Test Name

Comprehensive Hematologic Malignancy Sequencing Panel

Test Number

LAB9121R

Orderable Test Codes

CPT81455

Test Includes

The Comprehensive Hematologic Malignancy Sequencing Panel is designed to identify clinically relevant DNA mutations for the diagnosis, prognosis, and treatment of patients with acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndrome, myeloproliferative neoplasm, lymphoma and other hematologic malignancies. The appropriate panel should be selected. NovaSeq high throughput targeted sequencing technology is used to identify mutations within the following 221 genes. 
Comprehensive Hematologic Malignancy Sequencing Panel includes:

ABL1 BTK CHEK2 EPHA7 NRNPK KRAS NPM1 PRPF8 SGK1 TNFRSF14
ABL2 CALR CIITA EPOR HRAS LEF1 NRAS PTEN SH2B3 TP53
ALK CARD11 CREBBP ERG ID3 LRP1B NSD1 PTPN1 SMARCA4 TPMT
ANKRD26 CBL CRLF2 ETNK1 IDH1 LUC7L2 NSD2 PTPN11 SMC1A TRAF2
ARID1A CBLB CSF1R ETV6 IDH2 MAP2K1 NT5C2 PTPRD SMC3 TRAF3
ARID1B CBLC CSF3R EZH2 IKZF1 MAP3K14 NTRK1 RAD21 SOCS1 TYK2
ASXL1 CCND1 CTCF FANCL IKZF2 MAPK1 NTRK2 RARA SPEN U2AF1
ATM CCND2 CTLA4 FAS IKZF3 MAX NTRK3 RB1 SRP72 U2AF2
ATR CCND3 CTNNB1 FAT1 IL7R MBD4 PAX5 REL SRSF2 UBA1
ATRX CCR4 CUX1 FAT4 INO80 MECOM PDGFRA RHOA STAG2 WT1
B2M CD19 CXCR4 FBXO1 IRF4 MED12 PDGFRB RIT1 STAT3 XPO1
BCL10 CD274 DDX3X FBXW7 IRF8 MEF2B PHF6 RPL10 STAT5B ZMYM3
BCL11B CD28 DDX41 FGFR3 ITK MPL PIGA RPS15 STAT6 ZNF384
BCL2 CD40 DIS3 FLT3 JAK1 MTOR PIK3CA RRAGC SUZ12 ZRSR2
BCL6 CD58 DKC1 FOXO1 JAK2 MYC PIK3CD RUNX1 SYK  
BCL7A CD79A DNM2 GATA1 JAK3 MYD88 PIM1 SAMD9 TBL1XR1  
BCOR CD79B DNMT3A GATA2 KDM6A NBN PLCG1 SAMD9L TCF3  
BCORL1 CDKN1B EBF1 GATA3 KIT NF1 PLCG2 SAMHD1 TENT5C  
BIRC3 CDKN2A EED GNA13 KLF2 NFE2 POT1 SETBP1 TERC  
BLM CDKN2B EGFR GNAS KLHL6 NFKBIA PPM1D SETD2 TERT  
BRAF CDKN2C EGR2 GNB1 KMT2A NFKBIE PRDM1 SF1 TET2  
BRCC3 CEBPA ELANE H1-2 KMT2C NOTCH1 PRKCB SF3A1 TMEM30A
BTG1 CHD2 EP300 H1-4 KMT2D NOTCH2 PRPF40B SF3B1 TNFAIP3  

Performing Laboratory / Facility

UCLA Molecular Diagnostics Laboratories (MDL)

Performing Section

Molecular Pathology

Availability

Monday through Friday, 0700-1700

Turnaround Time

10-15 days from receipt of specimen in performing lab.

Methodology

The Comprehensive Hematologic Malignancy Sequencing Panel is a next-generation sequencing (NGS) test performed on DNA extracted from blood or bone marrow aspirate to detect DNA mutations in the 221 targeted genes.

