Table 2 Comparison of candidate driving genes of same cancer type from AYAs with those from all age group
| Â | 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 | Â | |||
 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 | Â | Â | Â | Â |
 SNVs/Indels | NF1 | SPOP | TP53 | CDKN2A |
| Â | RASA2 | TP53 | FAT1 | FAT1 |
| Â | ATAD5 | PTEN | MSX1 | TP53 |
| Â | Â | FOXA1 | USP6 | CASP8 |
| Â | Â | CDKN1B | ANK2 | AJUBA |
| Â | Â | ZNF595 | CHD5 | PIK3CA |
| Â | Â | THSD7B | FOXL2 | NOTCH1 |
| Â | Â | MED12 | ITGB4 | KMT2D |
| Â | Â | NIPA2 | LECT1 | NSD1 |
| Â | Â | PIK3CA | Â | HLA-A |
| Â | Â | C14orf9 | Â | TGFBR2 |
| Â | Â | SCN11A | Â | Â |
 CNVsa | NF1 | NAb | NOTCH1 | FADD |
| Â | SUZ12 | Â | SMAD4 | CDKN2A |
| Â | Â | Â | SETD2 | CSMD1 |
| Â | Â | Â | PTCH1 | SOX2 |
| Â | Â | Â | AXIN1 | LRP1B |
| Â | Â | Â | BAP1 | EGFR |
| Â | Â | Â | CDH1 | FAT1 |