Computational protocol: Common genetic variation in the glucokinase gene (GCK) is associated with type 2 diabetes and rates of carbohydrate oxidation and energy expenditure

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Protocol publication

[…] Single-nucleotide polymorphisms (SNPs) in exons and the putative promoter region (∼1.4 kb upstream of the translational start site) of GCK were obtained from whole-genome sequence data (30–40× coverage) of 234 individuals who were predominantly full-heritage Pima Indians (Complete Genomics, Mountain View, CA, USA; Illumina, San Diego, CA, USA). Individuals had been characterised for metabolic traits in our Clinical Research Center and were selected from different nuclear families to maximise identification of genetic variation. Genome sequence data were compared with the reference sequence GRCh37/hg19. SNPs not reported in NCBI dbSNP/1000 genomes (http://www.ncbi.nlm.nih.gov/SNP/; or http://browser.1000genomes.org/) were classified as ‘novel’. Linkage disequilibrium (LD) was determined using Haploview (version 4.2, Broad Institute, Cambridge, MA, USA). Tag SNPs were selected using the Tagger algorithm with a pairwise r2 ≥ 0.8 taken as indicative of redundancy.SNPs were genotyped for association analyses using the TaqMan Allelic Discrimination Assay on an ABI Prism 7900 (Applied Biosystems, Carlsbad, CA, USA) or BeadXpress System (Illumina). […]

Pipeline specifications

Software tools Haploview, Tagger
Databases dbSNP
Applications WGS analysis, GWAS
Diseases Diabetes Mellitus, Diabetes Mellitus, Type 2
Chemicals Glucose