Author | Leal, Thiago Peixoto | |
Author | Furlan, Vinicius C | |
Author | Gouveia, Mateus Henrique | |
Author | Duarte, Julia Maria Saraiva | |
Author | Fonseca, Pablo AS | |
Author | Tou, Rafael | |
Author | Scliar, Marilia de Oliveira | |
Author | Araujo, Gilderlanio Santana de | |
Author | Costa, Lucas F. | |
Author | Zolini, Camila | |
Author | Peixoto, Maria Gabriela Campolina Diniz | |
Author | Carvalho, Maria Raquel Santos | |
Author | Costa, Maria Fernanda Furtado Lima | |
Author | Gilman, Robert H | |
Author | Tarazona-Santos, Eduardo | |
Author | Rodrigues, Maíra Ribeiro | |
Access date | 2022-11-09T17:37:28Z | |
Available date | 2022-11-09T17:37:28Z | |
Document date | 2022 | |
Citation | LEAL,Thiago Peixoto et al. NAToRA, a relatedness-pruning method to minimize the loss of dataset size in genetic and omics analyses. Comput Struct Biotechnol J., v. 20, p. 1821–1828, 2022. doi: 10.1016/j.csbj.2022.04.009 | en_US |
ISSN | 2001-0370 | en_US |
URI | https://www.arca.fiocruz.br/handle/icict/55556 | |
Language | eng | en_US |
Publisher | Nature Publishing | en_US |
Rights | open access | en_US |
Title | NAToRA, a relatedness-pruning method to minimize the loss of dataset size in genetic and omics analyses | en_US |
Type | Article | en_US |
Abstract | Genetic and omics analyses frequently require independent observations, which is not guaranteed in real datasets. When relatedness cannot be accounted for, solutions involve removing related individuals (or observations) and, consequently, a reduction of available data. We developed a network-based relatedness-pruning method that minimizes dataset reduction while removing unwanted relationships in a dataset. It uses node degree centrality metric to identify highly connected nodes (or individuals) and implements heuristics that approximate the minimal reduction of a dataset to allow its application to complex datasets. When compared with two other popular population genetics methodologies (PLINK and KING), NAToRA shows the best combination of removing all relatives while keeping the largest possible number of individuals in all datasets tested and also, with similar effects on the allele frequency spectrum and Principal Component Analysis than PLINK and KING. NAToRA is freely available, both as a standalone tool that can be easily incorporated as part of a pipeline, and as a graphical web tool that allows visualization of the relatedness networks. NAToRA also accepts a variety of relationship metrics as input, which facilitates its use. We also release a genealogies simulator software used for different tests performed in this study. | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil/Lerner Research Institute. Genomic Medicine.Cleveland Clinic. Cleveland, OH, United States | en_US |
Affilliation | Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil/Center for Research on Genomics & Global Health. National Human Genome Research Institute. National Institutes of Health. Bethesda, MD, United States | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil/Centre for Genetic Improvement of Livestock. Department of Animal Biosciences. University of Guelph. Guelph, Ontario, Canadá | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Universidade de São Paulo. Instituto de Biociências. Centro de Estudos doGenoma Humano e Células-Tronco. São Paulo, SP, Brazil | en_US |
Affilliation | Universidade Federal do Pará. Instituto de Ciências Biológicas. Programa de Pós-Graduação em Biologia Molecular. Laboratório de Genética Humana e Médica. Belém, PA, Brazil | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil/Beagle. Belo Horizonte, MG, Brazil/Mosaico Translational Genomics Initiative, Belo Horizonte, MG, Brazil | en_US |
Affilliation | Embrapa Gado de Leite, Embrapa, Juiz de Fora, MG, Brazil | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Fundação Oswaldo Cruz. Instituto René Rachou. Belo Horizonte, MG, Brazil | en_US |
Affilliation | Universidad Peruana Cayetano Heredia.Lima, Lima, Perú/ Dept of International Health. Johns Hopkins School of Public Health Baltimore. Baltimore, MD, USA | en_US |
Affilliation | Universidade Federal de Minas Gerais. Instituto de Ciências Biológicas. Departamento de Genética, Ecologia e Evolução. Belo Horizonte, MG, Brazil/Mosaico Translational Genomics Initiative, Belo Horizonte, MG, Brazil/Dept of International Health. Johns Hopkins School of Public Health Baltimore. Baltimore, MD, USA | en_US |
Affilliation | Universidade de São Paulo. Instituto de Biociências. Departamento de Genética e Biologia Evolutiva. São Paulo, SP, Brazil | en_US |
Subject | Complex network theory | en_US |
Subject | Population genetics | en_US |
Subject | Genetic kinship | en_US |
Subject | Genealogies simulator | en_US |