lobSTR: A Short Tandem Repeat Profiler for Personal Genomes

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].