Comprehensive Somatic Mutation Analysis

The raw data were analyzed using the torrent suite software v3.6.2 (Life technologies). The coverage analysis was performed using the coverage analysis plug-in v3.6. Cases for which the number of mapped reads was <100000 and/or the average base coverage was <500x were considered as non informative. Mutations were detected using the Variant Caller plug-in v3.6 with low stringency settings (Life Technologies). In the variant list obtained, each mutation was verified in the Integrative genome viewer (IGV) from the Broad Institute (http://www.broadinstitute.org/igv/) [19 (link)]. Only mutations reported in the COSMIC (Sanger Institute Catalogue of Somatic Mutations in Cancer) database (http://www.sanger.ac.uk/cosmic) were taken into account and silent or intronic mutations were not reported.

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D’Haene N., Le Mercier M., De Nève N., Blanchard O., Delaunoy M., El Housni H., Dessars B., Heimann P., Remmelink M., Demetter P., Tejpar S, & Salmon I. (2015). Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers. PLoS ONE, 10(9), e0138245.

Publication 2015

torrent suite software v3.6.2 Variant Caller plug-in v3.6

Cancer Cosmic Genome Intronic Mutations Somatic

Corresponding Organization : KU Leuven

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Variable analysis

independent variables

Torrent suite software v3.6.2 (Life technologies)
Coverage analysis plug-in v3.6
Variant Caller plug-in v3.6 with low stringency settings (Life Technologies)

dependent variables

Number of mapped reads
Average base coverage
Detected mutations

control variables

Cases for which the number of mapped reads was <100000 and/or the average base coverage was <500x were considered as non informative
Only mutations reported in the COSMIC (Sanger Institute Catalogue of Somatic Mutations in Cancer) database were taken into account
Silent or intronic mutations were not reported

controls

Positive control: Not specified
Negative control: Not specified

Annotations

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