| lobSTR: A short tandem repeat profiler for personal genomes. | |
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MedLine Citation:
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PMID: 22522390 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat STR mapping as gapped alignment, which results in cumbersome processing times and a biased sampling of STR alleles. Here, we present lobSTR, a novel method for profiling STRs in personal genomes. lobSTR harnesses concepts from signal processing and statistical learning to avoid gapped alignment and to address the specific noise patterns in STR calling. The speed and reliability of lobSTR exceed the performance of current mainstream algorithms for STR profiling. We validated lobSTR's accuracy by measuring its consistency in calling STRs from whole-genome sequencing of two biological replicates from the same individual, by tracing Mendelian inheritance patterns in STR alleles in whole-genome sequencing of a HapMap trio, and by comparing lobSTR results to traditional molecular techniques. Encouraged by the speed and accuracy of lobSTR, we used the algorithm to conduct a comprehensive survey of STR variations in a deeply sequenced personal genome. We traced the mutation dynamics of close to 100,000 STR loci and observed more than 50,000 STR variations in a single genome. lobSTR's implementation is an end-to-end solution. The package accepts raw sequencing reads and provides the user with the genotyping results. It is written in C/C++, includes multi-threading capabilities, and is compatible with the BAM format. |
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Authors:
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Melissa Gymrek; David Golan; Saharon Rosset; Yaniv Erlich |
Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't Date: 2012-04-20 |
Journal Detail:
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Title: Genome research Volume: 22 ISSN: 1549-5469 ISO Abbreviation: Genome Res. Publication Date: 2012 Jun |
Date Detail:
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Created Date: 2012-06-04 Completed Date: 2012-12-07 Revised Date: 2013-02-19 |
Medline Journal Info:
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Nlm Unique ID: 9518021 Medline TA: Genome Res Country: United States |
Other Details:
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Languages: eng Pagination: 1154-62 Citation Subset: IM |
Affiliation:
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Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Electrophoresis / methods Female Genetic Variation Genome, Human* Genomics / methods* HapMap Project Humans Male Microsatellite Repeats* Pedigree Reproducibility of Results Software* |
| Comments/Corrections | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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