Sign in →

Test Code LAB9343 Cancer Panel Solid Tumor Somatic Mutations by Massively Parallel Sequencing

Genes Tested:

AKT1, ALK, APC, ARAF, BRAF, CDKN2A, CTNNB1, CYSLTR2, DDR2, EGFR, EIF1AX, ERBB2, ERBB4, ESR1, FBXW7, FGFR1, FGFR2, FGFR3, GNA11, GNAQ, GNAS, H3F3A, HIST1H3B, HRAS, IDH1, IDH2, KEAP1, KIT, KRAS, MAP2K1, MET, NOTCH1, NRAS, NTRK1, PDGFRA, PIK3CA, PLCB4, POLD1, POLE, PTEN, RAC1, RAF1, RET, RNF43, ROS1, SMAD4, STK11, TERT*, TP53

Collection:

Submit formalin-fixed paraffin-embedded (FFPE) or frozen block and a H&E stained slide matching the current block face. Also acceptable are 5-10 unstained slides with matching H&E stained slide or cytology smear with >20% tumor cell content for the entire slide.

Turnaround Time (TAT):

Results reported within 5 to 11 days after receipt of specimen.

Test Availability:

Batched once per week. DNA will be extracted on samples that are in the laboratory prior to 12pm on Friday and testing will be performed Monday through Wednesday with final results available on Thursday of the following week.

Performing Lab Section:

Cytogenetics Lab (Genomics) – EH218 University Hospital Extension

Send Specimen to Anatomic Pathology - EH314 Children's Hospital.  Fax MUSC Molecular Genetics Requisition Form to 843-792-9653.

Method Description

The Cancer Panel Solid Tumor Somatic Mutations by Massively Parallel Sequencing, also called “Focus Genomics”, is a targeted 49-cancer-related gene DNA panel that is relevant to the diagnosis, prognosis, or therapeutic decision-making for the patient that have been carefully selected for clinically relevant content from College of American Pathologist and National Comprehensive Cancer Network guidelines, relevant publications and late-phase clinical trials to provide single nucleotide, small insertion, and small deletion mutations. The variant and gene coverage is based on the NCCN guidelines for various solid tumor types and based on FDA approved drugs with companion diagnostics. The panel includes biomarkers listed in the NCCN guidelines for the following pathological diagnoses: non-small cell lung cancer, upper gastrointestinal tract cancer, colorectal cancer, pancreatic/hepatobiliary cancer, head and neck cancers (including thyroid carcinoma), skin cancers including melanoma, central nervous system tumors including astrocytic tumors, endocrine tumors, prostate cancer, breast cancer, gynecological malignancies, and metastatic cancer of unknown origin. This assay is intended for use in combination with other testing modalities as determined by the diagnosis. 

Disclaimer:

This test was developed and its performance characteristics determined by the Medical University of South Carolina. It has not been clearer or approved by the U.S. Food and Drug Administration. The FDA has determined that such clearance or approval is not necessary. This test is used for clinical purposes. It should not be regarded as investigational or for research. This laboratory is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) as qualified to perform high complexity clinical laboratory testing.

Limitations:

The lower limit of detection for this assay is 5% allele with coverage of each amplicon greater than 1,000X. The laboratory has determined that this technology cannot reliably detect mutations at coverage below 500X and tumor burden below 10%. Individuals being analyzed should understand that rare diagnostic errors may occur. Possible sources of diagnostic errors can include genotyping errors from trace contamination of PCR, mosaicism at levels below standard detection, rare variants that can interfere with analysis, and from other sources.

Variants predicted to be benign (such as synonymous coding changes and common population variants) and intronic variants are not reported. Any mutation with a variant frequency at or near 50% or 100% may represent a germline rather than somatic variation and not reported. If clinically indicated, patients with such results may be referred to a genetic counselor or clinical geneticist for further consideration and to assess for germline mutations and their causes and risks.