Score Tests for Association between Traits and Haplotypes when Linkage Phase Is Ambiguous
TLDR
New methods of testing the statistical association between haplotypes and a wide variety of traits, including binary, ordinal, and quantitative traits are developed, which allow adjustment for nongenetic covariates, which may be critical when analyzing genetically complex traits.Abstract:
A key step toward the discovery of a gene related to a trait is the finding of an association between the trait and one or more haplotypes. Haplotype analyses can also provide critical information regarding the function of a gene; however, when unrelated subjects are sampled, haplotypes are often ambiguous because of unknown linkage phase of the measured sites along a chromosome. A popular method of accounting for this ambiguity in case-control studies uses a likelihood that depends on haplotype frequencies, so that the haplotype frequencies can be compared between the cases and controls; however, this traditional method is limited to a binary trait (case vs. control), and it does not provide a method of testing the statistical significance of specific haplotypes. To address these limitations, we developed new methods of testing the statistical association between haplotypes and a wide variety of traits, including binary, ordinal, and quantitative traits. Our methods allow adjustment for nongenetic covariates, which may be critical when analyzing genetically complex traits. Furthermore, our methods provide several different global tests for association, as well as haplotype-specific tests, which give a meaningful advantage in attempts to understand the roles of many different haplotypes. The statistics can be computed rapidly, making it feasible to evaluate the associations between many haplotypes and a trait. To illustrate the use of our new methods, they are applied to a study of the association of haplotypes (composed of genes from the human-leukocyte-antigen complex) with humoral immune response to measles vaccination. Limited simulations are also presented to demonstrate the validity of our methods, as well as to provide guidelines on how our methods could be used.read more
Citations
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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
TL;DR: This work presents a statistical framework for calling SNPs, discovering somatic mutations, inferring population genetical parameters and performing association tests directly based on sequencing data without explicit genotyping or linkage-based imputation and demonstrates that this method achieves comparable accuracy to alternative methods for estimating site allele count, for inferring allele frequency spectrum and for association mapping.
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Complement Factor H Polymorphism in Age-Related Macular Degeneration
Robert J. Klein,Caroline J. Zeiss,Emily Y. Chew,Jen-yue Tsai,Richard S. Sackler,Chad Haynes,A. K. Henning,John Paul SanGiovanni,Shrikant Mane,Susan T. Mayne,Michael B. Bracken,Frederick L. Ferris,Jurg Ott,Colin J. Barnstable,Josephine Hoh +14 more
TL;DR: A genome-wide screen for polymorphisms associated with age-related macular degeneration revealed a polymorphism in linkage disequilibrium with the risk allele representing a tyrosine-histidine change at amino acid 402 in the complement factor H gene.
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Genome-wide association studies for common diseases and complex traits
TL;DR: Genome-wide association studies will soon become possible, and could open new frontiers in the understanding and treatment of disease, however, the execution and analysis of such studies will require great care.
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Complement Factor H Polymorphism and Age-Related Macular Degeneration
Albert O. Edwards,Robert C. Ritter,Kenneth Abel,Alisa K. Manning,Carolien I.M. Panhuysen,Lindsay A. Farrer +5 more
TL;DR: In this paper, single-nucleotide polymorphisms were tested for association with AMD in two independent case-control populations and significant association was identified within the regulation of complement activation locus and was centered over a tyrosine-402 --> histidine-402 protein polymorphism in the gene encoding complement factor.
Journal ArticleDOI
Genome-wide association study identifies novel breast cancer susceptibility loci
Douglas F. Easton,Karen A. Pooley,Alison M. Dunning,Paul D.P. Pharoah,Deborah J. Thompson,Dennis G. Ballinger,Jeffery P. Struewing,Jonathan J. Morrison,Helen I. Field,Robert Luben,Nicholas J. Wareham,Shahana Ahmed,Catherine S. Healey,Richard Bowman,Kerstin B. Meyer,Christopher A. Haiman,Laurence K. Kolonel,Brian E. Henderson,Loic Le Marchand,Paul Brennan,Suleeporn Sangrajrang,Valerie Gaborieau,Fabrice Odefrey,Chen-Yang Shen,Pei-Ei Wu,Hui-Chun Wang,Diana Eccles,D. Gareth Evans,Julian Peto,Olivia Fletcher,Nichola Johnson,Sheila Seal,Michael R. Stratton,Nazneen Rahman,Georgia Chenevix-Trench,Georgia Chenevix-Trench,Stig E. Bojesen,Børge G. Nordestgaard,C K Axelsson,Montserrat Garcia-Closas,Louise A. Brinton,Stephen J. Chanock,Jolanta Lissowska,Beata Peplonska,Heli Nevanlinna,Rainer Fagerholm,H Eerola,Daehee Kang,Keun-Young Yoo,Dong-Young Noh,Sei Hyun Ahn,David J. Hunter,Susan E. Hankinson,David G. Cox,Per Hall,Sara Wedrén,Jianjun Liu,Yen-Ling Low,Natalia Bogdanova,Peter Schu¨rmann,Do¨rk Do¨rk,Rob A. E. M. Tollenaar,Catharina E. Jacobi,Peter Devilee,Jan G. M. Klijn,Alice J. Sigurdson,Michele M. Doody,Bruce H. Alexander,Jinghui Zhang,Angela Cox,Ian W. Brock,Gordon MacPherson,Malcolm W.R. Reed,Fergus J. Couch,Ellen L. Goode,Janet E. Olson,Hanne Meijers-Heijboer,Hanne Meijers-Heijboer,Ans M.W. van den Ouweland,André G. Uitterlinden,Fernando Rivadeneira,Roger L. Milne,Gloria Ribas,Anna González-Neira,Javier Benitez,John L. Hopper,Margaret R. E. McCredie,Margaret R. E. McCredie,Margaret R. E. McCredie,Melissa C. Southey,Melissa C. Southey,Graham G. Giles,Chris Schroen,Christina Justenhoven,Christina Justenhoven,Hiltrud Brauch,Hiltrud Brauch,Ute Hamann,Yon-Dschun Ko,Amanda B. Spurdle,Jonathan Beesley,Xiaoqing Chen,_ kConFab,Arto Mannermaa,Veli-Matti Kosma,Vesa Kataja,Jaana M. Hartikainen,Nicholas E. Day,David Cox,Bruce A.J. Ponder +109 more
TL;DR: To identify further susceptibility alleles, a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls was conducted, followed by a third stage in which 30 single nucleotide polymorphisms were tested for confirmation.
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