Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX' |
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Authors: | Tom R Gaunt Santiago Rodríguez Ian NM Day |
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Affiliation: | (1) Bristol Genetic Epidemology Laboratories (BGEL) and MRC Centre for Causal Analyses in Translational Epidemiology (CAiTE), University of Bristol, Canynge Hall, Whiteladies Road, Bristol, BS8 2PR, UK |
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Abstract: | Background The frequency of a haplotype comprising one allele at each of two loci can be expressed as a cubic equation (the 'Hill equation'), the solution of which gives that frequency. Most haplotype and linkage disequilibrium analysis programs use iteration-based algorithms which substitute an estimate of haplotype frequency into the equation, producing a new estimate which is repeatedly fed back into the equation until the values converge to a maximum likelihood estimate (expectation-maximisation). |
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