Hereditary Cancer Predisposition Sequencing

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).