Alternative Applications of Genotyping Array Data Using Multivariant Methods

One of the forerunners that pioneered the revolution of high-throughput genomic technologies is the genotyping microarray technology, which can genotype millions of single-nucleotide variants simultaneously. Owing to apparent benefits, such as high speed, low cost, and high throughput, the genotyping array has gained lasting applications in genome-wide association studies (GWAS) and thus accumulated an enormous amount of data. Empowered by continuous manufactural upgrades and analytical innovation, unconventional applications of genotyping array data have emerged to address more diverse genetic problems, holding promise of boosting genetic research into human diseases through the re-mining of the rich accumulated data. Here, we review several unconventional genotyping array analysis techniques that have been built on the idea of large-scale multivariant analysis and provide empirical application examples. These unconventional outcomes of genotyping arrays include polygenic score, runs of homozygosity (ROH)/heterozygosity ratio, distant pedigree computation, and mitochondrial DNA (mtDNA) copy number inference. High-throughput genotyping arrays have been the driving force for identifying genetic variant associations with traits and phenotypes, but they can be used for far more.Novel statistical and bioinformatics methods have been developed to leverage the data from genotyping arrays, allowing a new and broader application of this established technology. These new techniques include: polygenic scores, detection of runs of homozygosity or the heterozygosity ratio, distant pedigree reconstruction, and inference of mitochondrial DNA copy number and heteroplasmy.A large amount of genotyping data has been accumulated in publicly accessible data repositories, forming a valuable resource for the use of these alternative applications to greatly extend the information that can be obtained from existing genetics studies.