DOI: 10.5061/dryad.k8b8n
title: Data from: Reducing cryptic relatedness in genomic datasets via a central node exclusion algorithm

description: Cryptic relatedness is a confounding factor in genetic diversity and
 genetic association studies. Development of strategies to reduce cryptic
 relatedness in a sample is a crucial step for downstream genetic analyzes.
 The present study uses a node selection algorithm, based on network
 degrees of centrality, to evaluate its applicability and impact on
 evaluation of genetic diversity and population stratification. 1,036
 Guzerá (Bos indicus) females were genotyped using Illumina Bovine SNP50 v2
 BeadChip. Four strategies were compared. The first and second strategies
 consists on a iterative exclusion of most related individuals based on
 PLINK kinship coefficient (φij) and VanRaden’s φij, respectively. The
 third and fourth strategies were based on a node selection algorithm. The
 fourth strategy, Network G matrix, preserved the larger number of
 individuals with a better diversity and representation from the initial
 sample. Determining the most probable number of populations was directly
 affected by the kinship metric. Network G matrix was the better strategy
 for reducing relatedness due to producing a larger sample, with more
 distant individuals, a more similar distribution when compared with the
 full dataset in the MDS plots and keeping a better representation of the
 population structure. Resampling strategies using VanRaden’s φij as a
 relationship metric was better to infer the relationships among
 individuals. Moreover, the resampling strategies directly impact the
 genomic inflation values in Genome-wide association studies. The use of
 the node selection algorithm also implies better selection of the most
 central individuals to be removed, providing a more representative sample.
description: Gwas_simulations_All_AnimalsGWAS simulation results obtained for the full data set (1036 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.Gwas_simulations_centralityGGWAS simulation results obtained for the Network G matrix sample (286 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.Gwas_simulations_CentralityIBDGWAS simulation results obtained for the full Network IBD sample (210 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.Gwas_simulations_threshold_GmatrixGWAS simulation results obtained for the Threshold G matrix (286 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.Gwas_simulations_thresholdIBDGWAS simulation results obtained for the Threshold IBD sample (203 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.Tabular_kinship_AllAnimalsThis file contains the Kinship values between each pair of individuals present in the All animals sample. Theses kinship values were used in each resampling approach applied in the present study.Tabular_Gmatrix_All_animalsThis file contains the G matrix (VanRaden, 2009) values between each pair of individuals present in the All animals sample. Theses kinship values were used in each resampling approach applied in the present study.Supplementary_file1This file contains the R script used to perform the threshold resampling applied in this study.