From: Next-generation sequencing: recent applications to the analysis of colorectal cancer
Samples | NGS | Application | Interesting genes | Ref. |
---|---|---|---|---|
15 CRCs | Illumina HiSeq (3′-seq library) | APA changes | PPIE, DMKN, PDXK | Morris et al. [96] |
3 CRC cell lines | Roche GS Junior (primers framing CD44 variable region) | CD44 ASP | CD44 CRC specific isoforms | BÃ nky et al. [97] |
1 stage III CRC patient (distant, adjacent mucosa and cancer) | Illumina GAIIx (TruSeq RNA) | RNA-seq (novel and fusion transcripts, alternative splicings) | List of 14 genes with cancer-associated differential-splicing, PTGFRN-NOTCH2 fusion product | Wu et al. [98] |
70 CRCs/normal pairs | Illumina HiSeq (TruSeq RNA) | RNA-seq | RSPO2/3 fusion transcript | Seshagiri et al. [99] |
20 CRC cell lines | Illumina (ChIP-seq) | RNA-seq (genes involved in irinotecan resistance) | 20 top-genes CDC20, CTNNAL1, FZD7, CITED2, ABR, ARHGEF7 and RNMT validated by qPCR | Li et al. [100] |
21 CRC cell lines | Illumina (ChIP-seq) | RNA-seq (genes involved in oxaliplatin resistance) | 58 top-genes 15 further validated by qPCR (e.g. HNF1A, NOTCH1, FZD5, KCND1, FDZ2) | Li et al. [101] |
175 CRCs/normal tissue pairs | Illumina HiSeq (TruSeq) | RNA_seq (CRC vs. normal differentially expressed genes) | 1138 up-regulated 695 down-regulated | Slattery et al. [102] |
HCT116 CRC cell line | Illumina HiSeq | RNA-seq (SNP profiles from single cell and bulk CRC) | Genes in WNT, PI3KCA, p53, TGF-β, MMR pathways, fusion transcripts | Chen et al. [103] |
5 paired primary, mCRC, normal colon and liver tissues | Illumina HiSeq | RNA-seq (comparative transcriptome analysis) | Similar expression profiling in CRC and metastasis, RNF43-SUPT4H1 fusion transcript frequent in primary CRCs | Lee et al. [104] |
217 CRCs/normal mucosa pairs | Illumina HiSeq (TruSeq) | RNA-seq (oncogenes, tumor suppressors’ differential expression) | 22 tumor suppressor genes and 27 oncogenes significantly differentially expressed in CRC vs. normal mucosa | Slattery et al. [105] |