TagSNP selection based on bovine microarray data

Realized by: Adrian Drożdż
Boss: Joanna Szyda

SNP markers are widely distributed in genomes. In human we have over 4 000 000 of verified SNPs. It is obvious this number will increase. The amount of SNPs is expected to be on the same level in other mammals. But there is an enormous delay with genotyping other mammals than human. Nowadays one can analyse over 50 000 SNPs per one bovine.

But we don’t have to take whole SNPs for study. Not every SNP is informative, furthermore each can be more or less informative. Less SNPs to analyse is the less computation time and less cost of genotyping.

The aim of the project is to reduce the amount of SNPs by Linkage Disequilibrium (LD) criterion. Briefly : LD is an opposite to Hardy-Weinberg Equilibrium (HWE). It is disequilibrium of random allele association. Picture below shows LD plot in some chromosome region. These red triangles corresponds to LD blocks which are inherited together with high probability.

Each of these 5 triangles could be represented even by only one SNP. This process is called tagging and it can reduce number of SNPs even by 60%.