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JAX SOMASEQ
Clinical Genetic Test
Help
offered by
The Jackson Laboratory for Genomic Medicine
GTR Test Accession: Help GTR000596290.4
CAP
Last updated in GTR: 2024-10-24
View version history
Last annual review date for the lab: 2024-09-30 LinkOut
At a Glance
Test purpose: Help
Diagnosis; Drug Response; Predictive; ...
Conditions (1): Help
Solid tumor
Genes (517): Help
ABL1 (9q34.12); ABL2 (1q25.2); ABRAXAS1 (4q21.23); ACVR1 (2q24.1); ACVR1B (12q13.13) more...
Methods (5): Help
Molecular Genetics - Deletion/duplication analysis: Next-Generation (NGS)/Massively parallel sequencing (MPS); ...
Target population: Help
Solid tumors with metastatic disease or not; FFPE samples with …
Clinical validity: Help
Not provided
Clinical utility: Help
Not provided
Ordering Information
Offered by: Help
The Jackson Laboratory for Genomic Medicine
View lab's website
Test short name: Help
SOMASEQ
Manufacturer's name: Help
Illumina TruSight Oncology 500
Specimen Source: Help
  • FFPE
Who can order: Help
  • Genetic Counselor
  • Health Care Provider
  • Licensed Physician
  • Nurse Practitioner
  • Physician Assistant
Test Order Code: Help
JAX SOMASEQ
Lab contact: Help
Melissa Kelly, PhD, CC(ABB), HCLD(ABB), Lab Director
[email protected]
Contact Policy: Help
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: Help
Yes
Pre-test genetic counseling required: Help
Decline to answer
Post-test genetic counseling required: Help
Decline to answer
Recommended fields not provided:
How to Order, Test strategy, Test development
Conditions Help
Total conditions: 1
Condition/Phenotype Identifier
Test Targets
Genes Help
Total genes: 517
Gene Associated Condition Germline or Somatic Allele (Lab-provided) Variant in NCBI
Methodology
Total methods: 5
Method Category Help
Test method Help
Instrument
Deletion/duplication analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Microsatellite instability testing (MSI)
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
RNA analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Sequence analysis of the entire coding region
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Targeted variant analysis
Next-Generation (NGS)/Massively parallel sequencing (MPS)
Illumina NovaSeq 6000
Clinical Information
Test purpose: Help
Diagnosis; Drug Response; Predictive; Prognostic; Recurrence; Screening; Therapeutic management
Target population: Help
Solid tumors with metastatic disease or not; FFPE samples with greater than or equal to 30% neoplastic content
Variant Interpretation:
What is the protocol for interpreting a variation as a VUS? Help
If a variant is uncharacterized or listed as unknown in the knowledgebases with no other functional studies identified, and is not classified in ClinVar for the patient's tumor type, the molecular impact is classified as unknown.

Are family members with defined clinical status recruited to assess significance of VUS without charge? Help
No.

Will the lab re-contact the ordering physician if variant interpretation changes? Help
No. The lab does not re-contact the ordering physicians as routine practice.
Sample reports:
Sample Positive Report Help
Sample Positive Report
Recommended fields not provided:
Clinical validity, Clinical utility, Is research allowed on the sample after clinical testing is complete?, Sample negative report
Technical Information
Test Platform:
Illumina NovaSeq 6000
Availability: Help
Tests performed
Entire test performed in-house
Analytical Validity: Help
The JAX SOMASEQ assay is >99% sensitive in detecting SNVs, Indels, Fusions/Splicing variants and MSI. JAX SOMASEQ has a >85% sensitivity for TMB and CNVs. Accuracy for SNVs, Indels, CNVs, and Fusions/Splicing variants and MSI are all greater than 97%. JAX SOMASEQTM has a >89% accuracy for TMB. Specificity for … View more
Proficiency testing (PT):
Is proficiency testing performed for this test? Help
Yes

Method used for proficiency testing: Help
Formal PT program

PT Provider: Help
College of American Pathologists, CAP

Description of PT method: Help
PT assessments are completed biannually.

CAP Testing Information Help
Copy Number Variant Solid Tumor; Copy number variant-solid tumor; CNVST
Fusion RNA; RNA sequencing; RNA
Next-Generation Sequencing-Solid Tumor; Next-generation sequencing; NGSST
Next-Generation Sequencing-Solid Tumor; Next-generation sequencing; TMB
VUS:
Software used to interpret novel variations Help
Illumina Connected Analysis

Laboratory's policy on reporting novel variations Help
Novel variants are interpreted in the context of the patient’s disease according the AMP/ASCO/CAP guidelines in which the variant is given a tier classification to signify the level of scientific literature associated with therapeutic, prognostic, and/or diagnostic evidence. All detected variants are reported on a clinical laboratory report that is … View more
Recommended fields not provided:
Test Confirmation, Assay limitations, Description of internal test validation method, Citations for Analytical validity
Regulatory Approval
FDA Review: Help
Not provided
Additional Information
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.