Genome-wide profiling of heritable and de novo STR variations

• Published in: Nature methods Vol. 14; no. 6; pp. 590 - 592
• Main Authors: Willems, Thomas, Zielinski, Dina, Yuan, Jie, Gordon, Assaf, Gymrek, Melissa, Erlich, Yaniv
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.06.2017; Nature Publishing Group
• Subjects: 631/114/2785; 631/208/212; Algorithms; Alleles; Bioinformatics; Biological Microscopy; Biological Techniques; Biomedical Engineering/Biotechnology; brief-communication; Chemical elements; Chromosome Mapping - methods; Disease; DNA Fingerprinting - methods; Forensic engineering; Forensic science; Gene mutation; Gene sequencing; Genetic Predisposition to Disease - genetics; Genetic Variation - genetics; Genetics; Genome, Human - genetics; Genomes; Genotyping; Haplotypes; High-Throughput Nucleotide Sequencing; Humans; Identification and classification; Life Sciences; Microsatellite Repeats - genetics; Mutation; Next-generation sequencing; Population genetics; Proteomics; Sequence Alignment; Sequence Analysis, DNA; Short tandem repeats; Software
• ISSN: 1548-7091; 1548-7105
• DOI: 10.1038/nmeth.4267

HipSTR accurately genotypes and phases short tandem repeats, enabling robust genome-wide analyses of short tandem repeat variations. Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, it has proven problematic to genotype STRs from high-throughput sequencing data. Here, we describe HipSTR, a novel haplotype-based method for robustly genotyping and phasing STRs from Illumina sequencing data, and we report a genome-wide analysis and validation of de novo STR mutations. HipSTR is freely available at https://hipstr-tool.github.io/HipSTR .