JAX SOMASEQTM reports on 517 cancer related genes for assessment of all DNA and RNA variant types such as SNVs, CNVs, indels, and fusions, in addition to MSI and TMB.
Test Overview
Molecular profiling of tumors is performed to identify genetic alterations that accumulate in cancer cells, in particular driver mutations that can serve as treatment targets. Genetic alterations identified in tumors usually include single nucleotide variants (SNVs), deletions and duplications. Fusion genes were originally associated with hematologic cancers; however, more than 300 gene fusions have been identified in almost every kind of solid tumor (sarcomas, carcinomas and tumors of the central nervous system). Identifying and characterizing the mutations in tumors therefore can have both diagnostic and therapeutic applications. The advent of Next-Generation sequencing has enabled high-throughput, low cost, accurate molecular profiling across many tumor types.
Test Description
The JAX SOMASEQTM test reports on 517 cancer related genes for assessment of all DNA and RNA variant types such as SNVs, copy number variants (CNVs), indels, and fusions, in addition to MSI and TMB. Analyzed using Next-Generation sequencing (NGS), JAX SOMASEQTM allows for calculation of MSI and TMB, markers that are used in predicting response to immunotherapy. All identified variants are assessed for clinical relevance based on associations in the biomedical literature with response or resistance to FDA approved targeted therapies. Evidence of association between genomic variants and potential response to therapy or availability of clinical trials curated from the peer-reviewed literature, publicly available databases, and The Jackson Laboratory Clinical Knowledgebase (CKB).
If you are interested in receiving PD-L1 immunohistochemistry results, please select JAX SOMASEQTM Complete when completing your requisition.
Methods
JAX SOMASEQTM uses genomic DNA and RNA extracted from macro dissection‐enriched FFPE tissue sections (≥30% neoplastic content), followed by enrichment of target exons and introns by hybrid‐capture (Illumina). Illumina sequencers generate 101bp paired‐end sequence reads with a median exon coverage of greater than or equal to 150X. Variants within regions that do not meet our coverage thresholds are not reported. For a list of these regions, please contact CGL_CS@jax.org. The LOD (limit of detection) for SNVs and indels was determined as 5%. The LOD for CNVs was 5 copies for amplifications and 1 copy for deletions. Mutational analysis is performed using the TSO500 bioinformatic pipeline. Variants were called against human genome build GRCh37. Results returned in as little as a week from sample receipt.
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Specimen Requirements:
- Formalin-fixed paraffin embedded (FFPE) specimens, including unstained cut slide specimens are acceptable.
- Decalcified specimens are not accepted.
- Purified nucleic acids are not accepted.
- Surface Area: minimum of 3x3mm tumor area.
- Neoplastic Content: Minimum 30% neoplastic content within the tumor area
- For more information on specimen requirements and shipping information, please refer to JAX SOMASEQTM Specimen Instructions.
Please deliver samples to:
The Jackson Laboratory for Genomic Medicine
Attn: Clinical Genomics Laboratory
10 Discovery Drive
Farmington, CT 06032
For more information on specimen requirements and shipping information, please refer to JAX SOMASEQTM Specimen Instructions.
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