PREVENTEST - Clinical Genetic Test - GTR

Genetic Testing Registry

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PREVENTEST

Clinical Genetic Test

offered by

GeneID Lab - Advanced Molecular Diagnostics

View lab's test page

GTR Test Accession: GTR000567625.2

CAP

INHERITED DISEASECANCERINHERITED DISEASE SUSCEPTIBILITY ... View more

Last updated in GTR: 2019-07-03

Last annual review date for the lab: 2024-04-03

At a Glance

Test purpose:

Risk Assessment

Conditions (60):

Familial adenomatous polyposis 1; Acute lymphoid leukemia; Aplastic anemia; ...

Genes (34):

APC (5q22.2), ATM (11q22.3), BARD1 (2q35), BMPR1A (10q23.2), BRCA1 (17q21.31), ...

Methods (2):

Molecular Genetics - Deletion/duplication analysis: Multiplex Ligation-dependent Probe Amplification (MLPA); ...

Target population:

Individuals that meet NCCN criteria for Hereditary Cancer

Clinical validity:

Not provided

Clinical utility:

Predictive risk information for patient and/or family members

Ordering Information

Offered by:

GeneID Lab - Advanced Molecular Diagnostics
View lab's website
View lab's test page

Specimen Source:

Buccal swab
Saliva
View specimen requirements

Who can order:

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

Test Order Code:

PVT

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:

All testing must be ordered by a qualified health care provider. Also, the results are only sent to the health care provider who then will disclosed the findings to the patient.
Order URL

Test service:

Clinical Testing/Confirmation of Mutations Identified Previously

Informed consent required:

Yes

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Yes

Recommended fields not provided:

Lab contact for this test, Test strategy, Test development

Conditions

Total conditions: 60

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 34

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

Methodology

Total methods: 2

Method Category

Test method

Instrument

Deletion/duplication analysis

Multiplex Ligation-dependent Probe Amplification (MLPA)

Other

Sequence analysis of the entire coding region

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

Thermofisher Ion S5XL
Illumina MiniSeq

Clinical Information

Test purpose:

Risk Assessment

Clinical utility:

Predictive risk information for patient and/or family members

View citations (2)

https://www.nccn.org/store/login/login.aspx?ReturnURL=https://www.nccn.org/professionals/physician_gls/pdf/genetics_colon.pdf
https://www.nccn.org/store/login/login.aspx?ReturnURL=https://www.nccn.org/professionals/physician_gls/pdf/genetics_screening.pdf

Target population:

Individuals that meet NCCN criteria for Hereditary Cancer

View citations (3)

ACOG Committee Opinion. Hereditary Cancer Syndromes and Risk Assessment. Committee on Genetics, Number 634, June 2015. Reaffirmed 2017.
NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines ®). Genetic/Familial High-Risk Assesssment: Breast and Ovarian. Version 1.2019 - July 11, 2018. NCCN.org
NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines ®). Genetic/Familial High-Risk Assesssment: Colorectal. Version 1.2018 - July 12, 2018. NCCN.org

Variant Interpretation:

What is the protocol for interpreting a variation as a VUS?
All sequence alterations are described and reported according to the Human Genome Variation Society (HGVS) nomenclature guidelines. All the VUS are imputed into a Data bank that is periodically checked for reclassification.

Are family members with defined clinical status recruited to assess significance of VUS without charge?
Yes. We notify the health care provider about the possibility of contacting family members.

Will the lab re-contact the ordering physician if variant interpretation changes?
Yes. A reclassification report is sent to the Physician office, also we contact the office via phone to explain the new interpretation, why did it change, and implication for patients.

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:

We utilize two NGS platforms in parallel: Miniseq - Illumina(clonal bridge amplification/reversible dye terminator) and Ion Torrent - Thermofisher (Ion sphere particles- Chef System/S5XL). All translated exons and immediately adjacent intronic regions of the relevant genes are sequenced. Discrepancies between platforms, if any, are resolved by selective incorporation of chain-terminating … View more

Test Confirmation:

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

To establish analytical sensitivity and specificity, reference samples that contain both disease-associated and non-disease associated sequence variations were analyzed. Analytical sensitivity: The likelihood of the assay to detect a sequence variation when present within the analyzed genomic region (the test’s false negative rate) was established. All samples tested that have … To establish analytical sensitivity and specificity, reference samples that contain both disease-associated and non-disease associated sequence variations were analyzed. Analytical sensitivity: The likelihood of the assay to detect a sequence variation when present within the analyzed genomic region (the test’s false negative rate) was established. All samples tested that have a positive result (“targeted mutation detected”) were correctly classified as positive after sequencing. Because the germline origin of the samples tested, the lower limit of detection was determined empirically as the allelic read percentage or allelic fraction (>35%, considering ideally an allelic read percentage of 50). Analytical specificity: The likelihood of the assay to detect only the target regions and not interfering regions, was established. The assay did not detect sequence variations when none were present within the analyzed genomic region (the test’s false positive rate). These parameters were established by comparing a platform test results to both methods that have been independently validated (Ion Torrent or Illumina, plus Sanger sequencing). Reportable range: The span of test result values over which the laboratory can establish the accuracy of the instrument, was established. There are areas of the targeted region that cannot be sequenced reliably and therefore are excluded from the reportable range. Unless otherwise indicated, all targeted regions were sequenced with >50x depth or supplemented with additional analysis. Reads were aligned to a reference sequence (GRCh37) and sequence changes were identified and interpreted in the context of a single clinically relevant transcript. Enrichment and analysis focus on the coding sequence of the indicated transcripts, 20 bp of flanking intronic sequence, and other specific genomic regions demonstrated to be causative of disease at the time of assay design. Promoters, untranslated regions and other non-coding regions, highly homologous regions and long homopolymers (>12nt) were not interrogated. All clinical significance observations were confirmed by orthogonal technologies. Reference range: GRCh37 was used as the reference genome against which the sequence reads were aligned and compared. It includes SNPs and other sequence variations that occur in the general population. For Illumina validation, annotations from the manufacturer’s software (Illumina-VariantStudio) was used for variant interpretation and population data analysis. View more

View citations (3)

https://nam.edu/wp-content/uploads/2015/06/AnalyticValidityPersp.pdf '
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3827024/pdf/nihms525968.pdf
https://nam.edu/wp-content/uploads/2015/06/AnalyticValidityPersp.pdf

Proficiency testing (PT):

Is proficiency testing performed for this test?
Yes

Method used for proficiency testing:
Formal PT program

PT Provider:
American College of Medical Genetics / College of American Pathologists, ACMG/CAP

Recommended fields not provided:

Assay limitations, Description of internal test validation method, Description of PT method, Major CAP category, CAP category, CAP test list

Regulatory Approval

FDA Review:

Not provided

Additional Information

Reviews:

Genereviews

PubMed Clinical Queries

Reviews in PubMed