Genome-wide profiling of heritable and de novo STR variations

Thomas Willems; Dina Zielinski; Jie Yuan; Assaf Gordon; Melissa Gymrek; Yaniv Erlich

doi:10.1038/nmeth.4267

Genome-wide profiling of heritable and de novo STR variations

Nat Methods. 2017 Jun;14(6):590-592. doi: 10.1038/nmeth.4267. Epub 2017 Apr 24.

Authors

Thomas Willems^{1

2}, Dina Zielinski¹, Jie Yuan^{1

3}, Assaf Gordon¹, Melissa Gymrek^{4

5}, Yaniv Erlich^{1

3

6}

Affiliations

¹ New York Genome Center, New York, New York, USA.
² Computational and Systems Biology Program, MIT, Cambridge, Massachusetts, USA.
³ Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA.
⁴ Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA.
⁵ Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
⁶ Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA.

Abstract

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.

MeSH terms

Algorithms
Chromosome Mapping / methods*
DNA Fingerprinting / methods*
Genetic Predisposition to Disease / genetics*
Genetic Variation / genetics*
Genome, Human / genetics*
High-Throughput Nucleotide Sequencing
Humans
Microsatellite Repeats / genetics*
Sequence Alignment
Sequence Analysis, DNA
Software

Grants and funding

UM1 HG008901/HG/NHGRI NIH HHS/United States