Table 2.
Comparison of candidate driving genes of same cancer type from AYAs with those from all age group
| 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 | |||
aEmphasized results from published paper (q < 0.0001)
bThere was not available emphasized result of CNVs