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An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.

ABSTRACT: Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.

SUBMITTER: Lu TT

PROVIDER: S-EPMC2986489 | biostudies-literature | 2009 Jul

REPOSITORIES: biostudies-literature

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An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.

Lu Timothy Tehua TT Lao Oscar O Nothnagel Michael M Junge Olaf O Freitag-Wolf Sandra S Caliebe Amke A Balascakova Miroslava M Bertranpetit Jaume J Bindoff Laurence Albert LA Comas David D Holmlund Gunilla G Kouvatsi Anastasia A Macek Milan M Mollet Isabelle I Nielsen Finn F Parson Walther W Palo Jukka J Ploski Rafal R Sajantila Antti A Tagliabracci Adriano A Gether Ulrik U Werge Thomas T Rivadeneira Fernando F Hofman Albert A Uitterlinden André Gerardus AG Gieger Christian C Wichmann Heinz-Erich HE Ruether Andreas A Schreiber Stefan S Becker Christian C Nürnberg Peter P Nelson Matthew Roberts MR Kayser Manfred M Krawczak Michael M

European journal of human genetics : EJHG 20090121 7

Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of ...[more]

PMID: 19156175

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Project description:Following chicken domestication, diversified chicken breeds were developed by both natural and artificial selection, which led to the accumulation of abundant genetic and phenotypic variations, making chickens an ideal genetic research model. To better understand the genetic structure of chicken breeds under different selection pressures, we genotyped various chicken populations with specific selection targets, including indigenous, commercial, gamecock, and wild ancestral chickens, using the 600K SNP array. We analyzed the population structure, genetic relationships, run of homozygosity (ROH), effective population number (Ne), and other genetic parameters. The wild ancestral population, red junglefowl (RJF), possessed the highest diversity, in comparison with all other domesticated populations, which was supported by linkage disequilibrium decay (LD), effective population number, and ROH analyses. The gamecock breeds, which were subjected to stronger male-biased selection for fighting-related traits, also presented higher variation than the commercial and indigenous breeds. Admixture analysis also indicated that game breed is a relatively independent branch of Chinese local breeds. Following intense selection for reproductive and productive traits, the commercial lines showed the least diversity. We also observed that the European local chickens had lower genetic variation than the Chinese local breeds, which could be attributed to the shorter history of the European breed. ROH were present in a breed specific manner and 191 ROH island were detected on four groups (commercial, local, game and wild chickens). These ROH islands were involved in egg production, growth and silky feathers and other traits. Moreover, we estimated the effective sex ratio of these breeds to demonstrate the change in the ratio of the two sexes. We found that commercial chickens had a greater sex imbalance between females and males. The commercial lines showed the highest female-to-male ratios. Interestingly, RJF comprised a greater proportion of males than females. Our results show the population genetics of chickens under selection pressures, and can aid in the development of better conservation strategies for different chicken breeds.

Dataset Information

An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.

Publications

An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.

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