Similar protocols

Protocol publication

[…] taset while the rest were plotted in an MDS plot (). After QC 3, 223065 SNPs and 9068 individuals (2664 cases, 6408 controls) remained to perform further downstream analyses., Haplotype association studies were performed using PLINK V1.07 [] on three sub-groups of CORECT genotyping data, familial (n = 481), sporadic (n = 2183), and familial + sporadic (n = 2664) as cases, and Swedish Twin Registry [] as controls., Genomic DNA was extracted from peripheral blood using standard procedures. Genotyping of in total 587 individuals, familial CRC cases and their relatives, was performed using the Illumina HumanOmniExpress-12v1_H BeadChip. The results, 730,525 SNPs, were analyzed using the software GenomeStudio 2011.1 from Illumina Inc. Average sample call rate per SNP with sample call rate >0 was >99% and the overall reproducibility >99.99%. Arrays were processed according to manufactures protocol at the SNP&SEQ Technology Platform at Uppsala University and available on request (, Capture sequencing of 46 familial CRC patients was performed by Axeq Technologies, US, using a SureSelect target enrichment system process followed by 100 bp paired-end sequencing on an Illumina HiSeq2000 sequencer. After sequencing, bioinformatics analysis of the FASTQ files included alignment of sequence reads to the reference human genome (GRCh37/hg19) using BWA and SAMTools, applying GATK [, , ] base quality score recalibration, indel realignment, duplicate removal, variant calling and annotation (dbSNP and 1000 Genome Project)., Association studies were performed using Taqman SNP Genotyping Assay (Thermo Fisher Scientific)., All patients gave written informed consents in accordance with Swedish legislation (2003:460) and the study was approved by the Regional Research Ethics Committee, Dnr: 2002-20489, 2008/125-2031/2, 2014/1324-31 and 2016/24-31/1., Author contributions , JT analyzed targeted and exome sequencing results, performed haplotype association studies and participated in writing the draft. HM participated in quality control of genotyping data. TB performed S […]

Pipeline specifications

Software tools GenomeStudio, BWA, SAMtools, GATK
Diseases Neoplasms, Gastrointestinal Neoplasms, Digestive System Neoplasms, Intestinal Diseases