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Clinical Cancer Genomics Laboratory (CCGL): Requesting Assistance from All Tumor Boards
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UCSF 500 Cancer Gene Panel (538 genes, 40 with intronic regions)
ABCB1 BARD1 CDH5 CYP3A5 ERCC6L FLCN GTF2I JAK3 MAPK8IP1 NFKBIE PIK3R1 RAD51 SIN3A STAT6 TRRAP ABL1 BCL2 CDH20 DAXX ERG FLT1 GUCY1A2 JAZF1 MCL1 NIPBL PIK3R2 RAD51C SLITRK6 STK11 TSC1 ABL2 BCL2A1 CDK12 DCC ESPL1 FLT3 H3F3A JUN MCTP1 NKX2-1 PIM1 RAD51D SMAD2 STK19 TSC2 ACVR1 BCL2L12 CDK4 DDIT3 ESR1 FLT4 H3F3B KAT6A (MYST3) MDM2 NOTCH1 PKHD1 RAF1 SMAD3 SUFU TSHR ACVR1B BCL2L2 CDK6 DDR2 ESR2 FOXA1 H3F3C KDM5A MDM4 NOTCH2 PLCG1 RARA SMAD4 SUZ12 TSHZ2 ACVR2A BCL6 CDK8 DDX3X ETS1 FOXA2 HDAC9 KDM5C MECOM NOTCH3 PLCH2 RASA1 SMARCA2 TACC1 TSHZ3 AJUBA BCL10 CDKN1A DICER1 ETV6 FOXL2 HGF KDM6A MED12 NOTCH4 PMS2 RB1 SMARCA4 TADA1 TSPY1 AKT1 BCL11B CDKN1B DNMT3A EWSR1 FOXO1 HIF1A KDR MEF2B NPM1 POLD1 RBM10 SMARCB1 TADA2B U2AF1 AKT2 BCOR CDKN2A DOT1L EZH1 FOXO3 HIST1H1C KEAP1 MEN1 NRAS POLE REL SMC1A TAF1 UGT1A1 AKT3 BCORL1 CDKN2B DPYD EZH2 FOXP1 HIST1H3B KIT MET NSD1 POLQ RELA SMC3 TAS2R60 UGT1A7 ALDH7A1 BIRC3 CDKN2C DUSP2 FAM123B (WTX) FOXP4 HLAA KLF4 MGA NT5C2 POT1 RET SMG7 TBL1XR1 USP6 ALK BLM CEBPA DUSP4 FAM46C FSIP1 HNF1A KLHL6 MIR142 NTRK1 POU3F2 RHEB SMO TBX3 USP7 APC BRAF CHD4 DUSP6 FAM58A FUBP1 HOXA3 KMT2A MITF NTRK2 PPM1D RHOA SNX31 TBX22 USP9X APOBEC3G BRCA1 CHEK1 DYNC1I1 FANCA FUS HOXB13 KMT2B MLH1 NTRK3 PPP2R1A RHOT1 SOCS1 TCF3 VAT1L AR BRCA2 CHEK2 EBF1 FANCC FYN HRAS KMT2C MPL NUP93 PPP6C RICTOR SOS1 TCF4 VEZF1 ARAF BRD4 CIC EDNRB FANCD2 GAB2 HSPA2 KMT2D MRAS NUP98 PRDM1 RIT1 SOS2 TCF7L2 VHL ARFRP1 BRIP1 CKS1B EGFR FANCE GAK HSPA5 KRAS MRE11A NUTM1 PRKACA RNF43 SOX9 TCL1A WAPAL ARHGAP35 BTK CLDN18 EGR3 FANCF GATA1 HSP90AA1 LARS MSH2 OR5L1 PRKAR1A ROS1 SOX10 TERT WHSC1 ARID1A B4GALT3 COL1A1 EIFA2 FANCG GATA2 ICK LEF1 MSH6 PAK3 PRKCA RPL5 SOX17 TET2 WISP3 ARID1B CALR COL2A1 EIF1AX FANCL GATA3 ID3 LIFR MTOR PALB2 PRKDC RPL22 SOX2 TFE3 WRN ARID2 CARD11 CREBBP ELF3 FBXO43 GID4 (C17orf39) IDH1 LRP1B MUTYH PAX3 PRSS1 RPTOR SPEN TFEB WT1 ARID5B CBFB CRIPAK EMSY (C11orf30) FBXW7 GIGYF2 IDH2 LRP6 MYB PAX5 PRX RRAS SPOP TGFBR2 XPO1 ASH2L CBL CRKL EP300 FGF10 GIPC3 IGF1R LRRK2 MYBL1 PAX8 PTCH1 RRAS2 SPRED1 TLR4 XRCC2 ASXL1 CCND1 CRLF2 EPCAM FGF14 GLI1 IGF2R LTK MYC PBRM1 PTCH2 RUNX1 SPRY1 TNC XRCC3 ASXL2 CCND2 CSF1R EPHA3 FGF19 GLI2 IKBKE MAF MYCL PCBP1 PTEN RUNX1T1 SPRY2 TNFAIP3 XRCC5 ATF1 CCND3 CSF3R EPHA5 FGF23 GNA11 IKZF1 MAFB MYCN PDCD1LG2 PTK2B SDHA SPRY4 TNFRSF14 XRCC6 ATM CCNE1 CTCF EPHA6 FGF3 GNA13 IKZF2 MALAT1 MYD88 PDGFB PTPN1 SDHB SPTA1 TNKS YAP1 ATR CD163L1 CTNNA1 EPHA7 FGF4 GNAQ IKZF3 MAP2K1 MYH9 PDGFRA PTPN11 SDHC SRC TNKS2 YWHAE ATRX CD79A CTNNB1 EPHB1 FGF6 GNAS IL36A MAP2K2 NAV3 PDGFRB PTPRD SDHD SRSF2 TOP1 ZFHX3 ATXN1 CD79B CUL3 EPHB4 FGFR1 GPR124 IL7R MAP2K4 NBN PDK1 PTPRK SETBP1 SS18 TMPRSS2 ZMYM3 AURKA CD274 CUX1 EPHB6 FGFR2 GPSM1 INHBA MAP3K1 NCOR1 