A reference haplotype panel for genome-wide imputation of short tandem repeats

Shubham Saini, Ileena Mitra, Nima Mousavi, Stephanie Feupe Fotsing and Melissa Gymrek ()
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Shubham Saini: University of California San Diego
Ileena Mitra: University of California San Diego
Nima Mousavi: University of California, San Diego
Stephanie Feupe Fotsing: University of California San Diego
Melissa Gymrek: University of California San Diego

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract Short tandem repeats (STRs) are involved in dozens of Mendelian disorders and have been implicated in complex traits. However, genotyping arrays used in genome-wide association studies focus on single nucleotide polymorphisms (SNPs) and do not readily allow identification of STR associations. We leverage next-generation sequencing (NGS) from 479 families to create a SNP + STR reference haplotype panel. Our panel enables imputing STR genotypes into SNP array data when NGS is not available for directly genotyping STRs. Imputed genotypes achieve mean concordance of 97% with observed genotypes in an external dataset compared to 71% expected under a naive model. Performance varies widely across STRs, with near perfect concordance at bi-allelic STRs vs. 70% at highly polymorphic repeats. Imputation increases power over individual SNPs to detect STR associations with gene expression. Imputing STRs into existing SNP datasets will enable the first large-scale STR association studies across a range of complex traits.

Date: 2018
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DOI: 10.1038/s41467-018-06694-0

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