title: Asymmetric linkage disequilibrium: Tools for assessing multiallelic LD.
abstract: Standard measures of linkage disequilibrium (LD) provide an incomplete description of the correlation between two loci. Recently, Thomson and Single (2014) described a new asymmetric pair of LD measures (ALD) that give a more complete description of LD. The ALD measures are symmetric and equivalent to the correlation coefficient r when both loci are bi-allelic. When the numbers of alleles at the two loci differ, the ALD measures capture this asymmetry and provide additional detail about the LD structure. In disease association studies the ALD measures are useful for identifying additional disease genes in a genetic region, by conditioning on known effects. In evolutionary genetic studies ALD measures provide insight into selection acting on individual amino acids of specific genes, or other loci in high LD (see Thomson and Single (2014) for these examples). Here we describe new software for computing and visualizing ALD. We demonstrate the utility of this software using haplotype frequency data from the National Marrow Donor Program (NMDP). This enhances our understanding of LD patterns in the NMDP data by quantifying the degree to which LD is asymmetric and also quantifies this effect for individual alleles.
authors.affiliation: Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States. Electronic address: richard.single@uvm.edu.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Single
authors.affiliation: Department of Mathematics and Statistics, University of Vermont, Burlington, VT, United States.
authors.forename: Nick
authors.initials: N
authors.lastname: Strayer
authors.affiliation: University of California, Berkeley, CA, United States.
authors.forename: Glenys
authors.initials: G
authors.lastname: Thomson
authors.affiliation: National Marrow Donor Program, Minneapolis, MN, United States.
authors.forename: Vanja
authors.initials: V
authors.lastname: Paunic
authors.affiliation: National Marrow Donor Program, Minneapolis, MN, United States.
authors.forename: Mark
authors.initials: M
authors.lastname: Albrecht
authors.affiliation: National Marrow Donor Program, Minneapolis, MN, United States.
authors.forename: Martin
authors.initials: M
authors.lastname: Maiers
mesh_terms: D000483:Alleles; D019295:Computational Biology / Q000379:methods*; D005787:Gene Frequency; D006680:HLA Antigens / Q000235:genetics; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D012984:Software; D064878:Web Browser
chemical_list: D006680:HLA Antigens
keywords: Asymmetric; Linkage disequilibrium; Multiallelic data