Recent advances in the detection of repeat expansions with short-read next-generation sequencing

Abstract

Short tandem repeats (STRs), also known as microsatellites, are commonly defined as consisting of tandemly repeated nucleotide motifs of 2–6 base pairs in length. STRs appear throughout the human genome, and about 239,000 are documented in the Simple Repeats Track available from the UCSC (University of California, Santa Cruz) genome browser. STRs vary in size, producing highly polymorphic markers commonly used as genetic markers. A small fraction of STRs (about 30 loci) have been associated with human disease whereby one or both alleles exceed an STR-specific threshold in size, leading to disease. Detection of repeat expansions is currently performed with polymerase chain reaction–based assays or with Southern blots for large expansions. The tests are expensive and time-consuming and are not always conclusive, leading to lengthy diagnostic journeys for patients, potentially including missed diagnoses. The advent of whole exome and whole genome sequencing has identified the genetic cause of many genetic disorders; however, analysis pipelines are focused primarily on the detection of short nucleotide variations and short insertions and deletions (indels). Until recently, repeat expansions, with the exception of the smallest expansion (SCA6), were not detectable in next-generation short-read sequencing datasets and would have been ignored in most analyses. In the last two years, four analysis methods with accompanying software (ExpansionHunter, exSTRa, STRetch, and TREDPARSE) have been released. Although a comprehensive comparative analysis of the performance of these methods across all known repeat expansions is still lacking, it is clear that these methods are a valuable addition to any existing analysis pipeline. Here, we detail how to assess short-read data for evidence of expansions, reviewing all four methods and outlining their strengths and weaknesses. Implementation of these methods should lead to increased diagnostic yield of repeat expansion disorders for known STR loci and has the potential to detect novel repeat expansions.

ExpansionHunter Denovo: A computational method for locating known and novel repeat expansions in short-read sequencing data

“…Existing methods for repeat expansion detection rely upon predefined repeat catalogs [22][23][24][25][26]38 . Although these methods can analyze user-defined catalogs, defining the genomic locations of repeats is a complex task and there is a risk of missing many potentially-pathogenic loci.…”

High-throughput multiplexed tandem repeat genotyping using targeted long-read sequencing

“…These techniques are only applicable to a specific target region and not scalable to high-throughput analysis, which limits the possibility of genome-wide TR analysis. In the recent decade, significant progress has been made in utilising high throughput short-read sequencing data for genotyping STRs [10]. Our group and others have also demonstrated targeted sequencing approaches using short-read sequencing for TR analysis [11, 12].…”

Rapid diagnosis of SCA36 in a three-generation family using short-read whole genome sequencing data

“…Methodological advances in bioinformatics in the last two years have made the simultaneous testing for all known REs through whole genome sequencing (WGS) feasible [2] . Additionally, multiple novel REs have been discovered in neurological disorders using WGS in the last two years alone, including in epilepsy [3] and ataxia [4][5][6].…”