• Test Code:
    4600
  • Department:
  • Test Synonyms:
    Heme Malignancies Panel Leukemia PanelNext Gen Sequencing Comprehensive Heme Malignancies Panel Next Gen Sequencing Leukemia Panel ABL1AKT1ANKRD26ARID1AARID1BASXL1ASXL2ATG2BATMATRXBCL2BCL6BCORBCORL1BIRC3BIRC6BLMBRAFBRCA1BRCA2BRCC3BRD4BTKCALRCARD11CASP10CBLCBLBCBLCCCND1CCND3CCR4CD27CD79ACD79BCDH11CDKN2ACEBPACHD2CHEK2CREBBPCRLF2CSF1RCSF3RCTCFCTLA4CUX1CXCR4DAXXDDX41DDX54DHX15DHX29DIS3DNAH5DNAH9DNAJC21DNM2DNMT1DNMT3ADOCK8DTX1EEDEFTUD1EGFRELANEEP300ERBB4ETNK1ETV6EZH2FAM47AFAM5CFASFAT1FAT4FBXO11FBXW7FLT3FOXO1FYNGATA1GATA2GATA3GNA13GNASGNB1GSKIPHAX1HIST1H1EHNRNPKHRASHVCN1ID3IDH1IDH2IGLL5IKZF1IKZF3IL7RIRF4JAK1JAK2JAK3KDM6AKITKLF2KLHL6KMT2AKMT2CKMT2DKRASLLGL2LRRC4LUC7L2MAGT1MAML1MAP2K1MECOMMED12MEF2BMGAMLH1MPLMSH2MSH6MYCMYD88NAF1NBNNF1NFKBIENOTCH1NOTCH2NPATNPM1NRASNT5C2NXF1PAX5PCLOPDGFRAPHF6PIGAPIK3CDPIM1PLCG1PLCG2PMS2POT1PPM1DPRDM1PRKCBPRPF40BPRPF8PRPS1PSMB5PTCH1PTENPTPN11RAD21RB1RBBP6RELNRHOARIT1RPS15RTEL1RUNX1RYR1RYR2SAMD9SAMD9LSAMHD1SBDSSETBP1SETD2SETDB1SF1SF3A1SF3B1SH2B3SMARCA2SMARCB1SMC1ASMC3SOCS1SPENSPI1SRP72SRSF2STAG2STAT3STAT5BSTXBP2SUZ12SYKSYNE1TBL1XR1TCF3TCF4TERCTERTTET2TNFAIP3TNFRSF14TP53TRAF3U2AF1U2AF2UBR5USH2AVAV1WASWHSC1WT1XPO1ZBTB7AZRSR2
  • CPT Code(s):
    81455
Background:

Screening for mutations in oncogenes and tumor suppressor genes is increasingly important in delivering personalized cancer care. The GeneTrails® Hematologic Malignancies NGS Panel delivers information on alterations in a panel of 220 genes that play a role in pathogenesis of hematolymphoid malignancies and precursor lesions, including acute myelogenous and lymphoid leukemias, myelodysplasias, myeloproliferative disorders, and lymphomas. Mutations in these genes are known to have clinical significance in diagnosis, prognosis, response to therapy, disease monitoring, or cancer predisposition.  Some mutations detected on this panel may directly inform targeted or non-targeted treatment options.  This panel covers nearly all of the mutation sites in the 220 genes listed below and is supplemented by Sanger sequencing. In addition, the panel is complemented with single gene tests to detect internal tandem duplication insertions in FLT3 exons 14&15 and partial tandem duplications in KMT2A/MLL (aka MLL-PTD).  The panel has a sensitivity of ~2% mutant allele for single nucleotide substitutions and ~5 % mutant allele for short insertions/deletions, with strict next generation sequencing quality control parameters.

For the full list of Genes included in the panel, see the Gene Table

Reasons for Referral:

The GeneTrails® Hematologic Malignancies 220 Gene Panel is designed to molecularly subclassify hemato-lymphoid neoplasms, which is important in determining prognosis and, in some cases, predicting responses to targeted and/or non-targeted therapy.

Methodology:

The GeneTrails® Hematologic Malignancies ​220 Gene Panel is performed on DNA extracted from blood, bone marrow aspirate or biopsy, or formalin-fixed, paraffin-embedded (FFPE) bone marrow.  The assay uses massively parallel sequencing (next-generation sequencing) with a combination of multiplexed PCR (customized QIAseq Targeted DNA panel) and sequencing on an Illumina platform (NextSeq500). The panel
targets all or selected coding exons (with reported hotspot mutations) and their flanking intronic regions of the genes listed in the table above. An in-house bioinformatics analysis pipeline has been used that employs multiple established variant calling tools (FreeBayes, MuTect2 and Scalpel) and variant annotation tool (Oncotator). The genomic variants have been interpreted in accordance with the 2017 guideline recommendations by AMP/ASCO/CAP (PMID: 27993330). The assay is validated in accordance with the AMP guidelines (PMID: 28341590).

  • Input DNA: 40ng (100ng for FFPE specimens)
  • Number of targeted regions: 1080
  • Average read depth per target region: ~2000

Specimen Requirements:

  • Peripheral blood: 5 mL EDTA ( lavender top tube) or 5 mL Citrate tube or
  • Bone marrow aspirate: 5 mL in EDTA (lavender top tube) or
  • A paraffin block or
  • 10 unstained sections of a bone marrow biopsy (4-5 microns)

Test Performed (Days):

Once or twice per week

Turn Around Time:

10 - 14 days

Shipment Sensitivity Requirements:

  • Package and ship specimen to remain cold, but not frozen. 
  • Ship via overnight express, using the FedEx priority overnight label provided. 
  • Contact Client Services at (855) 535-1522 for shipping kits and instructions.

References:

  1. Li MM, et al; Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. 2017, J Mol Diagn. 19(1):4-23.
  2. Jennings LJ, et al; Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. 2017, J Mol Diagn. 19(3):341-365.

Additional Info:

The Knight Cancer Institute at Oregon Health & Science University is a pioneer in the field of precision cancer medicine. The institute's director, Brian Druker, M.D., helped prove it was possible to shut down just the cells that enable cancer to grow. This breakthrough has made once-fatal forms of the disease manageable and transformed how cancer is treated. The OHSU Knight Cancer Institute is the only National Cancer Institute-designated Cancer Center between Sacramento and Seattle – an honor earned only by the nation's top cancer centers. It is headquarters for one of the National Cancer Institute's largest research collaboratives, SWOG, in addition to offering the latest treatments and technologies as well as hundreds of research studies and clinical trials.

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