Target sequences are enriched using the capture method and sequenced on the NovaSeq 6000 sequencer (Illumina Inc.). This assay involves sequencing of the entire coding regions of the targeted genes, except for TERC.

Alternate methodologies may be used to detect specific DNA mutations in certain genes, such as FLT3, when definitive results for the genes cannot always be determined via NGS.

Variants which are thought to be clinically significant based on existing knowledge as well as variant of uncertain significance (VUS) of probable somatic origin will be reported.

Limitations

This test has been validated by the UCLA Molecular Diagnostics Laboratories. This assay can detect variants with an approximate mutant allele frequency (VAF) of 2%. A negative (no mutation detected) result does not rule out the presence of clinically relevant DNA mutations, as results depend on various factors. These include, but not limited to, mutant allele frequency, specimen integrity, presence of inhibitors, and/or interfering polymorphisms, availability of sufficient high-quality DNA, the genomic location of the mutations, and the current understanding of the clinical impact of the variants at the time of testing. 

Specimen Type

Whole blood

Bone marrow

Extracted DNA

Container

Lavender/EDTA

Collection Instructions

Shared tubes, such as CBC tubes, are not acceptable specimens due to risk of cross-contamination. Send whole blood to the Laboratory at ambient temperature or refrigerated. Do not freeze.

Volume

Whole blood – 4 mL

Bone marrow – 4 mL

Extracted DNA – 200ng

Minimum Volume

Whole blood – <1 mL, if sufficient DNA is extracted from the blood

Bone marrow – <1 mL, if sufficient DNA is extracted from the bone marrow

Extracted DNA – 100ng

Shipping and Handling Instructions

Transport specimen at room temperature.

Causes for Rejection

Shared tubes, such as CBC tubes

Clotted specimen

Improperly labelled specimen

Broken specimen tube

Specimen older than 7 days

Test Information

Test Name

Comprehensive Hematologic Malignancy Sequencing Panel

Test Number

LAB9121R

Orderable Test Codes

CPT81455

Test Includes

The Comprehensive Hematologic Malignancy Sequencing Panel is designed to identify clinically relevant DNA mutations for the diagnosis, prognosis, and treatment of patients with acute myeloid leukemia, acute lymphoblastic leukemia, myelodysplastic syndrome, myeloproliferative neoplasm, lymphoma and other hematologic malignancies. The appropriate panel should be selected. NovaSeq high throughput targeted sequencing technology is used to identify mutations within the following 221 genes. 
Comprehensive Hematologic Malignancy Sequencing Panel includes:

