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Table 4 NGS in transcriptomics analysis

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

Bànky 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]