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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Functional SNPs in CD244 increase the risk of rheumatoid arthritis in a Japanese population
Akari Suzuki,Ryo Yamada,Yuta Kochi,Tetsuji Sawada,Yukinori Okada,Koichi Matsuda,Yoichiro Kamatani,Mikako Mori,Kenichi Shimane,Yasuhiko Hirabayashi,Atsushi Takahashi,Tatsuhiko Tsunoda,Akihiko Miyatake,Michiaki Kubo,Naoyuki Kamatani,Yusuke Nakamura,Kazuhiko Yamamoto +16 more
TL;DR: It is demonstrated that the rheumatoid arthritis–susceptible alleles of rs3766379 and rs6682654 and their haplotype increased their expression in luciferase and allele-specific transcript quantification assays, and may have a role in the autoimmune process shared by rhethritis and systemic lupus erythematosus.
Journal ArticleDOI
Association of GSK3β Polymorphisms With Brain Structural Changes in Major Depressive Disorder
Becky Inkster,Thomas E. Nichols,Philipp G. Saemann,Dorothee P. Auer,Florian Holsboer,Pierandrea Muglia,Paul M. Matthews +6 more
TL;DR: The association of GSK3beta polymorphisms with structural variation in the temporal lobe and hippocampus is of particular interest in the context of other evidence for structural and functional abnormalities in the hippocampi of patients with MDD.
Journal ArticleDOI
Burden Testing of Rare Variants Identified through Exome Sequencing via Publicly Available Control Data
Michael H. Guo,Michael H. Guo,Michael H. Guo,Lacey Plummer,Yee-Ming Chan,Joel N. Hirschhorn,Joel N. Hirschhorn,Joel N. Hirschhorn,Margaret F. Lippincott +8 more
TL;DR: The approach "re-discovered" genes previously implicated in IHH and introduced an approach for highly adaptable variant quality filtering that leads to well-calibrated results, and developed a user-friendly software package for performing gene-based burden testing against public databases.
Journal ArticleDOI
HLA class II sequence variants influence tuberculosis risk in populations of European ancestry
Gardar Sveinbjornsson,Gardar Sveinbjornsson,Daniel F. Gudbjartsson,Daniel F. Gudbjartsson,Bjarni V. Halldorsson,Bjarni V. Halldorsson,Karl G. Kristinsson,Magnus Gottfredsson,Jeffrey C. Barrett,Larus J. Gudmundsson,Kai Blöndal,Arnaldur Gylfason,Sigurjon A. Gudjonsson,Hafdis T. Helgadottir,Adalbjorg Jonasdottir,Aslaug Jonasdottir,Ari Karason,Ljiljana Bulat Kardum,Jelena Knežević,Helgi Kristjansson,Helgi Kristjansson,Mar Kristjansson,Arthur Löve,Arthur Löve,Yang Luo,Olafur Th Magnusson,Patrick Sulem,Augustine Kong,Gisli Masson,Unnur Thorsteinsdottir,Unnur Thorsteinsdottir,Zlatko Dembic,Sergey Nejentsev,Thorsteinn Blondal,Ingileif Jonsdottir,Ingileif Jonsdottir,Ingileif Jonsdottir,Kari Stefansson,Kari Stefansson +38 more
TL;DR: Findings show that the HLA class II region contributes to genetic risk of tuberculosis, possibly through reduced presentation of protective M. tuberculosis antigens to T cells.
Journal ArticleDOI
Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation.
María Soler Artigas,Louise V. Wain,Suzanne Miller,Abdul Kader Kheirallah,Jennifer E. Huffman,Ioanna Ntalla,Nick Shrine,Ma'en Obeidat,Holly Trochet,Wendy L. McArdle,Alexessander Couto Alves,Jennie Hui,Jing Hua Zhao,Peter K. Joshi,Alexander Teumer,Eva Albrecht,Medea Imboden,Rajesh Rawal,Lorna M. Lopez,Jonathan Marten,Stefan Enroth,Ida Surakka,Ozren Polasek,Ozren Polasek,Leo-Pekka Lyytikäinen,Raquel Granell,Pirro G. Hysi,Claudia Flexeder,Anubha Mahajan,John Beilby,John Beilby,Yohan Bossé,Corry-Anke Brandsma,Harry Campbell,Christian Gieger,Sven Glaeser,Juan R. González,Harald Grallert,Christopher J Hammond,Sarah E. Harris,Anna-Liisa Hartikainen,Markku Heliövaara,John Henderson,Lynne J. Hocking,Momoko Horikoshi,Nina Hutri-Kähönen,Erik Ingelsson,Erik Ingelsson,Erik Ingelsson,Åsa Johansson,John P. Kemp,John P. Kemp,Ivana Kolcic,Ashok Kumar,Lars Lind,Erik Melén,Arthur W. Musk,Arthur W. Musk,Pau Navarro,David C. Nickle,Sandosh Padmanabhan,Sandosh Padmanabhan,Olli T. Raitakari,Janina S. Ried,Samuli Ripatti,Samuli Ripatti,Holger Schulz,Robert A. Scott,Don D. Sin,John M. Starr,Ana Viñuela,Henry Voelzke,Sarah H. Wild,Alan F. Wright,Tatijana Zemunik,Deborah Jarvis,Tim D. Spector,David M. Evans,David M. Evans,Terho Lehtimäki,Veronique Vitart,Mika Kähönen,Ulf Gyllensten,Igor Rudan,Ian J. Deary,Stefan Karrasch,Stefan Karrasch,Nicole Probst-Hensch,Nicole Probst-Hensch,Joachim Heinrich,Beate Stubbe,James F. Wilson,Nicholas J. Wareham,Alan James,Alan James,Andrew P. Morris,Andrew P. Morris,Andrew P. Morris,Marjo-Riitta Järvelin,Caroline Hayward,Ian Sayers,David P. Strachan,Ian P. Hall,Martin D. Tobin,Martin D. Tobin,Panos Deloukas,Anna Hansell,Richard Hubbard,Victoria E. Jackson,Jonathan Marchini,Ian D. Pavord,Neil C. Thomson,Eleftheria Zeggini +112 more
TL;DR: 14 novel loci are identified in or near ENSA, RNU5F-1, KCNS3, AK097794, ASTN2, LHX3, CCDC91, TBx3, TRIP11, RIN3, TEKT5, LTBP4, MN1 and AP1S2, providing a basis for new understanding of the genetic determinants of these traits and pulmonary diseases in which they are altered.
References
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Journal ArticleDOI
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.
Journal ArticleDOI
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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