Wavelet Screening: a novel approach to analysing GWAS data

Abstract

We present here an alternative method for genome-wide association study (GWAS) that is more powerful than traditional GWAS methods for locus detection. Single-variant GWAS methods incur a substantial multiple-testing burden because of the vast number of single nucleotide polymorphisms (SNPs) being tested simultaneously. Furthermore, these methods do not consider the functional genetic effect on the outcome because they ignore more complex joint effects of nearby SNPs within a region. By contrast, our method reduces the number of tests to be performed by screening the entire genome for associations using a sliding-window approach based on wavelets. In this context, a sequence of SNPs represents a genetic signal, and for each screened region, we transform the genetic signal into the wavelet space. The null and alternative hypotheses are modelled using the posterior distribution of the wavelet coefficients. We enhance our decision procedure by using additional information from the regression coefficients and by taking advantage of the pyramidal structure of wavelets. When faced with more complex signals than single-SNP associations, we show through simulations that Wavelet Screening provides a substantial gain in power compared to both the traditional GWAS modelling as well as another popular regional-based association test called SNP-set (Sequence) Kernel Association Test (SKAT). To demonstrate feasibility, we re-analysed data from the large Norwegian HARVEST cohort.