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Specimen Collection Manual and Test Catalog

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MYGENVAR RAPID ACUTE LEUKIEMIA GENE PANEL, NEXT GENERATION SEQUENCING

Geisinger Epic Procedure Code:  LAB6020    Geisinger Epic ID:  184262
Test Restriction:  LAB ORDER ONLY

SPECIMEN COLLECTION
Specimen type:  Bone marrow (preferred) or whole blood (also acceptable)
Preferred collection container: 
Alternate collection container: 
6 mL lavender-top K2 EDTA tube
Specimen required: 
Bone Marrow - Two (2) Lavender Top - K2 EDTA, 3 mL

SPECIMEN PROCESSING
Processing instructions: 
Mix well immediately. Do not centrifuge.
Transport temperature: 
Refrigerated, 2-8°C. Send/deliver all collection tubes to GMC Molecular Diagnostics Lab.
Specimen stability: 
Refrigerated, 2-8°C: 3 days. Specimen must be extracted within 3 days.
Rejection criteria: 
Wrong collection tube. Improper storage or transport temperature. Stability limits exceeded. Shared or comingled specimens.

TEST DETAILS
Reference interval: 
Negative (no mutations detected).
Additional information: 
For molecular testing, original tube is required.
CPT code(s):  81450
Note: The billing party has sole responsibility for CPT coding.  Any questions regarding coding should be directed to the payer being billed.
The CPT codes provided by GML are based on AMA guidelines and are for informational purposes only.

Test includes: 
This assay is both a next-generation sequencing (NGS)-based multigene panel with combined RNA and DNA components and a capillary electrophoresis assay for FLT3 internal tandem duplication (ITD).

Analysis: FLT3, IDH1, IDH2, NPM1 and TP53 mutations are detected by DNA-based analysis which includes single base-pair and small insertion/deletion alterations in the coding regions and adjacent intron/exon boundaries. Alterations deep in introns or copy number variants will not be reported. In general, this DNA-based assay has a sensitivity of >98% (TBD) in detection of variants at greater than or equal to 5% Minor Allele Frequency in the wild-type background. False negative results are possible due to mutant cell populations below the analytical sensitivity of the method, which is approximately 10% of cells for most mutations. FLT3 ITD mutations are detected by PCR followed by capillary electrophoresis. This assay can detect ITD mutations of up to 270 bp. The lower limit of detection (LLoD) for the detection of FLT3 ITD is 3% in a wild type background.

Gene GeneBank Accession Exons
FLT3 NM_004119 8, 11, 14, 15, 16, 20, 23, 24
IDH1 NM_005896 4
IDH2 NM_002168 5
KMT2A NM_001197104 2, 7, 8, 9, 10, 11
NPM1 NM_002520 11
TP53 NM_000546
NM_001276695		 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
10

Analysis: ABL1, CBFB, CREBBP, ETV6, MECOM, NUP214, RARA, and RUNX1 fusions (translocations) are detected by RNA-based analysis which provides qualitative information including fusion transcript type and/or isoform. Partial tandem duplication in KMT2A gene can also be detected by RNA-based analysis. This RNA-based assay has a sensitivity of > 97% (TBD) detection of the most common fusion transcripts at greater than 0.5% frequency in wild-type background. False negative results are possible if mutant cells are below the analytical sensitivity of the method or alternative break/fusion events that result in unusual transcript types.

Fusion Driver Gene Common Fusion Partners Tested 
ABL1 BCR t(9;22)
CBFB MYH11 inv(16)/t(16;16)
CREBBP KAT6A t(8;16)
ETV6  MECOM t(3;12), RUNX1 t(12;21), 
KMT2A  AFF1 t(4;11), MLLT3 t(9;11), MLLT4 t(6;11), MLLT10 t(10;11) 
MECOM ETV6 t(3;12), RUNX1 t(3;21)
NUP214 DEK t(6;9)
RARA PML t(15;17)
RUNX1 ETV6 t(12;21), MECOM t(3;21), RUNX1T1 t(8;21)

