AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data
| Autor: | Carlo Rivolta, Béryl Royer Bertrand, Virginie G. Peter, Arash Salmaninejad, Neda Sepahi, Raquel Rodrigues, Luisa Coutinho Santos, Alireza Pasdar, Katarina Cisarova, Mehran Piran, Mathieu Quinodoz, Nicola Bedoni, Ali Ghanbari Asad, Andrea Superti-Furga, Majid Mojarrad, Ana Berta Sousa |
|---|---|
| Přispěvatelé: | Repositório da Universidade de Lisboa |
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0301 basic medicine
medicine.medical_specialty Genotype Computer science Bioinformatics Science General Physics and Astronomy Computational biology Chromosome Mapping/methods Computational Biology/methods Genetic Predisposition to Disease/genetics Genome Human/genetics High-Throughput Nucleotide Sequencing/methods Homozygote Humans Internet Mutation Polymorphism Single Nucleotide Reproducibility of Results Software Whole Exome Sequencing/methods 030105 genetics & heredity General Biochemistry Genetics and Molecular Biology DNA sequencing Article 03 medical and health sciences Consanguinity Exome Sequencing medicine Genetic Predisposition to Disease Exome sequencing Whole genome sequencing Variant Call Format Multidisciplinary Genome Human Chromosome Mapping Computational Biology High-Throughput Nucleotide Sequencing General Chemistry Genomics Disease gene identification Human genetics 030104 developmental biology Next-generation sequencing Medical genetics Microsatellite |
| Zdroj: | Nature communications, vol. 12, no. 1, pp. 518 Repositório Científico de Acesso Aberto de Portugal Repositório Científico de Acesso Aberto de Portugal (RCAAP) instacron:RCAAP Nature Communications Nature Communications, Vol 12, Iss 1, Pp 1-7 (2021) |
| Popis: | © The Author(s) 2021. Open AccessThis article is licensed under a Creative CommonsAttribution 4.0 International License, which permits use, sharing,adaptation, distribution and reproduction in any medium or format, as long as you giveappropriate credit to the original author(s) and the source, provide a link to the CreativeCommons license, and indicate if changes were made. The images or other third partymaterial in this article are included in the article’s Creative Commons license, unlessindicated otherwise in a credit line to the material. If material is not included in thearticle’s Creative Commons license and your intended use is not permitted by statutoryregulation or exceeds the permitted use, you will need to obtain permission directly fromthe copyright holder. To view a copy of this license, visithttp://creativecommons.org/licenses/by/4.0/. Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|