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

Shubham Saini, Ileena Mitra, Nima Mousavi, Stephanie Feupe Fotsing, Melissa Gymrek
doi: https://doi.org/10.1101/277673
Shubham Saini
1Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
2Department of Medicine, University of California San Diego, La Jolla, CA USA
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Ileena Mitra
2Department of Medicine, University of California San Diego, La Jolla, CA USA
3Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA.
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Nima Mousavi
1Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
2Department of Medicine, University of California San Diego, La Jolla, CA USA
4Department of Electrical and Computer Engineering, University of California San Diego, La Jolla, CA USA
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Stephanie Feupe Fotsing
1Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
2Department of Medicine, University of California San Diego, La Jolla, CA USA
5Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
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Melissa Gymrek
1Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA USA
2Department of Medicine, University of California San Diego, La Jolla, CA USA
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  • For correspondence: mgymrek@ucsd.edu
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Abstract

Short tandem repeats (STRs) are involved in dozens of Mendelian disorders and have been implicated in a variety of complex traits. However, existing technologies focusing on single nucleotide polymorphisms (SNPs) have not allowed for systematic STR association studies. Here, we leverage next-generation sequencing data from 479 families to create a SNP+STR reference haplotype panel for genome-wide imputation of STRs into SNP data. Imputation achieved an average of 97% concordance between genotyped and imputed STR genotypes in an external dataset compared to 63% expected under a random model. Performance varied widely across STRs, with near perfect concordance at bi-allelic STRs vs. 70% at highly polymorphic forensics markers. We demonstrate that imputation increases power over individual SNPs to detect STR associations using simulated phenotypes and gene expression data. This resource will enable the first large-scale STR association studies using existing SNP datasets, and will likely yield new insights into complex traits.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted July 24, 2018.
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A reference haplotype panel for genome-wide imputation of short tandem repeats
Shubham Saini, Ileena Mitra, Nima Mousavi, Stephanie Feupe Fotsing, Melissa Gymrek
bioRxiv 277673; doi: https://doi.org/10.1101/277673
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A reference haplotype panel for genome-wide imputation of short tandem repeats
Shubham Saini, Ileena Mitra, Nima Mousavi, Stephanie Feupe Fotsing, Melissa Gymrek
bioRxiv 277673; doi: https://doi.org/10.1101/277673

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