lobSTR: A Short Tandem Repeat Profiler for Personal Genomes

  • Melissa Gymrek
  • David Golan
  • Saharon Rosset
  • Yaniv Erlich
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7262)

Abstract

Motivation. Short tandem repeats (STRs), also known as microsatellites, are a class of genetic variations consisting of repetitive elements of 2 to 6 nucleotides that comprise hundreds of thousands of loci in the human genome. The repetitive structure of these loci makes them prone to replication slippage events [5] that can reach a rate of 1/500 mutations per locus per generation [8], 200,000 fold higher than the rate of de novo single nucleotide polymorphims (SNPs) [1].

Given their high mutation rate and large allele space, STRs represent a significant source of genetic variation and have been used in a plethora of applications in human genetics including forensics [3], anthropological applications [7], and tracing cancer cell lineages [2]. Additionally, STR expansions are implicated in the etiology of a variety of genetic disorders, such as Huntingon Disease [6] and Fragile-X Syndrome [5].

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Melissa Gymrek
    • 1
    • 2
  • David Golan
    • 2
  • Saharon Rosset
    • 3
  • Yaniv Erlich
    • 2
  1. 1.Harvard-MIT Division of Health Sciences and TechnologyCambridgeUSA
  2. 2.Whitehead Institute for Biomedical ResearchCambridgeUSA
  3. 3.Department of Statistics and Operations ResearchTel Aviv UniversityTel AvivIsrael

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