Caris MI TumorSeek Comprehensive Genomic Profile - Clinical Genetic Test - GTR

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Caris MI TumorSeek Comprehensive Genomic Profile

Clinical Genetic Test

offered by

Caris Life Sciences

View lab's test page

GTR Test Accession: GTR000560898.6

NYS CLEP

CAP

CANCER

Last updated in GTR: 2022-12-27

Last annual review date for the lab: 2024-03-25

At a Glance

Test purpose:

Predictive; Therapeutic management

Conditions (1):

Neoplasm

Genes (591):

ABI1 (10p12.1); ABL1 (9q34.12); ABL2 (1q25.2); ACKR3 (2q37.3); ACSL3 (2q36.1) more...

Methods (2):

Molecular Genetics - RNA analysis: Whole Transcriptome Sequencing; ...

Target population:

Not provided

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Caris Life Sciences
View lab's website
View lab's test page

How to Order:

Order URL

Informed consent required:

Decline to answer

Pre-test genetic counseling required:

Decline to answer

Post-test genetic counseling required:

Decline to answer

Recommended fields not provided:

Test Order Code, Specimen source, Lab contact for this test, Contact policy, Test strategy, Test development

Conditions

Total conditions: 1

Condition/Phenotype	Identifier

Test Targets

Genes

Total genes: 591

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

Methodology

Total methods: 2

Method Category

Test method

Instrument

RNA analysis

Whole Transcriptome Sequencing

Sequence analysis of the entire coding region

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

Illumina NovaSeq 6000

Clinical Information

Test purpose:

Predictive; Therapeutic management

Recommended fields not provided:

Clinical validity, Clinical utility, Target population, What is the protocol for interpreting a variation as a VUS?, Is research allowed on the sample after clinical testing is complete?, Sample negative report, Sample positive report

Technical Information

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

The MI TumorSeek Comprehensive Genomic Profile (CGP) panel is validated with an overall accuracy of ≥ 95% when detecting Single Nucleotide Variants (SNV), Insertions and Deletions by looking at over 7500 variants in DNA from 500+ samples, including a comparison to Sanger Sequencing calls for 20 SNV target areas and … The MI TumorSeek Comprehensive Genomic Profile (CGP) panel is validated with an overall accuracy of ≥ 95% when detecting Single Nucleotide Variants (SNV), Insertions and Deletions by looking at over 7500 variants in DNA from 500+ samples, including a comparison to Sanger Sequencing calls for 20 SNV target areas and 20 Indel target areas across a total of 400 formalin-fixed, paraffin-embedded (FFPE) analyses with ≥ 95% concordance. All precision studies demonstrated ≥ 95% concordance. MSI Analysis by CGP from DNA on 1196 colorectal carcinoma samples, including 75 MSI-High samples, demonstrated accuracy, sensitivity, and specificity metrics ≥ 95%. When the sample set was supplemented with additional lineages (2192 total samples including 207 MSI-High samples) the accuracy, sensitivity, and specificity metrics remained ≥ 95%. Inter-assay (9 samples) and intra-assay (12 samples) precision studies specific to MSI analysis resulted in overall relative standard deviations of 2.89% and 3.48%, respectively. The copy number alteration (CNA) of each exon is determined by a calculation using the average sequencing depth of the sample along with the sequencing depth of each exon and comparing this calculated result to a pre-calibrated value. A total of 39 FFPE samples were extracted for DNA and analyzed for CNA status via CGP and compared to array comparative genomic hybridization (aCGH) results generated by an external laboratory. The results for all 442 genes overlapping the panels for each sample resulted in accuracy, sensitivity, and specificity metrics ≥ 95%. All precision studies demonstrated ≥ 95% concordance. Tumor Mutational Burden is calculated using only missense mutations found in DNA that have not been previously reported as germline alterations. A validation cohort of 34 samples was tested on each the CGP and a WES assay by an external laboratory. The interpretive results in the validation cohort were compared and the overall concordance was ≥95%. The correlation coefficient for results (mutations/Mb) for the validation cohort was ≥0.95, further demonstrating a high degree of concordance between methods. All precision studies demonstrated ≥ 95% concordance. As part of the CGP Gene fusion and variant transcript detection are performed on mRNA isolated from formalin-fixed paraffin-embedded tumor samples using the Agilent SureSelectXT Low Input Library prep chemistry, optimized for FFPE tissue, in conjunction with the SureSelect Human All Exon V7 bait panel (48.2 Mb) and the Illumina NovaSeq. This assay is designed to detect fusions occurring at known and novel breakpoints within genes. Analytical validation of this test demonstrated ≥95% Positive Percent Agreement (PPA), ≥95% Negative Percent Agreement (NPA) and ≥95% Overall Percent Agreement (OPA) with a validated comparator method using 400+ samples and 200+ fusions/variants. Precision studies demonstrated ≥ 90% concordance for positive calls and ≥ 95% concordance for negative calls. View more

Assay limitations:

RNA: LOD of 50 ng RNA input and validated 10% as the minimal percent tumor nuclei in a specimen. DNA: LOD of 25 ng DNA input and validated 20% as the minimal percent tumor nuclei in a specimen.

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:

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

Regulatory Approval

FDA Review:

Not provided

NYS CLEP Approval:

Number: 62841
Status: Approved

Additional Information

Reviews:

PubMed Clinical Queries

Clinical resources:

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.