Targeted Capture Sequencing of Cancer Genes

The entire coding regions of fifty-seven genes were included in a hybridisation capture panel (Supplementary File 1_Table 1), based on: recurrence in our WES tumour set; reported in the Catalogue of Somatic Mutations in Cancer (COSMIC) database; implicated in cancer^{65 (link)}; or reported in the TCGA or Bueno et al. studies^{4 (link),5 (link)}. Sequencing libraries were prepared from DNA extracted from tumours and normal tissue (whole blood) samples using the SureSelect QXT Target Enrichment System (Agilent, Santa Clara, USA) according to the manufacturer`s protocols. Sequencing was performed on a MiSeq or NextSeq500/550 platform (Illumina) with a mean read depth of 780.6X (all samples). Supplementary File 2_Table 3 contains a list of filtered somatic variants from targeted capture sequencing.

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Nastase A., Mandal A., Lu S.K., Anbunathan H., Morris-Rosendahl D., Zhang Y.Z., Sun X.M., Gennatas S., Rintoul R.C., Edwards M., Bowman A., Chernova T., Benepal T., Lim E., Taylor A.N., Nicholson A.G., Popat S., Willis A.E., MacFarlane M., Lathrop M., Bowcock A.M., Moffatt M.F, & Cookson W.O. (2021). Integrated genomics point to immune vulnerabilities in pleural mesothelioma. Scientific Reports, 11, 19138.

Publication 2021

SureSelect QXT Target Enrichment System NextSeq500/550

Blood Cancer Cosmic Genes Hybridisation Mutations Normal tissue Recurrence Somatic Tumours

Corresponding Organization :

Other organizations : Imperial College London, Medical Research Council, University of Cambridge, Papworth Hospital, Royal Brompton & Harefield NHS Foundation Trust, St George’s University Hospitals NHS Foundation Trust, Royal Marsden Hospital, McGill Genome Centre

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Variable analysis

independent variables

None explicitly mentioned

dependent variables

Somatic variants from targeted capture sequencing

control variables

DNA extracted from normal tissue (whole blood) samples

controls

Positive control: None mentioned
Negative control: DNA from normal tissue (whole blood) samples

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