Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes

Abstract

Short tandem repeats (STRs) are hyper-mutable sequences in the human genome. They are often used in forensics and population genetics and are also the underlying cause of many genetic diseases. There are challenges associated with accurately determining the length polymorphism of STR loci in the genome by next-generation sequencing (NGS). In particular, accurate detection of pathological STR expansion is limited by the sequence read length during whole-genome analysis. We developed TREDPARSE, a software package that incorporates various cues from read alignment and paired-end distance distribution, as well as a sequence stutter model, in a probabilistic framework to infer repeat sizes for genetic loci, and we used this software to infer repeat sizes for 30 known disease loci. Using simulated data, we show that TREDPARSE outperforms other available software. We sampled the full genome sequences of 12,632 individuals to an average read depth of approximately 30× to 40× with Illumina HiSeq X. We identified 138 individuals with risk alleles at 15 STR disease loci. We validated a representative subset of the samples (n = 19) by Sanger and by Oxford Nanopore sequencing. Additionally, we validated the STR calls against known allele sizes in a set of GeT-RM reference cell-line materials (n = 6). Several STR loci that are entirely guanine or cytosines (G or C) have insufficient read evidence for inference and therefore could not be assayed precisely by TREDPARSE. TREDPARSE extends the limit of STR size detection beyond the physical sequence read length. This extension is critical because many of the disease risk cutoffs are close to or beyond the short sequence read length of 100 to 150 bases.

Profiling the genome-wide landscape of tandem repeat expansions

“…Enclosing FRR Spanning Off-target FRR Estimates # rpts. Genome-wide Estimation limit LobSTR [12] X X X < Read Length HipSTR [44] X X X < Read Length STRetch [9] X X X X Only reports expanded TRs exSTRa [40] X X X Does not estimate TR length Tredparse [38] X X X X < Fragment Length ExpansionHunter [11] Figure 1: Schematic of GangSTR method. Paired end reads from an input set of alignments are separated into various read classes, each of which provides information about the length of the TR in the region.…”

“…STRetch [9] can perform genome-wide expansion identification but does not analyze short TRs, is limited to motifs of up to 6bp, and is computationally expensive. Tredparse [38] models multiple aspects of paired end reads but cannot estimate repeat lengths longer than the sequencing fragment length. Expansion-Hunter [11] produces accurate genotypes across a range of repeat lengths except when both alleles are close to or longer than the sequencing read length.…”

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.…”

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.…”