RNA fusion partners tested include: BCR::ABL1 t(9;22), EML1::ABL1 t(9;14), ETV6::ABL1 t(9;12), FOXP1::ABL1 t(3;9), INPP5D::ABL1 t(2;9), NUP214::ABL1, RANBP2::ABL1 t(2;9), RCSD1::ABL1 t(1;9), SFPQ::ABL1 t(1;9), SNX2::ABL1 t(5;9), ZBTB16::ABL1 t(9;11), ZMIZ1::ABL1 t(9;10), CBFB::MYH11 inv(16)/t(16;16), KAT6A::CREBBP t(8;16), KAT6B::CREBBP t(10;16), KMT2A::CREBBP t(11;16), ETV6::ABL2 t(1;12), ETV6::ACSL6 t(5;12), ETV6::ANLN t(7;12), ETV6::ARNT t(1;12), ETV6::CDX2 t(12;13), ETV6::CHIC2 t(4;12), ETV6::FGFR3 t(4;12), ETV6::FLT3 t(12;13), ETV6::FRK t(6;12), ETV6::GOT1 t(10;12), ETV6::INO80D t(2;12), ETV6::ITPR2 t(12;12), ETV6::JAK2 t(9;12), ETV6::LYN t(12;8), ETV6::MECOM t(3;12), ETV6::MN1 t(12;22), ETV6::NCOA2 t(8;12), ETV6::NTRK2 t(9;12), ETV6::NTRK3 t(12;15), ETV6::PDGFRA t(4;12), ETV6::PDGFRB t(5;12), ETV6::PER1 t(12;17), ETV6::PRDM16 t(1;12), ETV6::PTPRR inv(12), ETV6::RUNX1 t(12;12), ETV6::SYK t(9;12), KMT2A:AFF4 ins(5;11), KMT2A::APBB1IP t(10;11), KMT2A::ARHGAP26 t(5;11), KMT2A::ARHGEF12 del(11), KMT2A::ARHGEF17 t(11;11), KMT2A::ATG16L2 ins(4;11), KMT2A::BTBD18 inv(11), KMT2A::C11orf88, KMT2A::CASC5 t(11;15), KMT2A::CASP8AP2 t(6;11), KMT2A::CBL del(11), KMT2A::CDK6 t(7;11); KMT2A::CEP170B t(11;14), KMT2A::CT45A2 t(X;11), KMT2A::DAB2IP t(9;11), KMT2A::DCP1A t(3;11), KMT2A::DCPS t(11;11), KMT2A::ELL t(11;19), KMT2A::ENAH t(1;11), KMT2A::EP300 t(11;22), KMT2A::EPS15 t(1;11), KMT2A::FLNA ins(X;11), KMT2A::FNBP1 t(9;11), KMT2A::FOXO3 t(6;11), KMT2A::FOXO4 t(X;11), KMT2A::FRYL t(4;11), KMT2A::GAS7 t(11;17), KMT2A::GMPS t(3;11), KMT2A::GPHN t(11;14), KMT2A::KIAA1524 t(3;11), KMT2A-PTD, KMT2A::LASP1 t(11;17), KMT2A::LPP t(3;11), KMT2A::MAML2 inv(11), KMT2A::MAPRE1 t(11;20), KMT2A::MEF2C t(5;11), KMT2A::MLLT1 t(11;19), KMT2A::MLLT3 t(9;11), KMT2A::MLLT4 t(6;11), KMT2A::MLLT6 t(11;17), KMT2A::MLLT10 t(10;11), KMT2A::MLLT11 t(1;11), KMT2A::MYH11 t(11;16), KMT2A::MYO18A t(11;17), KMT2A::MYO1F t(11;19), KMT2A::NCKIPSD t(3;11), KMT2A::NEBL t(10;11), KMT2A::NKAIN2 t(6;11), KMT2A::NRIP3, KMT2A::PDS5A t(4;11), KMT2A::PICALM t(11;11), KMT2A::RABGAP1L t(1;11), KMT2A::RNF115 t(1;11), KMT2A::RPS3, KMT2A::SARNP t(11;12), KMT2A::SEPT2 t(2;11), KMT2A::SEPT5 t(11;22), KMT2A::SEPT6 t(X;11), KMT2A::SEPT9 t(11;17), KMT2A::SEPT11 t(4;11), KMT2A::SH3GL1 t(11;19), KMT2A::SMAP1 t(6;11), KMT2A::SORBS2 t(4;11), KMT2A::TECR t(11;19), KMT2A::TET1 t(10;11), KMT2A::TIRAP del(11), KMT2A::TOP3A t(11;17), KMT2A::USP2, KMT2A::UVRAG, KMT2A::ZFYVE19 t(11;15), NUP98::KMT2A inv(11), ETV6::MECOM t(3;12), PSMD2::MECOM inv(3), RUNX1-MECOM t(3;21), DEK::NUP214 t(6;9), NUP214::BRAF t(7;9), NUP214::XKR3 t(9;22), SET7::NUP214 t(9;9), ADAMTS17::RARA t(15;17), BCOR::RARA t(X;17), FIP1L1::RARA t(4;17), IRF2BP2::RARA t(1;17), NABP1::RARA t(2;17), NPM1::RARA t(5;17), NUMA1::RARA t(11;17), NUP98::RARA t(11;17), PML::RARA t(15;17), PRKAR1A:RARA t(17;17) del(17), STAT5B::RARA der(17), TBL1XR1::RARA t(3;17), ZBTB16::RARA t(11;17), RUNX1:AFF3 t(2;21), RUNX1::CBFA2T2 t(20;21), RUNX1::CBFA2T3 t(16;21), RUNX1::CEP76 t(18;21), RUNX1::CLCA2 t(1;21), RUNX1::EVX1 t(7;21), RUNX1::KIAA1549L t(11;21), RUNX1::LPXN t(11;21), RUNX1::MACROD1 t(11;21), RUNX1::MRPS6 t(21;21), RUNX1::NOL4L t(20;21), RUNX1::PRDM16 t(1;21), RUNX1::PRDX4 t(X;21), RUNX1::RPL22 t(1;21), RUNX1::RUNX1T1 t(8;21), RUNX1::SH3D19 t(4;21), RUNX1::TACC1 t(8;21), RUNX1::TRPS1 t(8;21), RUNX1::USP16 del(21), RUNX1::USP42 t(7;21), RUNX1::YTHDF2 t(8;21), RUNX1::ZFPM2 t(8;21) and RUNX1::ZNF687 t(1;21).

Methodology: 
Capillary Electrophoresis
DNA/RNA Extraction
Next Generation Sequencing
Synonyms: 
AML, FLT3, IDH1, IDH2, NPM1, TP53, RUNX1, RARA, CBFB, KMT2A, ETV6, MECOM, NUP214, BCR-ABL1, BCR, ABL, Rapid AML, MyGenVar, NGS, Next Generation Sequencing, ALL
Clinical significance: 
This test detects variants/fusions associated with acute leukemia that are informative in the diagnosis and management of disease.
Doctoral Director(s): 
Yi Ding MD, PhD
Review Date:  09/24/2024

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