UT San Antonio Heme Oncor DNA Panel by NGS

CPT Code(s)

81455, G0452

Synonym(s)

NGS, Next generation sequencing, Heme Panel, Myeloid, Lymphoid, Hematologic neoplasms, Oncor, Heme, Sequencing, Leukemia, Lymphoma, DNA, Molecular, Panel, AML, MDS, MPN, ALL, myelodysplastic syndrome, myeloproliferative disorders, clonal hematopoiesis of indeterminate potential, clonal cytopenia of undetermined significance

Performed

Molecular Diagnostics Laboratory

Clinical Indication and Relevance

The assay can identify molecular genomic alterations that may help provide a diagnosis and/or therapeutic information. Genomic alterations that can be identified include single nucleotide variants (SNVs) and small indels from the coding regions of 129 genes, FLT3 ITDs and presence of EBV & HHV8 viruses in hematologic samples.

Methodology

The UT San Antonio Heme Oncor DNA Panel by NGS is a targeted sequencing assay, created to detect genomic alterations found in hematological malignancies including myelodysplastic syndrome, myeloproliferative disorders, leukemia, lymphoma, clonal hematopoiesis of indeterminate potential (VAF limit of 2.5%) and other hematologic neoplasms, as clinically indicated. The UTHSA Heme Panel NGS assay is custom designed to detect single nucleotide variants (SNVs) and small indels of <91bp from the coding regions of 129 genes (see Table 1 for gene list), FLT3 ITDs and EBV and HHV8 presence in hematologic samples. This test allows capture-based enrichment of a custom set of genes from whole genome using IDT xGen Lockdown hybridization probes.  High quality libraries are generated using UMIs for sequencing on the Illumina next-generation sequencing (NGS) platform, MiSeq. After sequencing, the data is UMI extracted, FASTQ demultiplexed and then processed using the ICA DRAGEN Somatic Enrichment pipeline. An in-house secondary pipeline analyzes the FLT3 ITDs, oncogenic virus presence, region of interest coverage and other metrics. Variant and quality files are passed to GenomOncology (GO) variant reporting system for variant interpretation and reporting.

Alterations are assessed as Tier I, Tier II, Tier III or Tier IV (benign or likely benign) based on professional guidelines (Li M et. al, 2017, PMID 27993330). Tier I and Tier II will be reported clinically with information on variant significance, targeted therapy and available clinical trials after being assessed using public databases (such as OncoKB, dbSNP, GNOMAD, Genie, PubMed and others). Tier III alteration will be reported separately in a list format and Tier IV alterations will not be reported clinically.

TABLE 1: GENES WITH CODING REGION TARGETED BY TEST

ABL1 BIRC3 CEBPA ETV6 IDH2 KMT2A NOTCH1 PPM1D SF3A1 TCF3
ANKRD26 BRAF CHEK2 EZH2 IKZF1 KMT2D NOTCH2 PRPF8 SF3B1 TERT
ARAF BRCA1 CREBBP FBXW7 IKZF3 KRAS NPM1 PTEN SH2B3 TET2
ARID1A BRCA2 CSF3R FLT3 IL7R LUC7L2 NRAS PTPN11 SMARCA4 TNFAIP3
ASXL1 BTK CUX1 GATA1 IRF4 MAP2K1 NTRK1 RAD21 SMARCB1 TNFRSF14
ASXL2 CALR CXCR4 GATA2 IRF8 MAPK1 PAX5 RB1 SMC1A TP53
ATM CARD11 DDX3X GATA3 JAK1 MEF2B PDGFRA RHOA SMC3 U2AF1
ATRX CBL DDX41 GNA13 JAK2 MIR142 PHF6 RUNX1 SOCS1 U2AF2
B2M CBLB DNMT1 GNAS JAK3 MPL PIGA SAMD9 SRSF2 UBA1
BCL2 CD79A DNMT3A HNRNPK KDM6A MYC PIK3CA SAMD9L STAG2 WT1
BCL6 CD79B ELANE HRAS KIT MYD88 PLCG1 SETBP1 STAT3 XPO1
BCOR CDKN2A EP300 ID3 KLF2 NF1 PLCG2 SETD2 STAT5B ZRSR2
BCORL1 CDKN2B ETNK1 IDH1 KLHL6 NFKBIE POT1 SF1 SUZ12

Minimum Specimen Requirements

  • Peripheral blood (PB): 3-5mL EDTA tube (lavender top), ACD (yellow top) also acceptable, store and transport at 2-8°C (wet ice or cold packs), collected within 72 hours (if exceeds, call Lab Manager as samples >7 days old were tested in validation)
  • Bone marrow (BM): 3-5 EDTA tube (minimum 1 mL), ACD (yellow top) also acceptable, store and transport at 2-8°C (wet ice or cold packs), collected within 72 hours (if exceeds, call Lab Manager as samples >7 days old were tested in validation)
  • Fresh or frozen tissue: At least 0.3×0.3 cm tissue. Flash frozen tissue stored at -80C or fresh tissue in RPMI collected within 72 hours. Store and transport fresh tissue at 2-8C (wet ice or cold packs).
  • Select tissue from hematopathologic neoplasm/suspected neoplasm, ideally with more than 500 neoplastic cells. A H&E slide is also requested:
  • Formalin Fixed Paraffin Embedded (FFPE) tissue blocks, including core needle biopsies. The Histology lab will cut 10 unstained slides at 5-10 microns and 1 H&E.
  • Unstained FFPE tissue slides (10 slides at 5-10 microns size) and 1 H&E. o Fine needle aspirate (FNA) processed as FFPE cell blocks (cytospin). The Histology lab will cut 10 unstained slides at 5-10 microns and 1 H&E.

Transport:

  • FFPE should be transported to the laboratory at controlled temperatures. Sample temperature should not exceed 30C.
  • Peripheral blood or bone marrow or fresh tissue should be delivered immediately at 2-8°C (wet ice or cold packs). Do not freeze.

Unacceptable Samples:

  • FFPE samples fixed in Zenker’s B5 or Bouin’s fixatives.
  • FFPE samples decalcified with strong acids.
  • PB and BM samples less than 2 mL requires pathologist approval
  • Serum or plasma, frozen peripheral blood or bone marrow, clotted blood, severely hemolyzed samples.
  • FFPE tissue scrolls are not desired, as they cannot be macrodissected. They require pathologist approval. Unstained tissue slides should be accompanied by an H&E slide.

Turnaround time

Seven to fifteen working days.

View Requisition Sheet