Detection of long repeat expansions from PCR-free whole-genome sequence data

Abstract

Identifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) and fragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is an important step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that, using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger than the read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence of the C9orf72 repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter correctly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions (4). Additionally, 99.9% (2786/2789, 95% CI [0.997, 1.00]) of the wild-type samples were correctly classified as wild type by this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a set of 152 samples in which every sample had one of eight different pathogenic repeat expansions, including those associated with fragile X syndrome, Friedreich's ataxia, and Huntington's disease, and correctly flagged all but one of the known repeat expansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides researchers with a tool that can be used to identify new pathogenic repeat expansions.

Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing

“…The Although several computational tools can be used to study repeat elements in next-generation sequencing data (Dolzhenko et al, 2017;Liu, Zhang, Wang, Gu, & Wang, 2017;Tang et al, 2017), none of these has been specifically designed for the No-Amp Targeted sequencing protocol. We therefore decided to implement our own strategy, which is outlined in Figure 2A.…”

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.…”

Paragraph: A graph-based structural variant genotyper for short-read sequence data

“…The removed SVs chiefly come from the unexpected AF peak at 0.5 (dashed lines in Figure 5a ). 79% of these HWE-failed SVs are within TRs, which are likely to have higher mutation rates and be more variable in the population 33,34 . SVs that showed more genotyping errors in the discovery samples were more likely to fail the HWE test ( Table S3 ) 35 .…”