For Providers

Full exon coverage of 1,516 cancer-related genes is provided by UT Southwestern's Comprehensive Pan-Cancer Next Generation Sequencing Solid Tumor Panel. Full exon coverage of 179 Myelodysplsia, Leukemia, and Lymphoma related genes is provided by UT Southwestern's Comprehensive Pan-Cancer Next Generation Sequencing Heme Panel. Designed to detect point mutations, insertions, deletions, splice site defects, mutation burden, gene fusions, and translocations, this test is an effective tool to facilitate the personalized management of solid tumors and hematopoietic malignancies. The size of the panel is based on the knowledge that analysis of many cancer genes has a greater probability of detecting targetable alterations, prognostic and predictive markers including mutational load, and resistance mutations than small panels or single gene analysis. Cancer arises due to a combination of aberrant function in numerous cellular pathways. Thus, a more complete understanding of the breadth and depth of these abnormalities increases the likelihood of discovering therapeutic targets and accurate prognostic information. If you need to know about specific genes in the UT Southwestern assay, you can search for them here.

Peripheral blood, bone marrow aspirate, and unstained formalin-fixed, paraffin-embedded (FFPE) surgical pathology specimens are all acceptable for testing. Paired germline tissue from saliva or peripheral blood is used to get more accurate results. More detailed specimen collection instructions are available on this website for your review. Both DNA and RNA are extracted and sequenced in order to provide the most definitive assessment of tumor mutations, gene fusions, and gene expression data. This assay is validated to report fusions where both genes contribute to protein coding. Fusions involving only non-coding regulatory DNA (e.g. TMPRSS2::ERG, IGH-rearrangements) may have false negatives. Comparison of alterations found in the tumor tissue with the patient’s germline DNA sequence (when provided by the patient as a saliva or blood specimen, at no additional charge) provides unambiguous results as to which aberrations are truly potential tumor drivers rather than rare (<1%) germline variation. FFPE specimens are micro- or macrodissected to enrich for tumor tissue before sequencing. Greater than 94% of all exons in the panel have at least 100X coverage with a mean coverage of ≥300X and a mutant allele frequency limit of detection for single nucleotide variants of 5%, thus providing sensitive measurement of tumor heterogeneity. The turnaround time is approximately 3 weeks from receipt of all specimens. Specimens are picked up by courier service or can be shipped using pre-labeled postage-paid shipping boxes provided by the lab. The lab will contact insurance companies prior to specimen analysis for preauthorization.

Reports of sequencing results of your patient’s tumor are presented in an easy-to-read format. A table with all significant (driver) mutations, FDA approved therapeutics for that tumor type or even tumors of other organ systems, and ongoing clinical trials available locally and across the U.S. are presented on the front page. The remainder of the report gives additional details of each mutation’s significance and biology, available therapeutics, and links to clinical trials and cited articles. The report generation process references a partner database that has already annotated over 40,000 specific mutations described in cancer. The UT Southwestern Pathology Department faculty responsible for analyzing this assay has decades of experience in the molecular pathology of neoplasia of all types. Cases are routinely discussed amongst faculty in order to provide a comprehensive assessment of individual cases. Thus, reports also provide useful interpretive comments concerning cancer pathways and how they may synergize in your patient’s tumor, based on recent clinical and basic science publications. A sample report is available as a PDF document for your review.