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IRCC GENE PANEL

This document summarizes procedures for generating IRCC gene panel mutation data output.
Data analysis has been performed by Dr Aikaterini Chatzipli in Ultan McDermott group at the Wellcome Trust Sanger Intitute, UK.

Analysis

  • Baits corresponding to a cancer gene panel were designed using SureSelect DNA platform (Agilent genomics).
  • 75 pb paired-end Sequencing was done using a HISEQ 2000 v4 system (Illumina).
  • The algorithms used for the analysis are the following
    • Bioconductor package XenofilteR was used to separate human from mouse reads interrogating the bam files.
    • Calling for mutations ( substitutions, insertions and deletions) was done using Caveman and Pindel algorithms (versions
      1.5.3 and 4.2, respectively)
    • Calling for Copy Number analysis was done using CNVkit
IRCC GENE PANEL
ACVR1B ACVR2A APC ARFGEF1 ARID1A ARID2 ARID4A ASXL1 ATM ATR
ATRX AXIN2 BAI3 BCL9L BCLAF1 BCOR BRAF BRCA2 CARD11 CBL
CDC27 CDC73 CDH1 CDK12 CDK8 CDKN2A CLSPN CREBBP CSPP1 CTNNB1
DKK2 DUSP16 EGFR ELF3 EP300 EP400 ERBB2 ERBB3 ERBB4 EZH2
FAM123B FBXW7 FGFR1 FGFR2 FLT1 GATA3 GNAS H3F3A H3F3B HNF4A
IGF2 IKBKB IRS2 JAK2 KAT6A KDM3B KDM6A KDR KIT KLF5
KRAS LIG1 MAP2K4 MAP3K4 MARK1 MET MGA MLH1 MLH3 MLL2
MLL3 MSH2 MSH3 MSH6 MTOR MYC NF1 NF2 NRAS PCBP1
PDGFRA PIK3CA PIK3R1 PMS2 POLE PPP1R3A PTCH1 PTEN PTPN11 RB1
RET RNF43 RSPO2 RSPO3 SETD2 SMAD2 SMAD3 SMAD4 SOX9 STAG2
STK11 TBX3 TCF7L2 TGFBR2 TOP2B TP53 TP53BP1 TPTE TRIM23 TRRAP

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