Solid Tumors GeneTrails Comprehensive Solid Tumor Panel

Features included:

• Tumor mutation burden estimate (TMB)
• Identification of microsatellite instability (MSI)
• Genes related to resistance to immune checkpoint inhibitor treatment (HLA genes, B2M, JAK1, JAK2, IFNGR1, IFGR2)
• GeneTrails® Solid Tumor Fusion Gene panel (RNA sequencing panel)

The GeneTrails^® Comprehensive Solid Tumor Panel (CSTP) is a next-generation sequencing (NGS) test comprised of two amplicon-based libraries (one DNA, one RNA/cDNA) used to screen for clinically informative gene alterations that are important in making therapeutic decisions, including SNVs, in/dels, copy number alterations and gene fusion events. The test can detect microsatellite instability and provides an estimate of tumor mutation burden (TMB). CSTP is intended for the analysis of solid tumors from patients with clinically advanced disease (stage III or IV). It covers genes that are informative for the use of FDA-approved therapies in non-small cell lung cancer (EGFR, BRAF, ALK, ROS1), colorectal cancer (KRAS, NRAS, BRAF), breast cancer (PIK3CA), and bladder cancer (FGFR2/3). In addition, it can be used to select therapies that have pan-cancer approval (pembrolizumab for MSI-high, larotrectinib and entrectinib for NTRK gene fusions).

The partner-agnostic RNA gene fusion panel that is part of the CSTP encompasses all fusions for which FDA-approved therapies are available, as well as targets for ongoing clinical trials. The DNA panel includes genes recently linked to immuno-therapy resistance (HLA, B2M, TAP, TAPBP, JAK1, IFNGR1, IFGR2).

The GeneTrails® Comprehensive Solid Tumor Panel has national coverage for qualifying Medicare and Medicare Advantage patients across all solid tumors.

Gene List:

The test is performed on DNA and RNA extracted from tumor-rich regions of formalin-fixed/paraffin-embedded tissue. The DNA and RNA (cDNA) NGS library preparations are both based on custom QiaSeq chemistry (Qiagen) that includes unique molecular indices for the assessment of library complexity. Sequencing is performed on Illumina NextSeq500/550 instruments and the data are analyzed through custom bioinformatics pipelines. The DNA library is generated by 9,229 custom-designed primer extension assays covering 613,343 base pairs across 225 cancer-related genes (whole exons of 199 genes, hotspot regions of 26 genes). This panel is routinely sequenced to an average read depth of ~2,000, providing high sensitivity for SNVs, in/dels and copy number alterations. Variants are identified using both FreeBayes and MuTect2 algorithms in a custom sequencing analysis pipeline. Included in the panel are 227 short repeats that are used to assess microsatellite instability. TMB is estimated by determining the number of likely somatic mutations and normalizing this to mutations per megabase of sequence.

The RNA panel consists of 309 custom-designed primer extension assays covering common breakpoints across 24 genes involved in clinically informative gene fusions. Using Starfusion software, the panel can identify any partner fused to these target genes. The panel can also detect oncogenic splice variants such as EGFRvIII and MET ex14del. Using a minimum output of 200,000 unique reads, this panel achieves a high level of sensitivity.

• Input DNA: 50 ng
• Minimum read depth per amplicon:  250

• A paraffin block or
• 10 unstained sections of tumor (4-5 microns)(15 sections for small biopsies)
• Contact Client Services for shipping materials and procedures at (855) 535-1522.

Twice weekly

10-17 Calendar days

• Keep specimen cool during transit, but do not ship on dry ice.
• Please use the cold pack provided in the KDL shipping kit.
• Ship the specimen overnight express, using the FedEx priority overnight label provided.
• Contact Client Services for shipping materials and procedures at (855) 535-1522

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