Test Code LAB9342 The Myeloid Molecular Panel by Massively Parallel Sequencing
Genes Tested:
ABL1, ASXL1, BCOR, BCORL1, BRAF, CALR, CBL, CBLC, CEBPA, CSF3R, DDX41, DNMT3A, ETV6, EZH2, FLT3, GATA1, GATA2, IDH1, IDH2, IKZF1, JAK2, KDM6A, KIT, KMT2A, KRAS, MPL, MYD88, NF1, NOTCH1, NPM1, NRAS, PDGFRA, PHF6, PPM1D, PTEN, PTPN11, RHOA, RUNX1, SETBP1, SF3B1, SRSF2, STAG1, STAG2, STAT3, TET2, TP53, U2AF1, WT1, ZRSR2
Collection:
Specimen: Bone Marrow, peripheral blood or solid tumor sample.
Container: Lavender Top Tube
Volume: 4 mL; Minimum 1 mL
Storage Instructions:
Send specimen to Lab immediately after collection. Ship specimen at room temperature; if > 90° F, use refrigerated coolant.
Turnaround Time (TAT):
Results reported within 5 to 11 days after receipt of specimen.
Test Availability:
Batched once a week. DNA will be extracted on samples that are in the lab prior 12 pm on Wednesday and testing will be performed Thursday – Friday with final results available early the following week.
Method Description
The Myeloid Molecular Panel by Massively Parallel Sequencing performed in the Medical University of South Carolina (MUSC) Genomics Laboratory, also called “FocusHeme”, is a targeted 49-gene DNA panel that is relevant to the diagnosis, prognosis, and/or therapeutic decision-making in hematological malignancies. The target genes and regions have been carefully selected for clinical relevance using available guidelines and recommendations from College of American Pathologists and National Comprehensive Cancer Network, relevant publications, late-phase clinical trials, and FDA-approved drugs associated with specific genomic markers that are single nucleotide, small insertion, and small deletion mutations. The variant and gene coverage is designed for hematological malignancies including myeloid and lymphoid lineage tumors, often in combination with other testing modalities (e.g. FISH, cytogenetics, SNP microarray, etc.). Single gene assessments by NGS for hematological tumors will be determined from this panel by the masking of all other results prior to pathologist review. The use of targeted massively parallel sequencing panels is recommended by NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®) for several tumor types to replace algorithmic, reflexive molecular testing, as it is both cost effective and streamlines downstream data analysis. This panel is intended for use on peripheral blood, bone marrow aspirate, bone marrow core (formalin-fixed paraffin-embedded), or other FFPE samples containing hematological malignant processes such as lymph nodes and tumor resection specimens.
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.
Performing Lab Section:
Cytogenetics Lab (Genomics) – EH218 University Hospital Extension