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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)    
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]