a variant previously reported.

Recommended fields not provided:

Assay limitations, Citations to support 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: Not Applicable

NYS CLEP Approval:

Number: 50534
Status: Approved

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.