Genomic control for association studies.
Bernie Devlin,Kathryn Roeder +1 more
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The performance of the genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.Abstract:
A dense set of single nucleotide polymorphisms (SNP) covering the genome and an efficient method to assess SNP genotypes are expected to be available in the near future. An outstanding question is how to use these technologies efficiently to identify genes affecting liability to complex disorders. To achieve this goal, we propose a statistical method that has several optimal properties: It can be used with case control data and yet, like family-based designs, controls for population heterogeneity; it is insensitive to the usual violations of model assumptions, such as cases failing to be strictly independent; and, by using Bayesian outlier methods, it circumvents the need for Bonferroni correction for multiple tests, leading to better performance in many settings while still constraining risk for false positives. The performance of our genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.read more
Citations
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Journal ArticleDOI
Genome-wide association studies: implications for multiethnic samples
TL;DR: The conduct of genome-wide association studies will confront many of the challenges identified in the first generation of candidate gene and linkage studies, with a substantial increase in complexity.
Journal ArticleDOI
A genome-wide association study of production traits in a commercial population of Large White pigs: evidence of haplotypes affecting meat quality
Marie Pierre Sanchez,Marie Pierre Sanchez,Thierry Tribout,Thierry Tribout,Nathalie Iannuccelli,Marcel Bouffaud,Bertrand Servin,A.M.M. Tenghe,A.M.M. Tenghe,Patrice Dehais,Nelly Muller,Maria Pilar Del Schneider,Maria Pilar Del Schneider,Marie-José Mercat,Claire Rogel-Gaillard,Claire Rogel-Gaillard,Denis Milan,Jean Pierre Bidanel,Jean Pierre Bidanel,Hélène Gilbert +19 more
TL;DR: GWAS analyses with the PorcineSNP60 BeadChip enabled the detection of 23 QTL regions that affect feed consumption, carcass and meat quality traits in a LW population, of which 13 were novel QTL.
Journal ArticleDOI
Genome-wide Association of Copy-Number Variation Reveals an Association between Short Stature and the Presence of Low-Frequency Genomic Deletions
Andrew Dauber,Yongguo Yu,Michael C. Turchin,Charleston W. K. Chiang,Yan A. Meng,Ellen W. Demerath,Sanjay R. Patel,Stephen S. Rich,Jerome I. Rotter,Pamela J. Schreiner,James G. Wilson,Yiping Shen,Bai-Lin Wu,Joel N. Hirschhorn +13 more
TL;DR: It is found that subjects with short stature had a greater global burden of copy-number variants (CNVs) and a greater average CNV length than did controls, and an increased burden of lower-frequency deletions was associated with shorter stature.
Journal ArticleDOI
Association mapping of quantitative resistance for Leptosphaeria maculans in oilseed rape ( Brassica napus L.)
C. Jestin,Maryse Lodé,Patrick Vallée,C. Domin,Cyril Falentin,R. Horvais,S. Coedel,Maria J. Manzanares-Dauleux,Régine Delourme +8 more
TL;DR: This work characterized the molecular diversity of an oilseed rape collection of 128 lines showing a large spectrum of responses to infection by L. maculans, using 72 pairs of primers for simple sequence repeat and other markers.
Journal ArticleDOI
EigenGWAS: finding loci under selection through genome-wide association studies of eigenvectors in structured populations
TL;DR: This work develops a novel approach to identify regions of the genome underlying population genetic differentiation in any genetic data where the underlying population structure is unknown, or where the interest is assessing divergence along a gradient, and shows through theory and simulation that this approach can identify regions under selection along gradients of ancestry.
References
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Malay Ghosh,James O. Berger +1 more
Book
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TL;DR: An overview of statistical decision theory, which emphasizes the use and application of the philosophical ideas and mathematical structure of decision theory.
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James F. Crow,Motoo Kimura +1 more
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics theory, and more.
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