Generead cancer predisposition v2 kit

Library preparation and sequencing of the Mexican, Argentinian and Guatemalan samples was performed with the GeneRead Cancer Predisposition V2 Kit (Qiagen), as previously described (18 (link)). Briefly, the kit targets 143 genes associated with inherited cancers. The genes have been selected on the basis of their putative role in the susceptibility of different hereditary cancers. Most, but not all, are associated with hereditary breast and ovarian cancer and with an increased risk to 88 oncological syndromes such as colorectal, ovarian, endometrial, prostate, gastric, and pancreatic cancers among others; and almost all these genes have evidence supporting a >2-fold increase in risk. The libraries were sequenced in a MiSeq instrument (Illumina, Inc.; 2X150 cycles) to reach an average theoretical mean coverage of 80X for each sample (Supplementary Figures 1, 2). The DNA samples from Argentina were prepared with Generead Library L kit (Qiagen) and sequenced in a PGM (Ion Torrent-Thermo fisher- Scientific). The libraries from Colombia were prepared using the Trusight cancer panel (Illumina, Inc.), which includes a panel of 96 genes (40 genes overlap with the 143 gene panel) and sequenced in a MiSeq instrument (Illumina, Inc.; 2X150 cycles).

Library preparation was performed as described previously (Quezada Urban et al., 2018 (link)). Briefly, The GeneRead Cancer Predisposition V2 Kit (Qiagen) was used to prepare the library, which targets 143 genes whose loss of function is a well-known mechanism associated with more than 80 inherited oncologic diseases based on data from the College of American Pathologists (CAP) guidelines, the National Comprehensive Cancer Network (NCCN) guidelines, and The Cancer Genome Atlas (TCGA). The amplification was carried out in four-pool PCR reactions and all libraries were barcoded and diluted equimolarly. Sequencing was performed in a HiSeq 4000 (Illumina) with pair-end (2x150) chemistry and to a theoretical coverage of 2000X.