Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data

Abstract

Repeat expansions cause more than 30 inherited disorders, predominantly neurogenetic. These can present with overlapping clinical phenotypes, making molecular diagnosis challenging. Single-gene or small-panel PCR-based methods can help to identify the precise genetic cause, but they can be slow and costly and often yield no result. Researchers are increasingly performing genomic analysis via whole-exome and whole-genome sequencing (WES and WGS) to diagnose genetic disorders. However, until recently, analysis protocols could not identify repeat expansions in these datasets. We developed exSTRa (expanded short tandem repeat algorithm), a method that uses either WES or WGS to identify repeat expansions. Performance of exSTRa was assessed in a simulation study. In addition, four retrospective cohorts of individuals with eleven different known repeat-expansion disorders were analyzed with exSTRa. We assessed results by comparing the findings to known disease status. Performance was also compared to three other analysis methods (ExpansionHunter, STRetch, and TREDPARSE), which were developed specifically for WGS data. Expansions in the assessed STR loci were successfully identified in WES and WGS datasets by all four methods with high specificity and sensitivity. Overall, exSTRa demonstrated more robust and superior performance for WES data than did the other three methods. We demonstrate that exSTRa can be effectively utilized as a screening tool for detecting repeat expansions in WES and WGS data, although the best performance would be produced by consensus calling, wherein at least two out of the four currently available screening methods call an expansion.

ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions

“…ExpansionHunter was the first computational method for genotyping STRs from short-read sequencing data capable of consistently genotyping repeats longer than the read length and, hence, detecting pathogenic repeat expansions (Dolzhenko et al 2017). Since the initial release of ExpansionHunter, several other methods have been developed and were shown to accurately identify long (greater than read length) repeat expansions (Dashnow et al 2018;Tang et al 2017;Mousavi, Shleizer-Burko, and Gymrek 2018;Tankard et al 2018 An even more extreme example is the CAGG repeat in the CNBP gene whose expansions cause Myotonic Dystrophy type 2 (DM2). This repeat is adjacent to polymorphic CA and CAGA repeats (Liquori et al 2001) making it particularly difficult to accurately align reads to this locus.…”

Accuracy of short tandem repeats genotyping tools in whole exome sequencing data

“…Tools such as Expansion Hunter (Dolzhenko et al, 2017;Dolzhenko et al, 2019), TREDPARSE (Tang, Haibao et al, 2017), STRetch (Dashnow et al, 2018) and exSTRa (Tankard et al, 2018) were excluded from our analysis as well because they are classified as tools which specifically look for expansions that might be disease causing and are often longer than the physical read length or expansion relative to a control set.…”

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

“…WGS was performed for three affected individuals from the family (Figure 1) and the data was analysed for a pre-defined list of 12 candidate repeat expansions known to cause ataxia (SCA1,2,3,6,7,8,10,12,17,36, Friedreich's ataxia and CANVAS) using exSTRa [19] and ExpansionHunter [20]. This analysis identified the SCA36 RE in all three individual's WGS data, with none of the 167 controls exhibiting a RE.…”