TruGenome Cardiovascular Disease Test - Clinical Genetic Test - GTR

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TruGenome Cardiovascular Disease Test

Clinical Genetic Test

offered by

Illumina Laboratory Services

GTR Test Accession: GTR000604271.1

CARDIOVASCULARMETABOLIC DISEASEMUSCULOSKELETAL ... View more

Last updated in GTR: 2023-04-13

Last annual review date for the lab: 2024-03-08

At a Glance

Test purpose:

Diagnosis; Risk Assessment; Screening

Conditions (4):

Cardiomyopathy; Abnormal circulating lipid concentration; Cardiac arrhythmia; ...

Chromosomal regions/ Mitochondria (1):

Human genome

Methods (1):

Molecular Genetics - Sequence analysis of the entire coding region: whole genome sequencing

Target population:

Not provided

Clinical validity:

Not provided

Clinical utility:

Not provided

Ordering Information

Offered by:

Illumina Laboratory Services
View lab's website

Specimen Source:

Isolated DNA
Peripheral (whole) blood
View specimen requirements

Who can order:

Genetic Counselor
Health Care Provider
Licensed Physician
Nurse Practitioner

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:

Order URL

Test development:

Test developed by laboratory (no manufacturer test name)

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, Lab contact for this test, Test strategy

Conditions

Total conditions: 4

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 *

Sequence analysis of the entire coding region

whole genome sequencing

* Instrument: Not provided

Clinical Information

Test purpose:

Diagnosis; Risk Assessment; Screening

Recommended fields not provided:

Clinical validity, Clinical utility, Target population, 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

Availability:

Tests performed
Entire test performed in-house

Analytical Validity:

Whole-genome sequencing was performed on extracted DNA using sequencing-by-synthesis (SBS) (2X150bp reads) next generation sequencing(NGS) at a minimum mean sequencing depth of 40X. These data were processed using TruSight Software Suite (TSS) v2.6 on the Illumina DRAGENBio-IT Platform v3.8.4 including read alignment to the GRCh37/hg19 genome assembly, variant calling, variant … Whole-genome sequencing was performed on extracted DNA using sequencing-by-synthesis (SBS) (2X150bp reads) next generation sequencing(NGS) at a minimum mean sequencing depth of 40X. These data were processed using TruSight Software Suite (TSS) v2.6 on the Illumina DRAGENBio-IT Platform v3.8.4 including read alignment to the GRCh37/hg19 genome assembly, variant calling, variant annotation by Nirvana v3.17, and comprehensive variant filtering. At least 98% of the sequenced autosomal genome was callable. Only genomic positions with a minimum coverage of 8X and alternate allele frequency of 25% or higher are assessed for interpretation and reporting. Small insertion and deletion events were detected and reported for this assay. Insertions up to 31 bp and deletions up to 27 bp have a sensitivity and analytical PPV of at least 80%. For SNVs and small insertion and deletion events, interpretation is limited to variant positions that overlap an exon and 8 base pairs of flanking sequence. This assay has the capability to detect copy number variants (CNVs) greater than or equal to 10 kb, however sensitivity was only assessed for events greater than 20 kb and was found to be approximately 85%. CNV boundaries cannot be assessed with complete accuracy. The boundaries are estimated to lie within +/-1 kb of the event, unless otherwise noted. CNV analysis will not detect balanced alterations (reciprocal translocations, Robertsonian translocations, inversions, and balanced insertions/deletions), triploidy, or genomic imbalances in segmentally duplicated regions. Mitochondrial DNA is sequenced and analyzed using the same pipeline. Mitochondrial SNVs detected at an allele fraction greater than or equal to 5percent are assessed. Heteroplasmy will be reported for clinically significant variants. Only pathogenic or likely pathogenic mitochondrial DNA variants in genes associated with cardiovascular disease are reported. Mitochondrial CNVs and small insertions and deletions are not reported. Expansion Hunter is used to screen for disorders with cardiovascular phenotypes caused by repeat expansions in clinically relevant short tandem repeats (STRs). Sizes of some repeats can be underestimated due to somatic mosaicism and GC amplification bias. Only the repeats that are 'expanded' in the genes listed below will be included on the clinical report. The specific repeat number will not be reported. This test cannot distinguish between expansions in the premutation range and full mutation range for some conditions. For genes associated with autosomal recessive repeat expansion disorders, i.e., FXN, carrier status will not be reported. Orthogonal confirmation of all clinically significant expanded STRs will be performed and results reported in an addended report. The list of genes that are included in the Expansion Hunter analysis is given below: DMPK, CNBP and FXN. View more

Assay limitations:

A causal variant(s) associated with one of the genes and diseases tested may not be identified by this test. Reasons for this include limitations of testing and limitations in current scientific and clinical knowledge about certain genetic variants, genes, and the association with human genetic disease. Some regions of the … A causal variant(s) associated with one of the genes and diseases tested may not be identified by this test. Reasons for this include limitations of testing and limitations in current scientific and clinical knowledge about certain genetic variants, genes, and the association with human genetic disease. Some regions of the human genome are not covered by this assay, including stretches of the human reference genome that have not been completely resolved, low complexity regions, or regions where it is difficult to align fragments accurately. Deletion, duplication, or insertion variants between 50bpand 10,000bp in length are not evaluated. Such variants are very rare in aggregate in unselected populations. Additionally, genes that are associated with regions of high homology (pseudogenes) are difficult for this assay to resolve, unless specified to be part of this test. This assay is not designed to detect mosaicism and possible cases of mosaicism may be investigated at the discretion of the laboratory director. Possible sources of testing error include rare genetic variants that interfere with analysis, sample misidentification, and other sources. Unexpected combinations of risk allele variants and/or poor-quality calls of these variants will result in a result of no risk allele detected. This test is intended to detect genomic variation associated with inherited cardiovascular disease (CVD) and/or lipid disorder phenotypes in adults rather than neonatal or pediatric age groups. This comprehensive assay is focused on “high-evidence” genes that are deemed clinically relevant and appropriate for individuals with a personal and/or family history of aortopathy, arrhythmia, cardiomyopathy and/or dyslipidemia. The primary selection criterion for the list of genes is predicated on a clearly defined gene-disease relationship that has been classified as Definitive or Strong, based on theClinGen framework (PMID:28552198). This assay is designed as a “screening-like” test with variant classification that is performed in a phenotypically agnostic manner. As such, clinical sensitivity has not been determined for this assay. A negative result does not exclude the possibility of a heritable etiology of CVD in the patient being tested. Review of the gene list below is recommended to ensure that the gene(s) of clinical interest for the individual being tested corresponds to the gene(s) included in this assay. For all reported variants, clinical correlation is recommended. 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:

Not provided

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.