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Updated: Aug 11, 2026

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Improved power offered by a score test for linkage disequilibrium mapping of quantitative-trait loci by selective
Chris Wallace1, Juliet M Chapman, David G Clayton
1Department of Clinical Pharmacology, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, United Kingdom. c.wallace@qmul.ac.uk
Abstract:
Selective genotyping is used to increase efficiency in genetic association studies of quantitative traits by genotyping only those individuals who deviate from the population mean. However, selection distorts the conditional distribution of the trait given genotype, and such data sets are usually analyzed using case-control methods, quantitative analysis within selected groups, or a combination of both. We show that Hotelling's T(2) test, recently proposed for association studies of one or several tagging single-nucleotide polymorphisms in a prospective (i.e., trait given genotype) design, can also be applied to the retrospective (i.e., genotype given trait) selective-genotyping design, and we use simulation to demonstrate its improved power over existing methods.
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