An efficient algorithm for the extraction of HGVS variant descriptions from sequences
Motivation: Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficien...
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| Published in | Bioinformatics (Oxford, England) Vol. 31; no. 23; pp. 3751 - 3757 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
01.12.2015
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1367-4811 |
| DOI | 10.1093/bioinformatics/btv443 |
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| Abstract | Motivation: Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful.
Results: Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers.
Availability: The algorithm is accessible as an experimental service in the Mutalyzer program suite (https://mutalyzer.nl). The C++ source code and Python interface are accessible at: https://github.com/mutalyzer/description-extractor.
Contact: j.k.vis@lumc.nl |
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| AbstractList | Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful.MOTIVATIONUnambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful.Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers.RESULTSOur algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers.The algorithm is accessible as an experimental service in the Mutalyzer program suite (https://mutalyzer.nl). The C++ source code and Python interface are accessible at: https://github.com/mutalyzer/description-extractor.AVAILABILITYThe algorithm is accessible as an experimental service in the Mutalyzer program suite (https://mutalyzer.nl). The C++ source code and Python interface are accessible at: https://github.com/mutalyzer/description-extractor.j.k.vis@lumc.nl.CONTACTj.k.vis@lumc.nl. Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful. Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers. The algorithm is accessible as an experimental service in the Mutalyzer program suite (https://mutalyzer.nl). The C++ source code and Python interface are accessible at: https://github.com/mutalyzer/description-extractor. j.k.vis@lumc.nl. Motivation: Unambiguous sequence variant descriptions are important in reporting the outcome of clinical diagnostic DNA tests. The standard nomenclature of the Human Genome Variation Society (HGVS) describes the observed variant sequence relative to a given reference sequence. We propose an efficient algorithm for the extraction of HGVS descriptions from two sequences with three main requirements in mind: minimizing the length of the resulting descriptions, minimizing the computation time and keeping the unambiguous descriptions biologically meaningful. Results: Our algorithm is able to compute the HGVS descriptions of complete chromosomes or other large DNA strings in a reasonable amount of computation time and its resulting descriptions are relatively small. Additional applications include updating of gene variant database contents and reference sequence liftovers. Availability: The algorithm is accessible as an experimental service in the Mutalyzer program suite (https://mutalyzer.nl). The C++ source code and Python interface are accessible at: https://github.com/mutalyzer/description-extractor. Contact: j.k.vis@lumc.nl |
| Author | Vermaat, Martijn Laros, Jeroen F. J. Taschner, Peter E. M. Vis, Jonathan K. Kok, Joost N. |
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| Cites_doi | 10.1093/nar/gku1161 10.1145/357401.357404 10.1093/bioinformatics/btp319 10.1002/humu.20654 10.1038/nbt.2023 10.1145/321879.321880 10.1002/humu.21427 10.1002/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N 10.1017/CBO9780511574931 10.1016/0022-2836(81)90087-5 10.1145/321796.321811 |
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| References | Robinson (2023020202420587400_btv443-B6) 2015; 43 Abbasi (2023020202420587400_btv443-B1) 1997 Brandon (2023020202420587400_btv443-B2) 2009; 25 Tichy (2023020202420587400_btv443-B9) 1984; 2 Wagner (2023020202420587400_btv443-B10) 1974; 21 Wagner (2023020202420587400_btv443-B11) 1975; 22 Wildeman (2023020202420587400_btv443-B12) 2008; 29 Compeau (2023020202420587400_btv443-B3) 2011; 29 Den Dunnen (2023020202420587400_btv443-B4) 2000; 15 Gusfield (2023020202420587400_btv443-B5) 1997 Taschner (2023020202420587400_btv443-B8) 2011; 32 Smith (2023020202420587400_btv443-B7) 1981; 147 |
| References_xml | – volume: 43 start-page: 23 year: 2015 ident: 2023020202420587400_btv443-B6 article-title: The IPD and IMGT/HLA database: Allele variant databases publication-title: Nucleic Acids Res. doi: 10.1093/nar/gku1161 – volume: 2 start-page: 309 year: 1984 ident: 2023020202420587400_btv443-B9 article-title: The string-to-string correction problem with block moves publication-title: TOCS doi: 10.1145/357401.357404 – volume: 25 start-page: 1731 year: 2009 ident: 2023020202420587400_btv443-B2 article-title: Data structures and compression algorithms for genomic sequence data publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp319 – volume: 29 start-page: 6 year: 2008 ident: 2023020202420587400_btv443-B12 article-title: Improving sequence variant descriptions in mutation databases and literature using the Mutalyzer sequence variation nomenclature checker publication-title: Hum. Mutat. doi: 10.1002/humu.20654 – volume: 29 start-page: 987 year: 2011 ident: 2023020202420587400_btv443-B3 article-title: How to apply de Bruijn graphs to genome assembly publication-title: Nat. Biotechnol. doi: 10.1038/nbt.2023 – year: 1997 ident: 2023020202420587400_btv443-B1 – volume: 22 start-page: 177 year: 1975 ident: 2023020202420587400_btv443-B11 article-title: An extension of the string-to-string correction problem publication-title: JACM doi: 10.1145/321879.321880 – volume: 32 start-page: 507 year: 2011 ident: 2023020202420587400_btv443-B8 article-title: Describing structural changes by extending HGVS sequence variation nomenclature publication-title: Hum. Mutat. doi: 10.1002/humu.21427 – volume: 15 start-page: 7 year: 2000 ident: 2023020202420587400_btv443-B4 article-title: Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion publication-title: Hum. Mutat. doi: 10.1002/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N – volume-title: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology year: 1997 ident: 2023020202420587400_btv443-B5 doi: 10.1017/CBO9780511574931 – volume: 147 start-page: 195 year: 1981 ident: 2023020202420587400_btv443-B7 article-title: Identification of common molecular subsequences publication-title: J. Mol. Biol. doi: 10.1016/0022-2836(81)90087-5 – volume: 21 start-page: 168 year: 1974 ident: 2023020202420587400_btv443-B10 article-title: The string-to-string correction problem publication-title: JACM doi: 10.1145/321796.321811 |
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| SubjectTerms | Algorithms Genetic Variation Genome, Human Humans Sequence Analysis, DNA - methods |
| Title | An efficient algorithm for the extraction of HGVS variant descriptions from sequences |
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