• Test Code:
    4600
  • Department:
  • Test Synonyms:
    Heme Malignancies Panel Leukemia Panel AmpliSeq AML Panel Ion Torrent Next 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
CCND1
CDKN2A
JAK1
JAK2
JAK3
STAT3

Transcription
BCOR
BCL6
CEBPA
CREBBP
ETV6
EP300
FOXO1
GATA1
GATA2
MEF2B
MLL
MLL2
MYC
1D3
IKZF1
PAX5
PHF6
PRDM1
RUNX1
STAT3
TDF3
WT1

Epigenetic
ASXL1
DNMT3A
EZH2 KDM6A/UTX
PTEN
SUZ12
TET

RAS
HRAS
KRAS
NRAS

Adaptor
CBL
CBL-B
MYD88

Phosphatase
PTPN11

Ubiquitin
BIRC3
FBXW7
TNFAIP3
TNFRSF14

Receptor Tyrosine Kinase
FLT3
KIT

Splicing
SF3B1
SRSF2
U2AF35
ZRSR2

 

Cohesin-Complex gene
RAD21
SMC1A
SMC3
STAG2

Receptor
CSF3R
GNA13
IL7R
MPL
NOTCH1
NOTCH2

 

Other
CALR
CARD11
CD79A
BCL2
FAM5C
HNRNPK
IDH1
IDH2
NPM1


Gene

Primary Clinical Relevance

Target Regions

Exons

AML/MDS

Lymphoid

ALL

ABL

X

Selected exons

4-10

ASXL1

X

All coding

13

ATM

 

X

 

All coding

1-62

BCL2

 

X

 

All coding

1-2

BCL6

 

X

 

Selected exons

3,6-8

BCOR

X

All coding

1-14

BIRC3

 

X

 

Selected exons

2,5

BRAF

 

X

 

Selected exons

15

CALR

Rare

 

 

Selected exons

9

CARD11

 

X

 

Selected exons

1-8

CBL

X

Selected exons

7-9

CBL-B

X

Selected exons

7-9

CCND1

 

X

 

Selected exons

1

CD79B

 

X

 

Selected exons

5

CDKN2A

 

X

 

All coding

1-3

CEBPA

X

All coding

1

CREBBP

X

All coding

1-31

CSF3R

X

X

Selected exons

4-5, 12-15

DNMT3A

X

All coding

1-24

EP300

 

X

 

All coding

1-31

ETV6

X

All coding

1-8

EZH2

X

All coding

1-19

FAM5C

 

X

 

Selected exons

2,3,7

FBXW7

X

All coding

1-13

FLT3

X

Selected exons

11,12,14,16,20

FOXO1

 

X

 

Selected exons

1

GATA1

X

All coding

1-5

GATA2

X

Selected exons

4-5

GNA13

 

X

 

All coding

1-4

HNRNPK

 

X

 

Selected exons

3-5

HRAS

X

Selected exons

1-2

ID3

 

X

 

Selected exons

1

IDH1

X

Selected exons

2

IDH2

X

Selected exons

4

IKZF1

X

All coding

1-8

IL7R

X

Selected exons

5-6

JAK1

X

Selected exons

9,12-24

JAK2

X

Selected exons

10,12,14,18

JAK3

X

Selected exons

2-4, 11-16, 18-23

KDM6A/UTX

X

X

All coding

1-29

KIT

X

Selected exons

8-9,17

KRAS

X

Selected exons

1-4

MEF2B

 

X

 

Selected exons

2-8

MLL

X

Partial tandem duplication

PTD within exons 8-12

MLL2

 

X

 

All coding

1-54

MPL

X

Selected exons

4,9,10

MYC

 

X

 

All coding

1-3

MYD88

 

X

 

Selected exons

3,4

NOTCH1

X

Selected exons

26-28,34

NOTCH2

 

X

 

Selected exons

8,22,24,27,28,31,33,34

NPM1

X

Selected exons

11

NRAS

X

Selected exons

1-2

PAX5

X

All coding

1-10

PHF6

X

 

 

All coding

1-9

PRDM1

 

X

 

All coding

1-7

PTEN

 

X

 

All coding

1-9

PTPN11 (SHP2)

X

Selected exons

3,7,12,13

RAD21

X

 

 

Selected exons

5,6,9

RUNX1

X

All coding

1-8

SETBP1

X

 

 

Selected exons

3

SF3B1

X

All coding

1-25

SMC1A

X

 

 

Selected exons

4,5,11,16-18

SMC3

X

 

 

Selected exons

10,13,19,25,28

SOCS1

 

X

 

All coding

1

SRSF2

X

All coding

1-2

STAG2

X

 

 

Selected exons

18,23,27,28

STAT3

X

Selected exons

20

SUZ12

X

All coding

1-16

TCF3

 

X

 

Selected exons

9,17

TET2

X

All coding

1

TNFAIP3

 

 

X

All coding

1-8

TNFRSF14

 

 

X

All coding

1-8

TP53

X

All coding

1-10

U2AF35 (U2AF1)

X

All coding

1-9

WT1

X

All coding

1-10

ZRSR2

X

All coding

1-11


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 next-generation, semiconductor-based massively parallel sequencing (Ion Torrent PGM platform).  Input DNA is amplified using the AmpliSeq technology (Ion Torrent), after which the amplicons are modified with adaptors and subjected to emulsion PCR.  The final products are sequenced on a 316 or 318 chip.

  • Input DNA: 20ng
  • Number of multiplexed amplicons: 701
  • Average read depth per amplicon: 1750

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):

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:

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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