Genome-Wide Association

Genome-Wide Association (GWA) studies involve analysing a genome-wide set of genetic variants to probe the relationship between variants and phenotypes. In general, the variants examined are Single Nucleotide Polymorphisms (SNPs) and the traits are major human diseases. GWA has proven to be a powerful tool in identifying the complex genetic linkages that underpin some of the most common, yet complex, human diseases and represents a significant improvement over previous methods.

Imputing variants

At present, GWA studies using commercially available genotyping chips assay a huge number (> 100,000) of markers across the genome, but this represents a small percentage of the overall number of known SNPs. It is therefore unlikely that the true causal variant would be included on the chip. Geneticists have proposed that in order to increase the amount of information gained from a GWA study and to account for these unidentified variants, the data obtained must be subject to imputation to identify the untyped disease variants.

Evolutionary genetics analysis software

IMPUTE 5 is a software program for imputation/estimation of unobserved and missing SNP alleles in a dataset, consisting of genotype data on a set of individuals based upon a panel of known haplotype data and a recombination map.

The idea of imputing alleles is very popular in genetics studies of human disease and is being used to enable researchers to find new disease genes and share data.
The software allows more precise and efficient prediction than other algorithms available.

The main benefits of IMPUTE 5 include:

• Algorithm based on use of Positional Burrows-Wheeler Transform (PBWT).
• Best in class performance. Up to 30x faster than MINIMAC4 and up to 3x faster than BEAGLE5.
• Can be used with large reference panels, such as the Haplotype Reference Consortium or TopMed datasets.

Oxford Genome-Wide Analysis Software Suite

IMPUTE 5 is part of the Oxford Genome-Wide Analysis Software Suite (OGWASS) for statistical analysis of genetic information. Oxford University Innovation is seeking licensees who may wish to obtain a commercial licence to IMPUTE 5 or indeed the entire OGWASS family.