AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data.

Details

Ressource 1Download: NCs41467-020-20584-4.pdf (1765.48 [Ko])
State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_03712A3BC8BB
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data.
Journal
Nature communications
Author(s)
Quinodoz M., Peter V.G., Bedoni N., Royer Bertrand B., Cisarova K., Salmaninejad A., Sepahi N., Rodrigues R., Piran M., Mojarrad M., Pasdar A., Ghanbari Asad A., Sousa A.B., Coutinho Santos L., Superti-Furga A., Rivolta C.
ISSN
2041-1723 (Electronic)
ISSN-L
2041-1723
Publication state
Published
Issued date
22/01/2021
Peer-reviewed
Oui
Volume
12
Number
1
Pages
518
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
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.
Keywords
Chromosome Mapping/methods, Computational Biology/methods, Genetic Predisposition to Disease/genetics, Genome, Human/genetics, Genotype, High-Throughput Nucleotide Sequencing/methods, Homozygote, Humans, Internet, Mutation, Polymorphism, Single Nucleotide, Reproducibility of Results, Software, Whole Exome Sequencing/methods
Pubmed
Web of science
Open Access
Yes
Create date
08/02/2021 9:45
Last modification date
02/03/2021 7:25
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