Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France).īenestan, L. genetix 4.05, logiciel sous Windows™ pour la génétique des populations. Maximum‐likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Molecular Ecology Resources published by John Wiley & Sons Ltd.īeerli, P. ĪMOVA K-means genetic distances genetic diversity polyploidy population differentiation. genodive is available for computers running Mac OS X 10.7 or higher and can be downloaded freely from. In addition, genodive makes it possible to run several external programs (lfmm, structure, instruct and vegan) directly from its own user interface, avoiding the need for data reformatting and use of the command line. A unique feature of genodive is that it can also open data sets with nongenetic variables, for example environmental data or geographical coordinates that can be included in the analysis. The different types of analyses offered by genodive include multiple statistics for estimating population differentiation (φ ST, F ST, F' ST, G ST, G' ST, G'' ST, D est, R ST, ρ), analysis of molecular variance-based K-means clustering, Hardy-Weinberg equilibrium, hybrid index, population assignment, clone assignment, Mantel test, Spatial Autocorrelation, 23 ways of calculating genetic distances, and both principal components and principal coordinates analyses. One major feature of genodive is that it supports both diploid and polyploid data, up to octaploidy (2n = 8x) for some analyses, but up to hexadecaploidy (2n = 16x) for other analyses. Furthermore, genodive seamlessly supports 15 different file formats for importing or exporting data from or to other programs. genodive has an intuitive graphical user interface that allows direct manipulation of the data through transformation, imputation of missing data, and exclusion and inclusion of individuals, population and/or loci. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. Īny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.Genodive version 3.0 is a user-friendly program for the analysis of population genetic data. Īn original code used for determining ploidy (gene copy number) and allele genotype of KIR is available at with reference data curated from IPD-KIR allele database, both of which are publicly available ( ).Other web resources used in this study are listed in the key resources table. Accession numbers are listed in the key resources table. The genotype data of BBJ used in this study are available from the Japanese Genotype-phenotype Archive (JGA) through application at. The International Histocompatibility Working Group (IHWG) cell lines were obtained from ECACC HLA typed collection ( ). The genomic DNA we used for KIR sequencing were obtained from a cell line established by the Japan Biological Informatics Consortium (JBIC), and can be purchased at. Individual-level KIR alleles and KIR imputation reference panel used in this study are deposited at the National Bioscience Database Center (NBDC) Human Database ( ) and are publicly available as of the date of publication. Our pipeline presents a broadly applicable framework to evaluate innate immunity in large-scale datasets. We observe a dearth of genome-wide significant associations, even in immune traits implicated previously to be associated with KIR (the smallest p = 1.5 × 10 −4). We construct a KIR imputation reference panel (n reference = 689, imputation accuracy = 99.7%), apply it to biobank genotype (n total = 169,907), and perform phenome-wide association studies of 85 traits. We define 118 alleles in 13 genes and demonstrate a linkage disequilibrium structure within and across KIR centromeric and telomeric regions. We devise a bioinformatics pipeline incorporating copy number estimation and insertion or deletion (indel) calling for high-resolution KIR genotyping. Here we conduct deep sequencing of 16 KIR genes in 1,173 individuals. Despite its role in immunity, the complex genomic structure has limited a deep understanding of the KIR genomic landscape. The killer cell immunoglobulin-like receptor (KIR) recognizes human leukocyte antigen (HLA) class I molecules and modulates the function of natural killer cells.
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