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Table 2 Comparison of candidate driving genes of same cancer type from AYAs with those from all age group

From: Clinical application of genomic profiling to find druggable targets for adolescent and young adult (AYA) cancer patients with metastasis

  Prostate cancer HNSCC
AYA01 Barbieri, et al. AYA04 TCGA
Sequencing platform WES (n = 1) WES (n = 112) WES (n = 1) WES (n = 279)
 Exome capture kit Agilent SureSelect Agilent SureSelect Agilent SureSelect Agilent SureSelect
 Sequencing instrument Illumina HiSeq Illumina HiSeq Illumina HiSeq Illumina HiSeq
Depth (mean) 138X 118X 198X 95X
Age (median) 30 63 33 61
Bioinformatic pipeline  
 Alignment bwa (hg19)
 Deduplication Picard
 Realignment GATK
 Recalibration GATK
 Variant calling  
  SNVs MuTect
  Indels Somatic Indel Detector/Indelocator
Selection of candidate SNV/Indels Heuristic annotation MutSig Heuristic annotation MutSig
CNVs detection AffymetrixOncoScan Affymetrix SNP 6.0 AffymetrixOncoScan Affymetrix SNP 6.0
Selection of candidate CNVs Heuristic annotation GISTIC Heuristic annotation GISTIC
Candidate driving genes     
 SNVs/Indels NF1 SPOP TP53 CDKN2A
  RASA2 TP53 FAT1 FAT1
  ATAD5 PTEN MSX1 TP53
   FOXA1 USP6 CASP8
   CDKN1B ANK2 AJUBA
   ZNF595 CHD5 PIK3CA
   THSD7B FOXL2 NOTCH1
   MED12 ITGB4 KMT2D
   NIPA2 LECT1 NSD1
   PIK3CA   HLA-A
   C14orf9   TGFBR2
   SCN11A   
 CNVsa NF1 NAb NOTCH1 FADD
  SUZ12   SMAD4 CDKN2A
    SETD2 CSMD1
    PTCH1 SOX2
    AXIN1 LRP1B
    BAP1 EGFR
    CDH1 FAT1
  1. aEmphasized results from published paper (q < 0.0001)
  2. bThere was not available emphasized result of CNVs