Targeted Sequencing of Cancer Genes

A customized panel, encompassing all the exons of 39 cancer-related genes, including genes frequently reported to be involved in advanced CRCs and serrated lesions [2 (link),25 (link),26 (link)], was created using the Ion Torrent System with an Ion AmpliSeq Designer (Thermo Fisher Scientific) (S1 Fig). Genes within oncogene-induced senescence pathways detected in patients with multiple serrated polyps were also investigated [30 (link)]. The assay design consisted of 1,455 amplicons ranging from 125 to 175 bp in length, covering 94% of the 112.8 kb target sequence.
Library preparation and sequencing with the Ion Torrent sequencer were performed as previously described [34 (link)–36 (link)]. The templates were sequenced after emulsion PCR was performed with 24 samples per Ion PI chip using the Ion PI HI-Q Chef kit (Thermo Fisher Scientific).

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Nakanishi H., Sawada T., Kaizaki Y., Ota R., Suzuki H., Yamamoto E., Aoki H., Eizuka M., Hasatani K., Takahashi N., Inagaki S., Ebi M., Kato H., Kubota E., Kataoka H., Takahashi S., Tokino T., Minamoto T., Sugai T, & Sasaki Y. (2020). Significance of gene mutations in the Wnt signaling pathway in traditional serrated adenomas of the colon and rectum. PLoS ONE, 15(2), e0229262.

Publication 2020

Ion Torrent System Ion AmpliSeq Designer Ion PI HI-Q Chef kit

Assay Chip Crcs Emulsion Exons Genes Genes cancer Library Oncogene Patients Polyps

Corresponding Organization : Aichi Medical University

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Variable analysis

independent variables

Customized panel, encompassing all the exons of 39 cancer-related genes, including genes frequently reported to be involved in advanced CRCs and serrated lesions

dependent variables

Genetic variants in the 39 cancer-related genes

control variables

The assay design consisted of 1,455 amplicons ranging from 125 to 175 bp in length, covering 94% of the 112.8 kb target sequence
Library preparation and sequencing with the Ion Torrent sequencer were performed as previously described [34 (link)–36 (link)]
The templates were sequenced after emulsion PCR was performed with 24 samples per Ion PI chip using the Ion PI HI-Q Chef kit (Thermo Fisher Scientific)

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