NAToRA, a relatedness-pruning method to minimize the loss of dataset size in genetic and omics analyses

• DOI: 10.1016/j.csbj.2022.04.009
• Publication Date: 2022-04-09T15:17:41Z
• Authors: Thiago Peixoto Leal; Vinicius C Furlan; Mateus Henrique G...; Julia Maria Sarai...; Pablo AS Fonseca; Rafael Tou; Marilia de Olivei...; Gilderlanio Santa...; Lucas F. Costa; Camila Zolini; Maria Gabriela Ca...; Maria Raquel Sant...; Maria Fernanda Li...; Robert H Gilman; Eduardo Tarazona-...; Maíra Ribeiro Rod...
• Keywords: Pruning; Heuristics

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 network-based relatedness-pruning method that minimizes dataset while unwanted relationships dataset. It uses node degree centrality metric to identify highly connected nodes individuals) implements heuristics approximate the minimal allow its application complex compared with two other popular population genetics methodologies (PLINK KING), NAToRA shows best combination all relatives keeping largest possible number datasets tested also, similar effects on allele frequency spectrum Principal Component Analysis than PLINK KING. freely available, both as standalone tool can easily incorporated part pipeline, graphical web allows visualization networks. also accepts variety relationship metrics input, facilitates use. release genealogies simulator software used for different tests performed this study.