title: Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations.
abstract: Copy number variations represent a substantial source of genetic variation and are associated with a plethora of physiological and pathophysiological conditions. Joint copy number and allelic variations (CNAVs) are difficult to analyze and require new strategies to unravel the properties of genotype distributions. We developed a Bayesian hidden Markov model (HMM) approach that allows dissecting intrinsic properties and metastructures of the distribution of CNAVs within populations, in particular haplotype phases of genes with varying copy numbers. As a key feature, this approach incorporates an extension of the Hardy-Weinberg equilibrium, allowing both a comprehensive and parsimonious model design. We demonstrate the quality of performance and applicability of the HMM approach with a real data set describing the Fcγ receptor (FcγR) gene region. Our concept, using a dynamic process to analyze a static distribution, establishes the basis for a novel understanding of complex genomic data sets.
authors.affiliation: 1] Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany [2] Department of Dermatology, Allergology and Venereology, University of Lübeck, Lübeck, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Recke
authors.affiliation: Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
authors.forename: Klaus-Günther
authors.initials: KG
authors.lastname: Recke
authors.affiliation: Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
authors.forename: Saleh
authors.initials: S
authors.lastname: Ibrahim
authors.affiliation: Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.
authors.forename: Steffen
authors.initials: S
authors.lastname: Möller
authors.affiliation: 1] Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany [2] Center for Clinical Studies, University of Lübeck, Lübeck, Germany.
authors.forename: Reinhard
authors.initials: R
authors.lastname: Vonthein
mesh_terms: D000483:Alleles; D000818:Animals; D001499:Bayes Theorem; D056915:DNA Copy Number Variations; D008040:Genetic Linkage; D014644:Genetic Variation; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D008390:Markov Chains; D008957:Models, Genetic; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide; D017452:Receptors, IgG / Q000235:genetics
chemical_list: D017452:Receptors, IgG