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popSTR2 enables clinical and population-scale genotyping of microsatellites

popSTR2 enables clinical and population-scale genotyping of microsatellites

Title: popSTR2 enables clinical and population-scale genotyping of microsatellites
Author: Kristmundsdottir, Snædis
Eggertsson, Hannes P
Arnadottir, Gudny A
Halldórsson, Bjarni   orcid.org/0000-0003-0756-0767
Date: 2019-12-05
Language: English
Scope: 2269-2271
University/Institute: Reykjavík University (RU)
Háskólinn í Reykjavík (HR)
School: Tæknisvið (HR)
School of Technology (RU)
Department: Verkfræðideild (HR)
Department of Engineering (RU)
Series: Bioinformatics;36(7)
ISSN: 1367-4803
DOI: https://doi.org/10.1093/bioinformatics/btz913
Subject: Statistics and Probability; Computational Theory and Mathematics; Biochemistry; Molecular Biology; Computational Mathematics; Computer Science Applications; Líkindafræði; Tölfræði; Tölvunarfræði; Lífefnafræði; Sameindalíffræði
URI: https://hdl.handle.net/20.500.11815/2646

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Kristmundsdottir, S., Eggertsson, H. P., Arnadottir, G. A. og Halldorsson, B. V. (2020). popSTR2 enables clinical and population-scale genotyping of microsatellites. Bioinformatics, 36(7), 2269–2271. https://doi.org/10.1093/bioinformatics/btz913


Summary: popSTR2 is an update and augmentation of our previous work ‘popSTR: a population-based microsatellite genotyper’. To make genotyping sensitive to inter-sample differences, we supply a kernel to estimate sample-specific slippage rates. For clinical sequencing purposes, a panel of known pathogenic repeat expansions is provided along with a script that scans and flags for manual inspection markers indicative of a pathogenic expansion. Like its predecessor, popSTR2 allows for joint genotyping of samples at a population scale. We now provide a binning method that makes the microsatellite genotypes more amenable to analysis within standard association pipelines and can increase association power. Availability and implementation: https://github.com/DecodeGenetics/popSTR. Contact: snaedisk@decode.is or bjarni.halldorsson@decode.is Supplementary information: Supplementary data are available at Bioinformatics online.


VC The Author(s) 2019. Published by Oxford University Press. 2269 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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