GangSTR—New Algorithm Applied to Genome-Wide Genotyping of Short Tandem Repeat (STR) Expansions, Such As Those Implicated in Huntington’s Disease, Fragile X Syndrome, & Myotonic Dystrophy

(BY SALLY G. PASION, PhD, Associate Professor of Biology, San Francisco State University). On October 18, at the 2018 American Society for Human Genetics (ASHG) Annual Meeting in San Diego, California ( (October 16-20), software engineer Nima Mousavi, PhD (@nmmsv), in the Electrical and Computer Engineering Department, University of California San Diego (UCSD), in the laboratory of Dr. Melissa Gymrek (, highlighted GangSTR, a novel algorithm for genome-wide profiling of both normal and expanded tandem repeats (TRs). GangSTR provides a new way to identify short tandem repeats (STRs) from next-generation sequencing (NGS) data. STRs are 1-6 base-pair (bp) sequences, repeated in tandem in the genome. Dr. Mousavi’s presentation was one of six that were delivered in a late-morning meeting session (#51) titled ““What Are We Missing? Identification of Previously Underappreciated Mendelian Variants.” The session is described at the following link: Dr. Mousavi’s presentation (#188) was titled “GangSTR: Genome-Wide Genotyping Short Tandem Repeat Expansions” ( STRs exhibit a higher mutation rate compared to insertion-deletions (indels) or single nucleotide polymorphisms (SNPs). Three percent of the human genome contains STRs, and the presence of the repeats may affect the coding region and thus the protein sequence, or it may occur in the non-coding region and affect gene expression. There are STRs that are implicated in trinucleotide repeat diseases such as Huntington’s disease (HD), fragile X syndrome, Friedreich ataxia, spinocerebellar ataxia, and myotonic dystrophy.
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