ColoGene Lynch - Clinical Genetic Test - GTR

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ColoGene Lynch

Clinical Genetic Test

offered by

GeneID Lab - Advanced Molecular Diagnostics

GTR Test Accession: GTR000596791.1

INHERITED DISEASECANCERINHERITED DISEASE SUSCEPTIBILITY ... View more

Last updated in GTR: 2021-11-12

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

At a Glance

Test purpose:

Risk Assessment

Conditions (9):

Lynch syndrome; Colorectal cancer, hereditary nonpolyposis, type 2; Endometrial carcinoma; ...

Genes (5):

EPCAM (2p21), MLH1 (3p22.2), MSH2 (2p21-16.3), MSH6 (2p16.3), PMS2 (7p22.1)

Methods (1):

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

Target population:

Individuals that meet NCCN criteria for Lynch Syndrome

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

GeneID Lab - Advanced Molecular Diagnostics
View lab's website

Specimen Source:

Saliva
View specimen requirements

Test Order Code:

CGL

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.

Informed consent required:

Yes

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

How to Order, Lab contact for this test, Test strategy, Test development

Conditions

Total conditions: 9

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 5

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 MiniSeq

Clinical Information

Test purpose:

Risk Assessment

Target population:

Individuals that meet NCCN criteria for Lynch Syndrome

Recommended fields not provided:

Clinical validity, Clinical utility, What is the protocol for interpreting a variation as a VUS?, 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 Platform:

None/not applicable

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://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/pmc/articles/PMC3827024/pdf/nihms525968.pdf
https://nam.edu/wp-content/uploads/2015/06/AnalyticValidityPersp.pdf '
https://nam.edu/wp-content/uploads/2015/06/AnalyticValidityPersp.pdf

Proficiency testing (PT):

Is proficiency testing performed for this test?
No

Recommended fields not provided:

Test Confirmation, Assay limitations, Description of internal test validation method, PT Provider, 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