Table 2 NGS to detect lesions in actionable genes
From: Next-generation sequencing: recent applications to the analysis of colorectal cancer
Samples | NGS platform | # of analyzed genes/assay | Mutant genes analyzed | Therapy | Ref. |
|---|---|---|---|---|---|
320 mCRC | 454 GS FLX | 9 Targeted-seq (KRAS, NRAS, EGFR, BRAF, PTEN, PI3KCA, AKT, TP53, CTNNB1) | K/NRAS, BRAF, PI3KCA, TP53, PTEN, EGFR, AKT, CTNNB1 | Panitumumab | Peeters et al. [75] |
468 CRC (77 KRAS analyzed) | GAIIx Illumina | 1321 Targeted-seq (SureSelect Agilent) | KRAS | Anti-EGFR | Kothari et al. [76] |
182 mCRC KRAS ex2 wt | Ion Torrent | 22 Targeted-seq (AmpliSeq colon and lung cancer panel) | KRAS (29/182pts) frequently mutant: TP53, RAS, PI3KCA, BRAF | Folfiri/Cetuximab | Ciardiello et al. [77] |
91 CRC | Ion Torrent | 22 | KRAS, TP53, APC, FBXW7, PI3KCA, BRAF, CTNNB1, ERBB2, SMAD4 | Anti-EGFR | Bai et al. [78] |
188 mCRC | 454 GS Junior | 2 Targeted-seq (KRAS, NRAS) | KRAS, NRAS | Anti-EGFR | Harlé et al. [79] |
1054 stage III CRC | Ion Torrent | 22 | KRAS, NRAS, BRAF | Folfox/cetuximab | Taieb et al. [80] |
63 Iranian CRC | Ion Torrent | 15 Targeted-seq (AMER1, APC, ARID1A, BRAF, FBXW7, KRAS, MSH3, MSH6, NRAS, PIK3CA, SMAD4, SOX9, TCF7L2, TGFBR2 and TP53) | MSH3, MSH6, AMER1, APC, BRAF, KRAS, PI3KCA, TGFBR2A, SMAD4, SOX9, TCF7L2, TP53 | Suggested informed genetic diagnosis and personalized strategies | Ashktorab et al. [81] |
Illumina | 20 Targeted-seq (ACVR2A, AMER1, APC, ARID1A, BRAF, FBXW7, KRAS, MSH2, MSH3, MSH6, NRAS, PIK3CA, POLE, PTEN, SMAD2, SMAD4, SOX9, TCF7L2, TGFBR2 and TP53) | Â | Â | Â | |
138 stage IV CRC | FoundationOne method | 315 cancer related genes + introns of 28 frequently rearranged genes | RAS, RAF, ERBB2, AKT, PI3KCA, PTEN, MET, POLE | Anti-EGFR, anti-HER2, anti-PD1 | Gong et al. [82] |
7 CRC cell lines 25 CRC | Illumina MiSeq | 48 Targeted-seq (TruSeq Amplicon Cancer) | ATM, E-cadherin | Anti-EGFR | Geiβler et al. [83] |
3 mCRC positive for NTRK1 rearrangement | Illumina MiSeq | 5 gene rearrangements (NTRK1/2/3, ROS, ALK) | NTRK1 | Entrectinib | Lee et al. [84] |
54 mCRCs + liver metastasis KRAS ex2 wt | Ion Torrent | 22 | KRAS, NRAS, TP53, PI3KCA, FBXW7, PTEN | Anti-EGFR | Adua et al. [85] |
53 KRAS ex2 WT mCRC | Ion Torrent | 20 Targeted-seq (EGFR, KRAS, HRAS, NRAS, BRAF, PIK3CA, AKT1, PTEN, HER2, HER4, TP53) | KRAS, NRAS, BRAF | Anti-EGFR | Hsu et al. [86] |