Genome-wide profiling of heritable and de novo STR variations
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...
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| Published in | Nature methods Vol. 14; no. 6; pp. 590 - 592 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.06.2017
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | 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
. |
|---|---|
| AbstractList | 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. 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 . Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic casework. However, STRs have proven problematic to genotype 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 report a genome-wide analysis and validation of de novo STR mutations. |
| Audience | Academic |
| Author | Gordon, Assaf Yuan, Jie Erlich, Yaniv Gymrek, Melissa Zielinski, Dina Willems, Thomas |
| AuthorAffiliation | 1 New York Genome Center, New York, New York 10013, USA 3 Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York 10027, 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 10032, USA 4 Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA 2 Computational and Systems Biology Program, MIT, Cambridge, Massachusetts 02139, USA |
| AuthorAffiliation_xml | – name: 1 New York Genome Center, New York, New York 10013, USA – name: 2 Computational and Systems Biology Program, MIT, Cambridge, Massachusetts 02139, USA – name: 6 Center for Computational Biology and Bioinformatics, Columbia University, New York, New York 10032, USA – name: 5 Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA – name: 3 Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York 10027, USA – name: 4 Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA |
| Author_xml | – sequence: 1 givenname: Thomas surname: Willems fullname: Willems, Thomas email: tfwillems@gmail.com organization: New York Genome Center, Computational and Systems Biology Program, MIT – sequence: 2 givenname: Dina surname: Zielinski fullname: Zielinski, Dina organization: New York Genome Center – sequence: 3 givenname: Jie surname: Yuan fullname: Yuan, Jie organization: New York Genome Center, Department of Computer Science, Fu Foundation School of Engineering, Columbia University – sequence: 4 givenname: Assaf surname: Gordon fullname: Gordon, Assaf organization: New York Genome Center – sequence: 5 givenname: Melissa surname: Gymrek fullname: Gymrek, Melissa organization: Analytic and Translational Genetics Unit, Massachusetts General Hospital, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard – sequence: 6 givenname: Yaniv surname: Erlich fullname: Erlich, Yaniv email: yaniv@cs.columbia.edu organization: New York Genome Center, Department of Computer Science, Fu Foundation School of Engineering, Columbia University, Center for Computational Biology and Bioinformatics, Columbia University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28436466$$D View this record in MEDLINE/PubMed |
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| Snippet | HipSTR accurately genotypes and phases short tandem repeats, enabling robust genome-wide analyses of short tandem repeat variations.
Short tandem repeats... Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic... Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases, population genetics applications, and forensic... |
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| SubjectTerms | 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 |
| Title | Genome-wide profiling of heritable and de novo STR variations |
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