5 Genomic variant studies

In this chapter, we deal with genetic variants other than SNPs. As the proportion of genetic variation explained by SNPs for complex traits appears to be limited, more complex genetic variants are likely to play an important role in complex traits or disease susceptibility. We explain how SNP array data can be used to detect other structural variants (SV) such as copy number (CNV), genetic mosaicisms and polymorphic inversions. In particular, we discuss how CNVs and mosaicisms can be called using the log R ratio (LRR) and B-allele frequencies (BAF) of raw microarray data, and how polymorphic inversions can be called using SNP genotypes. We demonstrate how to assess its association with quantitative and qualitative outcomes.

The R code to reproduce the results and figures of this chapter can be found:

• here for CNVs and Genetic Mosaicism.

• here for genetic inversions.