ABL1 BTK CHEK2 EPHA7 NRNPK KRAS NPM1 PRPF8 SGK1 TNFRSF14
ABL2 CALR CIITA EPOR HRAS LEF1 NRAS PTEN SH2B3 TP53
ALK CARD11 CREBBP ERG ID3 LRP1B NSD1 PTPN1 SMARCA4 TPMT
ANKRD26 CBL CRLF2 ETNK1 IDH1 LUC7L2 NSD2 PTPN11 SMC1A TRAF2
ARID1A CBLB CSF1R ETV6 IDH2 MAP2K1 NT5C2 PTPRD SMC3 TRAF3
ARID1B CBLC CSF3R EZH2 IKZF1 MAP3K14 NTRK1 RAD21 SOCS1 TYK2
ASXL1 CCND1 CTCF FANCL IKZF2 MAPK1 NTRK2 RARA SPEN U2AF1
ATM CCND2 CTLA4 FAS IKZF3 MAX NTRK3 RB1 SRP72 U2AF2
ATR CCND3 CTNNB1 FAT1 IL7R MBD4 PAX5 REL SRSF2 UBA1
ATRX CCR4 CUX1 FAT4 INO80 MECOM PDGFRA RHOA STAG2 WT1
B2M CD19 CXCR4 FBXO1 IRF4 MED12 PDGFRB RIT1 STAT3 XPO1
BCL10 CD274 DDX3X FBXW7 IRF8 MEF2B PHF6 RPL10 STAT5B ZMYM3
BCL11B CD28 DDX41 FGFR3 ITK MPL PIGA RPS15 STAT6 ZNF384
BCL2 CD40 DIS3 FLT3 JAK1 MTOR PIK3CA RRAGC SUZ12 ZRSR2
BCL6 CD58 DKC1 FOXO1 JAK2 MYC PIK3CD RUNX1 SYK  
BCL7A CD79A DNM2 GATA1 JAK3 MYD88 PIM1 SAMD9 TBL1XR1  
BCOR CD79B DNMT3A GATA2 KDM6A NBN PLCG1 SAMD9L TCF3  
BCORL1 CDKN1B EBF1 GATA3 KIT NF1 PLCG2 SAMHD1 TENT5C  
BIRC3 CDKN2A EED GNA13 KLF2 NFE2 POT1 SETBP1 TERC  
BLM CDKN2B EGFR GNAS KLHL6 NFKBIA PPM1D SETD2 TERT  
BRAF CDKN2C EGR2 GNB1 KMT2A NFKBIE PRDM1 SF1 TET2  
BRCC3 CEBPA ELANE H1-2 KMT2C NOTCH1 PRKCB SF3A1 TMEM30A
BTG1 CHD2 EP300 H1-4 KMT2D NOTCH2 PRPF40B SF3B1 TNFAIP3  

Performing Laboratory / Facility

UCLA Molecular Diagnostics Laboratories (MDL)

Performing Section

Molecular Pathology

Availability

Monday through Friday, 0700-1700

Turnaround Time

10-15 days from receipt of specimen in performing lab.

Methodology

The Comprehensive Hematologic Malignancy Sequencing Panel is a next-generation sequencing (NGS) test performed on DNA extracted from blood or bone marrow aspirate to detect DNA mutations in the 221 targeted genes.

Target sequences are enriched using the capture method and sequenced on the NovaSeq 6000 sequencer (Illumina Inc.). This assay involves sequencing of the entire coding regions of the targeted genes, except for TERC.

Alternate methodologies may be used to detect specific DNA mutations in certain genes, such as FLT3, when definitive results for the genes cannot always be determined via NGS.

Variants which are thought to be clinically significant based on existing knowledge as well as variant of uncertain significance (VUS) of probable somatic origin will be reported.

Limitations

This test has been validated by the UCLA Molecular Diagnostics Laboratories. This assay can detect variants with an approximate mutant allele frequency (VAF) of 2%. A negative (no mutation detected) result does not rule out the presence of clinically relevant DNA mutations, as results depend on various factors. These include, but not limited to, mutant allele frequency, specimen integrity, presence of inhibitors, and/or interfering polymorphisms, availability of sufficient high-quality DNA, the genomic location of the mutations, and the current understanding of the clinical impact of the variants at the time of testing. 
Specimen Collection and Handling

Specimen Type

Whole blood

Bone marrow

Extracted DNA

Container

Lavender/EDTA

Collection Instructions

Shared tubes, such as CBC tubes, are not acceptable specimens due to risk of cross-contamination. Send whole blood to the Laboratory at ambient temperature or refrigerated. Do not freeze.

Volume

Whole blood – 4 mL

Bone marrow – 4 mL

Extracted DNA – 200ng

Minimum Volume

Whole blood – <1 mL, if sufficient DNA is extracted from the blood

Bone marrow – <1 mL, if sufficient DNA is extracted from the bone marrow

Extracted DNA – 100ng

Shipping and Handling Instructions

Transport specimen at room temperature.

Causes for Rejection

Shared tubes, such as CBC tubes

Clotted specimen

Improperly labelled specimen

Broken specimen tube

Specimen older than 7 days

Result Interpretation