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GeneTrails AML MDS Genotyping Panel

Test Code: 4025 Department: Hematological Malignancies
Test Synonyms: Leukemia Panel AmpliSeq AML Panel Ion Torrent AML / MDS Next Gen Sequencing Leukemia Panel ABL ASXL1 BCOR CBL CBL-B CEBPA CREBBP CSF3R DNMT3A ETV6 EZH2 FBXW7 FLT3 GATA1 GATA2 HRAS IDH1 IDH2 IKZF1 IL7R JAK1 JAK2 JAK3 KDM6A/UTX KIT KRAS MLL MPL NOTCH1 NPM1 NRAS PAX5 PTPN11 (SHP2) RUNX1 SF3B1 SRSF2 STAT3 SUZ12 TET2 TP53 U2AF35 (U2AF1) WT1 ZRSR2
CPT Code(s): 81403 x 6 81404 x 2 81405 x 2 81479 x 34

Background:
Screening for mutations in oncogenes and tumor suppressor genes is increasingly important in delivering personalized cancer care.  The GeneTrails® AML/MDS Genotyping Panel delivers information on predictive and prognostic mutations commonly involved in acute myelogenous leukemia and myelodysplasias, as well as detecting some mutations that may directly inform targeted or non-targeted treatment options.  This panel covers nearly all of the mutation sites in the 43 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

Transcription

Epigenetic

RAS

ABL1

BCOR

ASXL1

HRAS

JAK1

CEBPA

DNMT3A

KRAS

JAK2

CREBBP

EZH2

NRAS

JAK3

ETV6

KDM6A/UTX

Adaptor

Receptor Tyrosine Kinase

GATA1

SUZ12

CBL

FLT3

GATA2

TET2

CBL-B

KIT

MLL

Phosphatase

Ubiquitin

Receptor

IKZF1

PTPN11

FBXW7

CSF3R

PAX5

Splicing

Other

IL7R

RUNX1

SF3B1

IDH1

MPL

STAT3

SRSF2

IDH2

NOTCH1

WT1

U2AF35

NPM1

 

Tumor suppressor

ZRSR2

 

 

TP53

 

 




OHSU Knight Diagnostic Labs 43 Gene Next-Gen Sequencing Panel for Leukemias

Gene

Primary Clinical Relevance

 

 

Target Regions

Exons

 

AML/MDS

 

ALL

 

 

ABL

 

 

X

Selected exons

4-10

ASXL1

X

 

 

All coding

13

BCOR

X

 

 

All coding

1-14

CBL

X

 

 

Selected exons

7-9

CBL-B

X

 

 

Selected exons

7-9

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

ETV6

X

 

 

All coding

1-8

EZH2

X

 

 

All coding

1-19

FBXW7

 

 

X

All coding

1-13

FLT3

X

 

 

Selected exons

11,12,14,16,20

GATA1

X

 

 

All coding

1-5

GATA2

X

 

 

Selected exons

4-5

HRAS

X

 

 

Selected exons

1-2

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

MLL

X

Partial tandem duplication

PTD within exons 8-12

MPL

X

 

 

Selected exons

4,9,10

NOTCH1

 

 

X

Selected exons

26-28,34

NPM1

X

 

 

Selected exons

11

NRAS

X

 

 

Selected exons

1-2

PAX5

 

 

X

All coding

1-10

PTPN11 (SHP2)

X

 

 

Selected exons

3,7,12,13

RUNX1

X

 

 

All coding

1-8

SF3B1

X

 

 

All coding

1-25

SRSF2

X

 

 

All coding

1-2

STAT3

X

 

 

Selected exons

20

SUZ12

 

 

X

All coding

1-16

TET2

X

 

 

All coding

1

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


Methodology:

The AML/MDS Genotyping 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: 20 ng
  • 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)
A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES.  Please include detailed clinical information.

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:
Recommended Use: 

The AML/MDS Genotyping Panel is designed to molecularly subclassify leukemias and myelodysplasias, which is important in determining prognosis and, in some cases, predicting responses to targeted and/or non-targeted therapy.