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HEME-STAMP (STANFORD ACTIONABLE MUTATION PANEL FOR HEMATOPOIETIC AND LYMPHOID NEOPLASMS)

Test Code: HSTAMP, HSTAMPB
Description: This assay detects single nucleotide variants (SNVs), short insertion-deletions and selected gene fusions in 164 genes recurrently altered in myeloid and lymphoid neoplasms. The Heme Stanford Actionable Mutation Panel for Hematopoietic and Lymphoid Malignancies (Heme-STAMP) is a targeted next generation sequencing method. The workflow includes acoustic shearing of isolated genomic DNA, followed by efficient preparation of sequencing libraries and a targeted enrichment approach to capture genomic regions of interest. The enrichment is accomplished using custom designed libraries of capture oligonucleotides that target a specific set of genomic regions. This panel targets 164 genes, either in part or fully, with the genes selected on the basis of their known impact as actionable targets of existing and emerging anti-cancer therapies, their prognostic features, and/or their mutation recurrence frequency across patients with hematopoietic neoplasms. These genomic features are interrogated to achieve a minimum analytic detection-limit of 5% for SNVs and insertion-deletion variants. Pooled libraries are sequenced on an Illumina sequencing instrument.

This assay detects single nucleotide variants (SNVs), short insertion-deletions and selected gene fusions in 164 genes recurrently altered in myeloid and lymphoid neoplasms. The Heme Stanford Actionable Mutation Panel for Hematopoietic and Lymphoid Malignancies (Heme-STAMP) is a targeted next generation sequencing method. The workflow includes acoustic shearing of isolated genomic DNA, followed by efficient preparation of sequencing libraries and a targeted enrichment approach to capture genomic regions of interest. The enrichment is accomplished using custom designed libraries of capture oligonucleotides that target a specific set of genomic regions. This panel targets 164 genes, either in part or fully, with the genes selected on the basis of their known impact as actionable targets of existing and emerging anti-cancer therapies, their prognostic features, and/or their mutation recurrence frequency across patients with hematopoietic neoplasms. These genomic features are interrogated to achieve a minimum analytic detection-limit of 5% for SNVs and insertion-deletion variants. Pooled libraries are sequenced on an Illumina sequencing instrument.

Due to inherent limitations of the NGS method, insertion-deletion variants larger than 25 bp are not reliably detected. To detect larger insertion and deletions in key regions of CALR and FLT3 PCR amplification of these regions is performed, followed by capillary electrophoresis fragment analysis. Genes tested by NGS:

ABL1 EGR1 JAK2 PTEN
AKT1 EP300 JAK3 PTPN11
ALK EPOR KDM6A RAD21
ANKRD26-promoter ETNK1 KIT RB1
APLNR ETV6 KLF2 RHOA
ARID1A EZH2 KLHL6 RPS15
ASXL1 FAS KMT2A RUNX1
ATM FBXW7 KRAS S1PR2
B2M FGFR3 MALT1 SETBP1
BCL2 FLT3** MAP2K1 SETD2
BCL6 FOXO1 MAPK1 SF3B1
BCOR FYN MEF2B SGK1
BCR GATA1 MPL SH2B3
BIRC3 GATA2 MTOR SMC1A
BRAF GATA3 MYC SMC3
BTK GNA13 MYD88 SOCS1
CALR** GNAS MYH11 SRSF2
CARD11 GNB1 NF1 STAG2
CBL HRAS NFKB2 STAT1
CBLB ID3 NFKBIE STAT3
CCND1 IDH1 NOTCH1 STAT5B
CCND3 IDH2 NOTCH2 STAT6
CCR4 IGHA1 NPM1 STIL
CD274 IGHA2 NRAS STX11
CD28 IGHG1 NT5C2 TAL1
CD58 IGHG2 PAX5 TCF3
CD79A IGHG3 PDCD1 TERT-promoter
CD79B IGHG4 PDCD1LG2 TET2
CD83 IGHJ1 PDGFRA TNFAIP3
CDKN2A IGHJ2 PDGFRB TNFRSF14
CDKN2C IGHJ3 PHF6 TNFRSF1B
CEBPA* IGHJ4 PIGA TP53
CIITA IGHJ5 PIK3CA U2AF1
CKS1B IGHJ6 PIK3CD VAV1
CREBBP IGHM PIM1 WHSC1
CRLF2 IKZF1 PLCG1 WT1
CSF3R IKZF3 PLCG2 XPO1
CTLA4 IL7R PML ZRSR2
CXCR4 IRF4 POLE  
DDX3X IRF8 POT1  
DDX41 ITK PPM1D  
DNMT3A JAK1 PRDM1  

For specific regions covered, contact Molecular Pathology Fellows at 650-723-6574.

*CEBPA is tested using Sanger Sequencing. This gene is only sequenced on diagnostic AML samples.
**FLT3 and CALR are tested by NGS and PCR/fragment analysis to ensure the identification of large indels.


 
 


 
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