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
Haplotype structure and phenotypic associations in the chromosomal regions surrounding two Arabidopsis thaliana flowering time loci.
Jenny Hagenblad,Chunlao Tang,John Molitor,Jonathan D. Werner,Keyan Zhao,Honggang Zheng,Paul Marjoram,Detlef Weigel,Detlef Weigel,Magnus Nordborg +9 more
TL;DR: It is demonstrated that LD could have been used to fine-map the FRI gene to a roughly 30-kb region and to identify two common loss-of-function alleles, and the effect of population structure in causing false positives was evident.
Journal ArticleDOI
Trans-ethnic genome-wide association study of colorectal cancer identifies a new susceptibility locus in VTI1A
Hansong Wang,Terrilea Burnett,Suminori Kono,Christopher A. Haiman,Motoki Iwasaki,Lynne R. Wilkens,Lenora W. M. Loo,David Van Den Berg,Laurence N. Kolonel,Brian E. Henderson,Temitope O. Keku,Robert S. Sandler,Lisa B. Signorello,William J. Blot,Polly A. Newcomb,Mala Pande,Christopher I. Amos,Dee W. West,Stéphane Bézieau,Sonja I. Berndt,Brent W. Zanke,Li Hsu,Noralane M. Lindor,Robert W. Haile,John L. Hopper,Mark A. Jenkins,Steven Gallinger,Graham Casey,Stephanie L. Stenzel,Fredrick R. Schumacher,Ulrike Peters,Stephen B. Gruber,Shoichiro Tsugane,Daniel O. Stram,Loic Le Marchand +34 more
TL;DR: A new pan-ethnic CRC risk locus is revealed at 10q25 (rs12241008, intronic to VTI1A; P=1.4×10−9), providing additional insight into the etiology of CRC and highlighting the value of association mapping in diverse populations.
Book ChapterDOI
Applications of Linkage Disequilibrium and Association Mapping in Maize
TL;DR: Association mapping, also known as linkage disequilibrium mapping, is a relatively new and promising genetic method for complex trait dissection as discussed by the authors, which utilizes ancestral recombinations and natural genetic diversity within a population to dissect quantitative traits.
Book ChapterDOI
Common genetic variation and human disease.
Nick Orr,Stephen J. Chanock +1 more
TL;DR: An overview of the field of complex disease genetics pertaining to mapping by association and the many pitfalls and caveats that have arisen is provided.
Journal ArticleDOI
Frequentist p-values for large-scale-single step genome-wide association, with an application to birth weight in American Angus cattle
Ignacio Aguilar,Andres Legarra,Fernando Flores Cardoso,Fernando Flores Cardoso,Yutaka Masuda,Daniela Lourenco,Ignacy Misztal +6 more
TL;DR: The use of a p-value for SSGWAS is a very general and efficient strategy to identify quantitative trait loci (QTL) and can be used for complex datasets such as those used in animal breeding, where only a proportion of the pedigreed animals are genotyped.
References
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Stastical Decision Theory and Bayesian Analysis.
Malay Ghosh,James O. Berger +1 more
Book
Statistical Decision Theory and Bayesian Analysis
TL;DR: An overview of statistical decision theory, which emphasizes the use and application of the philosophical ideas and mathematical structure of decision theory.
Journal ArticleDOI
The Future of Genetic Studies of Complex Human Diseases
TL;DR: The identification of the genetic basis of complex human diseases such as schizophrenia and diabetes has proven difficult as mentioned in this paper, and Risch and Merikangas proposed that they can best accomplish this goal by combining the power of the human genome project with association studies.
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An Introduction to Population Genetics Theory
James F. Crow,Motoo Kimura +1 more
TL;DR: An introduction to population genetics theory, An introduction to Population Genetics Theory, Population Genetics theory, Population genetics theory as discussed by the authors, Population genetics, population genetics, and population genetics theories, Population Genetic Theory
Book
An introduction to population genetics theory
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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