Whole Exome Sequencing for Familial CRC

The entire cohort of 39 patients underwent germline WES similarly to previous reported studies performed by our research group in familial CRC (20 (link)–22 (link)). Briefly, WES was characterized using the HiSeq2000 platform (Illumina, San Diego, CA) and SureSelectXT Human All Exon V5 for exon enrichment (Agilent, Santa Clara, CA). Indexed libraries were pooled and massively parallel sequenced using a paired-end 2 × 75 bp read length protocol. Mean coverage was >95× in all samples, and 51 Mb was the target size that required about 4 Gb of sequencing per sample. Burrows-Wheeler Aligner was used for read mapping to the human reference genome (build hs37d5, based on NCBI GRCh37) (23 (link)). Polymerase chain reaction duplicates were discarded using the MarkDuplicates tool from Picard, and then indel realignment and base quality score recalibration were performed with the Genome Analysis Toolkit. The HaplotypeCaller Genome Analysis Toolkit tool was used for variant calling (24 (link)).

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Toma C., Díaz-Gay M., Soares de Lima Y., Arnau-Collell C., Franch-Expósito S., Muñoz J., Overs B., Bonjoch L., Carballal S., Ocaña T., Cuatrecasas M., Díaz de Bustamante A., Castells A., Bujanda L., Cubiella J., Balaguer F., Rodríguez-Alcalde D., Fullerton J.M, & Castellví-Bel S. (2019). Identification of a Novel Candidate Gene for Serrated Polyposis Syndrome Germline Predisposition by Performing Linkage Analysis Combined With Whole-Exome Sequencing. Clinical and Translational Gastroenterology, 10(10), e00100.

Publication 2019

HiSeq2000 platform SureSelectXT Human All Exon V5

Exon Genome Germline Human Human genome Indel Patients Polymerase chain reaction

Corresponding Organization : Consorci Institut D'Investigacions Biomediques August Pi I Sunyer

Other organizations : Neuroscience Research Australia, Hospital Universitario de Móstoles, Biogipuzkoa Health Research Institute

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