Association mapping using PLINK software

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PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. • The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results. • PLINK (one syllable) is being developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard MIT, with the support of others. • Association mapping also known as linkage disequilibrium mapping , is a method of mapping quantitative trait loci(QTLs). In this video the software is demonstrated based on the study of Lumbar Disc Degenerative Disease in human. The study involves 58 SNPs,35 candidate genes in 342 individuals. To run this software the major requirements are three files namely ped, map and phenotype files. After running the software the final results are interpreted based on the P values obtained in the associated file. From this the gene (i.e) SNPs associated with the phenotype is found using the list of candidate genes. Finally the SNP location on the chromosome is showed in the Haploview 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