Stanford Health Care
About Stanford Clinical LaboratoryLicensureContact Us

Home
Test Directory

Test Requisitions Specimen Collection
Critical Values
Administrative Department
Clinical DepartmentsDepartment of PathologyEsoteric DepartmentsFeatured Services



STANFORD SOLID TUMOR ACTIONABLE MUTATION PANEL

Test Code: STAMP
Description:

The STAMP assay has been updated effective July 18, 2016, to include more driver genes across a broad range of solid tumors (STAMP V2). See below for a complete list of genes.

This assay detects potentially clinically actionable mutations, as well as additional genes that are frequently mutated in cancers. The Stanford Solid Tumor Actionable Mutation Panel (STAMP) is a targeted next generation sequencing method that uses target enrichment to capture genomic regions of interest. The targeted sequencing approach and integrated bioinformatics workflow is optimized for ultra-deep sequencing of formalin fixed tumor biopsy tissue specimens. The workflow includes acoustic shearing of isolated genomic DNA, followed by efficient preparation of sequencing libraries and a target enrichment approach to capture genomic regions of interest for sequencing. The enrichment is done using custom designed libraries of capture oligonucleotides that target a specific set of genomic regions. This panel targets 130 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 known cancer types. These genomic features are interrogated to achieve a minimum analytic detection-limit of at least 5%. Pooled libraries are sequenced on the Illumina® MiSeq system.

This test covers 130 genes, either in part or fully, at a minimum analytic detection limit of 5%.

Genomic positions are given in reference to the GRCh37 (hg19) assembly of the human genome.

Genes entirely or partly covered:

ABL1 EGFR MAP2K1 PPP2R1A
AKT1 EP300 MAP2K2 PTCH1
ALK EPHA2 MDM2 PTEN
APC EPHA3 MDM4 PTPN11
AR ERBB2 MED12 RAC1
ARAF ERBB3 MET RAF1
ARID1A ERBB4 MLH1 RB1
AURKA ESR1 MPL RET
BAP1 EZH2 MSH2 RHEB
BCL2 FBXW7 MTOR RHOA
BCR FGF3 MYC RIT1
BRAF FGF4 MYCL ROS1
BRCA1 FGFR1 MYCN SDHD-promoter
BRCA2 FGFR2 MYD88 SETBP1
CASP8 FGFR3 NF1 SETD2
CCND1 FLT3 NF2 SF3B1
CCND2 FOXO1 NFE2L2 SMAD4
CCND3 GATA3 NKX2-1 SMO
CCNE1 GNA11 NOTCH1 SOX2
CDH1 GNAQ NRAS SPOP
CDK12 GNAS NTRK1 SRC
CDK4 HGF NTRK2 SRSF2
CDK6 HNF1A NTRK3 STK11
CDKN1B HRAS PALB2 TERT-promoter
CDKN2A IDH1 PCBP1 TP53
CDKN2B IDH2 PDGFRA TP63
CHEK2 IGF1R PDGFRB TSC1
CREBBP JAK2 PIK3CA TSC2
CTNNB1 JAK3 PIK3R1 U2AF1
CUL3 KDR PLEKHS1-promoter VEGFA
DDR2 KEAP1 POLD1 VHL
DNMT3A KIT POLE YAP1
DPH3-promoter KRAS    

Examples of mutations potentially considered actionable in cancers and targeted by this assay include:

AKT1: E17K
BRAF: V600G, V600A, V600E, V600K, L597V, Y472C, G469L, G469V, G469A, G466V
CTNNB1: D32N, D32H, D32Y, D32A, D32G, D32V, S33Y, S33C, S33F, G34E, G34V, S37T, S37P, S37A, S37Y, S37C, S37F, T41P, T41A, T41S, T41N`1q2wsx, T41I, S45T, S45P, S45A, S45Y, S45C, S45F
DDR2: S768R
EGFR: G719S, G719C, G719D, G719A, E746_A750delELREA, A763_Y764insFQEA, T790M, L858Q, L858R, L861Q, L861R
ERBB2: E770_A771insAYVM, V777_G778insGSP
KRAS: G12V, G12A, G12D, G12C, G12R, G12S, G13V, G13A, G13D, G13C, G13R, G13S, Q61H, Q61L, Q61R, Q61P, Q61E, Q61K
MAP2K1: Q56P, K57N, D67N
MYD88: L265P
NOTCH1: L1600P, L1574P
NRAS: Q61H, Q61L, Q61R, Q61P, Q61E, Q61K, G13V, G13A, G13D, G13C, G13R, G13S, G12V, G12A, G12D, G12C, G12R, G12S
PIK3CA: R88Q, E542K, E542Q, E545K, E545Q, Q546K, Q546E, Q546P, Q546R, Q546L, H1047Y, H1047R, H1047L, G1049S, G1049R
PTEN: R130R, R130G, R130*, R173C, R173H, R233R, R233*, K267fs*9, K267fs*9
SF3B1: K666N, K666R, K666T, K666Q, R625L, R625C, E622D
TP53: R306*, R273L, R273H, R273C, R248L, R248P, R248Q, R248W, R248G, G245C, G245R, G245S, R175L, R175H

For information regarding genes tested by STAMP v1, please call the Molecular Pathology Lab at 650-723-6574.

In addition, STAMP targets the kinase domains of several genes that are directly or indirectly targeted by clinically available kinase inhibitors. [Note: identification of a mutation in one or more of these genes does not guarantee activity of the drug in a given indication; this list is intended to give examples of potential utility of this information]

 Gene/Kinase  Tumor Type (Cancer Gene Census) Kinase Inhibitor
ABL1 CML, ALL, T-ALL Bosutinib; Imatinib; Ponatinib; Dasatinib; Regorafenib; Nilotinib; Crizotinib;
BRAF melanoma, colorectal, papillary thyroid, borderline ovarian, NSCLC, cholangiocarcinoma, pilocytic astrocytoma Sorafenib; Regorafenib; Dabrafenib; Vemurafenib;
DDR2   Regorafenib;
EGFR NSCLC, glioma Erlotinib; Afatinib; Lapatinib; Vandetanib; Gefitinib;
ERBB2 breast, ovarian, other tumor types, NSCLC, gastric Afatinib; Lapatinib;
ERBB4   Afatinib;
FGFR1 MPD, NHL Ponatinib; Regorafenib; Pazopanib;
FGFR2 gastric, NSCLC, endometrial Ponatinib; Regorafenib;
FGFR3 bladder, MM, T-cell lymphoma Ponatinib; Pazopanib;
KIT GIST, AML, TGCT, mastocytosis, mucosal melanoma Cabozantinib; Imatinib; Ponatinib; Sorafenib; Dasatinib; Regorafenib; Sunitinib; Nilotinib; Pazopanib;
MAP2K1 NSCLC, melanoma, colorectal Trametinib;
MAP2K2 NSCLC, melanoma Trametinib;
MET papillary renal, head-neck squamous cell Crizotinib; Cabozantinib;
PDGFRA GIST, idiopathic hypereosinophilic syndrome, pediatric glioblastoma Regorafenib; Sunitinib; Pazopanib;
PDGFRB MPD, AML, CMML, CML Sorafenib; Dasatinib; Regorafenib; Sunitinib; Pazopanib; Ponatinib; Nilotinib;
RAF1 pilocytic astrocytoma Sorafenib; Dabrafenib; Vemurafenib; Regorafenib;
RET medullary thyroid, papillary thyroid, pheochromocytoma, NSCLC Vandetanib; Cabozantinib; Ponatinib; Sorafenib; Regorafenib; Sunitinib;

References
Newman AM, Bratman SV, To J, Wynne JF, Eclov NC, Modlin LA, Liu CL, Neal JW, Wakelee HA, Merritt RE, Shrager JB, Loo BW Jr, Alizadeh AA, Diehn M. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014 May;20(5):548-54.

Hadd AG, Houghton J, Choudhary A, et al. Targeted, high-depth, next-generation sequencing of cancer genes in formalin-fixed, paraffin-embedded and fine-needle aspiration tumor specimens. J Mol Diagn. 2013 Mar;15(2):234-47.

Wong SQ, Li J, Tan AYC, et al. Sequence artefacts in a prospective series of formalin-fixed tumours tested for mutations in hotspot regions by massively parallel sequencing. BMC Medical Genomics. 2014 7:23.


 
 


 
Home | About Stanford Clinical Laboratories | Careers | Contact Us | Legal Notices & Disclaimer