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Estimating Disequilibrium Coefficients

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1666)

Abstract

Gametic phase disequilibrium is the nonrandom association of alleles within gametes. Linkage disequilibrium (LD) describes the special case of deviation from independence between alleles at two linked genetic loci. Estimation of allelic LD requires knowledge of haplotypes. Genotype-based LD measures dispense with the haplotype estimation step and avoid bias in LD estimation. In this chapter, the most important measures for allelic and genotypic LD are introduced. The use of software packages for LD estimation is illustrated.

Key words

Allelic linkage disequilibrium Coefficient of determination Composite linkage disequilibrium Gametic phase disequilibrium Genotypic linkage disequilibrium Haplotype Hardy–Weinberg equilibrium LDheatmap Lewontin’s D′ Linkage disequilibrium PLINK snpStats 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Institut für Medizinische Biometrie und EpidemiologieUniversitätsklinikum Hamburg-EppendorfHamburgGermany
  2. 2.Institut für Medizinische Biometrie und Statistik & Zentrum für klinische StudienUniversität zu Lübeck, Universitätsklinikum Schleswig-HolsteinLübeckGermany

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