PDPK1 PTPRT SETD2 STAG1 TP53 ZNF217 AURKB CDC42 CXCR4 EPPK1 FGFR3 GRIN2A INSR MAP3K2 NF1 PDS5B PYDC2 SF3B1 STAG2 TP63 ZNF668 AXIN1 CDC73 CYLD ERBB2 FGFR4 GRM3 IRF4 MAP3K5 NF2 PHF6 RAC1 SGK1 STAT3 TPMT ZNF703 AXIN2 CDH1 CYP2C8 ERBB3 FH GSK3A IRS2 MAP3K7 NFE2L3 PHLPP2 RAC2 SH2B3 STAT4 TRAF7 ZRSR2 AXL CDH2 CYP2D6 ERBB4 FHIT GSK3B JAK1 MAP3K9 NFE2L2 PIK3CA RAD21 SHH STAT5A TRPM1 BAP1 CDH4 CYP3A4 ERCC2 FKBP9 GSTP1 JAK2 MAPK1 NFKBIA PIK3CG RAD50 SHOC2 STAT5B TRPM3 538 genes, 40 with intronic regions.
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UCSF 500 Sequencing Pipeline
DNA Extraction & Library Prep UCSF 500 Targeted Capture Sequencing on HiSeq FASTQ Sequence Files SNV/Small Indels (Unified Genotyper, FreeBayes, Mutect) Alignment to Human Genome (BWA) Post-alignment processing (Picard, GATK) Variant Calls: Tumor/Normal Comparison Variant Annotation, Interpretation & Reporting Medium/Large Indels (Pindel) Copy Number (CNVkit) Rearrangements/Translocations (CREST or Delly)
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Variant Classification
Pathogenic Mutation Predictive Prognostic Diagnostic Variant, Likely Pathogenic (VLP) Variant, Unknown Significance (VUS) Variant, Likely Benign (VLB) Benign
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Variant Classification
Pathogenic Mutation Predictive Prognostic Diagnostic Variant, Likely Pathogenic (VLP) Variant, Unknown Significance (VUS) Variant, Likely Benign (VLB) Benign Would like to increase sensitivity of this category, especially for variants that change management
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To increase sensitivity, we need a list of tumor-specific hotspots that are critical for management
GI Tumor Board Breast Tumor Board Tumor Type Gene Variant PMID Biliary FGFR2 rearrangement KRAS codon 12, 13, 61 Colorectal APC any , BRAF V600E , , V600 (other than E) CTNNB1 EGFR S492R amplification , ERBB2 , G13D FDA codon 12, 13 (nonG13D), 61 codon 146 NRAS codon 12, 61 , , NTRK1 J Clin Oncol 2014; abstr 2502 Gastric codon 12, 13 , MET GIST , KIT V654A V559I, H687Y, T670, V654A, A829P, D816, N822, Y823D , , exon 9 p exon 11 p exon 14 p exon 17 p Tumor-Type Gene Variant PMID Breast AKT1 E17K , AKT3 rearrangement ERBB2 L755S G309A del D769Y D769H R896C V777L P780_Y781insGSP V842I amplification FDA V659E ESR1 ERS1-YAP1 rearrangement E380Q , , codon 537 codon 538 L536 , P535H FGF3 FGF4 FGFR1 Ann Oncol 2012; 23(suppl 9): abstr 3190; J Clin Oncol 2011; 29(Suppl): abstr 508; AACR 2013, abstr LB-145. FGFR2 Ann Oncol 2012; 23(suppl 9): abstr 3190 GATA3 any HGF MET NOTCH1 NOTCH2 NTRK3 , PDPK1 PIK3CA
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https://gmi.ucsf.edu/clinicians/#clinician-input
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Molecular Tumor Board Lurie Conference Room
Chaired by W. Michael Korn, M.D. UCSF Divisions of Gastroenterology and Hematology/Oncology
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