• Test Code:
    4600
  • Department:
    Hematological Malignancies
  • Test Synonyms:
    Heme Malignancies Panel Leukemia Panel AmpliSeq AML Panel NextSeqNext Gen Sequencing Heme Malignancies Panel Next Gen Sequencing Leukemia Panel ABL ATM ASXL1 BCL2 BCL6 BCOR BIRC3 BRAF CALRCARD11 CBL CBL-B CCND1 C79B CDKN2A CEBPA CREBBP CSF3R DNMT3A EP300 ETV6 EZH2FAM5C FBXW7 FLT3 FOXO1GNA13 GATA1 GATA2 HNRNPK HRAS IDH1 IDH2 ID3 IKZF1 IL7R JAK1JAK2 JAK3 KDM6A/UTX KIT KRAS MEF2BMLLMLL2MPL MYCMYD88NOTCH1 NOTCH2NPM1NRASPAX5PHF6PRDM1PTENPTPN11 (SHP2)RAD21RUNX1SETBP1SF3B1SMC1ASMC3SOCS1SRSF2STAG2STAT3SUZ12TCF3TET2TNFAIP3TNFRSF14 TP53U2AF35 (U2AF1)WT1ZRSR2
  • 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 76 Gene Panel delivers information on predictive and prognostic mutations commonly involved in hematolymphoid malignancies and precursor lesions, including acute myelogenous and lymphoid leukemias, myelodysplasias, myeloproliferative disorders, and lymphomas.  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 76 genes listed below and is supplemented by Sanger sequencing.  The panel has a sensitivity of ~5 % mutant allele with strict next generation sequencing quality control parameters.

Gene Categories

Kinase

ABL1

ATM

BRAF

Transcription

BCOR

BCL6

CEBPA

Epigenetic

ASXL1

DNMT3A

EZH2

RAS

HRAS

KRAS

NRAS

CCND1

CDKN2A

JAK1

JAK2

CREBBP

ETV6

EP300

FOXO1

KDM6A

PTEN

SUZ12

TET2

Adaptor

CBL

CBLB

MYD88

JAK3

STAT3

GATA1

GATA2

Phosphatase

PTPN11

Ubiquitin

BIRC3

Receptor Tyrosine Kinase

FLT3

MEF2B

KMT2D

WT1

Splicing

SF3B1

SRSF2

FBXW7

TNFAIP3

TNFRSF14

KIT

MYC

U2AF1

Cohesin-Complex gene

Receptor

ID3

ZRSR2

RAD21

CRLF2

CSF3R

GNA13

IL7R

IKZF1

PAX5

PHF6

 

SMC1A

SMC3

STAG2

MPL

NOTCH1

NOTCH2

PRDM1

RUNX1

STAT3

TCF3

 

 

Other

CALR

CARD11

CD79B

BCL2

FAM5C

HNRNPK

IDH1

IDH2

NPM1

SETBP1


Gene

Primary Clinical Relevance

Target Regions

Myeloid

Lymphoid

ABL1

X

X

All coding exons

ASXL1

X

All coding exons

ATM

 

X

All coding exons

BCL2

 

X

All coding exons

BCL6

 

X

All coding exons

BCOR

X

All coding exons

BIRC3

 

X

All coding exons

BRAF

 

X

All coding exons

CALR

X

 

All coding exons

CARD11

 

X

Selected exons

(CCDS5336.2: 3-9, 15, 21)

CBL

X

All coding exons

CBLB

X

All coding exons

CCND1

 

X

All coding exons

CD79B

 

X

All coding exons

CDKN2A

 

X

All coding exons

CEBPA

X

All coding exons

CREBBP

X

All coding exons

CRLF2

X

 

All coding exons

CSF3R

X

X

All coding exons

DNMT3A

X

All coding exons

EP300

 

X

All coding exons

ETV6

X

All coding exons

EZH2

X

All coding exons

FAM5C

 

X

All coding exons

FBXW7

X

All coding exons

FLT3

X

All coding exons

FOXO1

 

X

All coding exons

GATA1

X

All coding exons

GATA2

X

All coding exons

GNA13

 

X

All coding exons

HNRNPK

 

X

All coding exons

HRAS

X

All coding exons

ID3

 

X

All coding exons

IDH1

X

All coding exons

IDH2

X

All coding exons

IKZF1

X

All coding exons

IL7R

X

All coding exons

JAK1

X

All coding exons

JAK2

X

All coding exons

JAK3

X

All coding exons

KMT2A

X

 

PTD

KDM6A

X

X

All coding exons

KIT

X

All coding exons

KRAS

X

All coding exons

MEF2B

 

X

All coding exons

KMT2D/MLL2

 

X

All coding exons

MPL

X

All coding exons

MYC

 

X

All coding exons

MYD88

 

X

All coding exons

NOTCH1

X

All coding exons

NOTCH2

 

X

All coding exons

NPM1

X

All coding exons

NRAS

X

All coding exons

PAX5

X

All coding exons

PHF6

X

 

All coding exons

PRDM1

 

X

All coding exons

PTEN

 

X

All coding exons

PTPN11 (SHP2)

X

All coding exons

RAD21

X

 

All coding exons

RUNX1

X

All coding exons

SETBP1

X

 

All coding exons

SF3B1

X

All coding exons

SMC1A

X

 

All coding exons

SMC3

X

 

All coding exons

SOCS1

 

X

All coding exons

SRSF2

X

All coding exons

STAG2

X

 

All coding exons

STAT3

X

All coding exons

SUZ12

X

All coding exons

TCF3

 

X

All coding exons

TET2

X

All coding exons

TNFAIP3

 

X

All coding exons

TNFRSF14

 

X

All coding exons

TP53

X

All coding exons

U2AF1

X

All coding exons

WT1

X

All coding exons

ZRSR2

X

All coding exons



Reasons for Referral:

The GeneTrails® Hematologic Malignancies 76 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 76 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: