Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes

Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci.

Source: The American Journal of Human Genetics - November 2, 2017 Category: Genetics & Stem Cells Authors: Haibao Tang, Ewen F. Kirkness, Christoph Lippert, William H. Biggs, Martin Fabani, Ernesto Guzman, Smriti Ramakrishnan, Victor Lavrenko, Boyko Kakaradov, Claire Hou, Barry Hicks, David Heckerman, Franz J. Och, C. Thomas Caskey, J. Craig Venter, Amalio Tel Tags: Article Source Type: research