publication . Article . Other literature type . 2010

An evaluation of statistical approaches to rare variant analysis in genetic association studies.

Morris, Andrew P.; Zeggini, Eleftheria;
English
  • Published: 01 Feb 2010 Journal: Genetic epidemiology, volume 34, issue 2 (issn: 0741-0395, eissn: 1098-2272, Copyright policy)
  • Country: United Kingdom
Abstract
Genome-wide association (GWA) studies have proved to be extremely successful in identifying novel common polymorphisms contributing effects to the genetic component underlying complex traits. Nevertheless, one source of, as yet, undiscovered genetic determinants of complex traits are those mediated through the effects of rare variants. With the increasing availability of large-scale re-sequencing data for rare variant discovery, we have developed a novel statistical method for the detection of complex trait associations with these loci, based on searching for accumulations of minor alleles within the same functional unit. We have undertaken simulations to evalua...
Subjects
free text keywords: Genetics(clinical), Epidemiology, Genetic association, Genome-wide association study, Genetic variation, Biology, Population, education.field_of_study, education, Allele, Genotype, Locus (genetics), Trait, Genetics, Original Article, rare variant association, re-sequencing data, genome-wide association data
Funded by
WT| Applied statistical genetics.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 088885
  • Funding stream: Cellular and Molecular Neuroscience
,
WT| Statistical methods for the analysis of whole genome association studies.
Project
  • Funder: Wellcome Trust (WT)
  • Project Code: 081682
  • Funding stream: Genetics, Genomics and Population Research
20 references, page 1 of 2

Anderson, CA, Pettersson, FH, Barrett, JC, Zhuang, JJ, Ragoussis, J, Cardon, LR, Morris, AP. Evaluating the effects of imputation on the power, coverage, and cost-efficiency of genome-wide SNP platforms. Am J Hum Genet. 2008; 83: 112-119 [OpenAIRE] [PubMed]

Aulchenko, YS, Ripatti, S, Lindqvist, I, Boomsma, D, Heid, IM, Pramstaller, PP, Penninx, BW, Janssens, AC, Wilson, JF, Spector, T, Martin, NG, Pedersen, NL, Kyvik, KO, Kaprio, T, Hofman, A, Freimer, NB, Jarvelin, MR, Gyllensten, U, Campbell, H, Rudan, I, Johansson, A, Marroni, F, Hayward, C, Vitart, V, Jonasson, I, Pattaro, C, Wright, A, Hastle, N, Pichler, I, Hicks, AA, Falchi, M, Willemsen, G, Hottenga, JJ, de Geus, EJ, Montgomery, GW, Whitfield, J, Magnusson, P, Sabarinen, J, Perola, M, Silander, K, Isaacs, A, Sijbrands, EJ, Uitterlindcn, AG, Witteman, JC, Oostra, BA, Elliott, P, Ruokonen, A, Sabatti, C, Gieger, C, Meitinger, T, Kronenberg, F, Doring, A, Wichmann, HE, Smit, JH, McCarthy, MI, van Duijn, CM, Peltonen, L. Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. Nat Genet. 2009; 41: 47-55 [OpenAIRE] [PubMed]

Barrett, JC, Hansoul, S, Nicolae, DL, Cho, JH, Duerr, RH, Rioux, JD, Brant, SR, Silverberg, MS, Taylor, KD, Barmada, MM, Bitton, A, Dassopoulos, T, Datta, LW, Green, T, Griffiths, AM, Kistner, EO, Murtha, MT, Regueiro, MD, Rotter, JI, Schumm, LP, Steinhart, AH, Targan, SR, Xavier, RJ, Libioulle, C, Sandor, C, Lathrop, M, Belaiche, J, Dewit, O, Gut, I, Heath, S, Laukens, D, Mni, M, Rutgeerts, P, Van Gossum, A, Zelenika, D, Franchimont, D, Hugot, TP, de Vos, M, Vermeire, S, Louis, E, Cardon, LR, Anderson, CA, Drummond, H, Nimmo, E, Ahmad, T, Prescott, NJ, Onnie, CM, Fisher, SA, Marchini, J, Ghori, T, Bumpstead, S, Gwilliam, R, Tremelling, M, Deloukas, P, Mansfield, J, Jewell, D, Satsangi, J, Mathew, CG, Parkes, M, Georges, M, Daly, MT. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008; 40: 955-962 [OpenAIRE] [PubMed]

Cohen, JC, Kiss, RS, Pertsemlidis, A, Marcel, YL, McPherson, R, Hobbs, HH. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science. 2004; 305: 869-872 [PubMed]

Cooper, JD, Smyth, DJ, Smiles, AM, Plagnol, V, Walker, NM, Allem, JE, Downes, K, Barrett, JC, Healy, BC, Mychaleckyj, JC, Warram, JH, Todd, JA. Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet. 2008; 40: 1399-1401 [OpenAIRE] [PubMed]

Excoffier, L, Slatkin, M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol. 1995; 12: 921-927 [OpenAIRE] [PubMed]

Griffiths, RD, Marjoram, P, Donnelly, P, Tavare, S. An ancestral recombination graph. Progress in Population Genetics and Human Evolution. 1997: 257-270 [OpenAIRE]

Hudson, RR. Generating samples under a Wright-Fisher neutral model. Bioinformatics. 2002; 18: 337-338 [PubMed]

Li, B, Leal, S. Novel methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008; 83: 311-321 [OpenAIRE] [PubMed]

Morris, RW, Kaplan, NL. On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles. Genet Epidemiol. 2002; 23: 221-233 [PubMed]

Nordborg, M, Balding, DJ, Bishop, M, Cannings, C. Coalescent theory. Handbook of Statistical Genetics. 2001: 179-212

Prokopenko, I, Langenberg, C, Florez, JC, Saxena, R, Soranzo, N, Thorleifsson, G, Loos, RJ, Manning, AK, Jackson, AU, Aulchenko, Y, Potter, SC, Erdos, MR, Sanna, S, Hottenga, JJ, Wheeler, E, Kaakinen, M, Lyssenko, V, Chen, WM, Ahmadi, K, Beckmann, JS, Bergman, RN, Bochud, M, Bonnycastle, LL, Buchanan, TA, Cao, A, Cervino, A, Coin, L, Collins, FS, Crisponi, L, de Geus, EJ, Dehghan, A, Deloukas, P, Doney, AS, Elliott, P, Freimer, N, Gateva, V, Herder, C, Hofman, A, Hughes, TE, Hunt, S, Illig, T, Inouye, M, Isomaa, B, Johnson, T, Kong, A, Krestyaninova, M, Kuusisto, J, Laakso, M, Lim, N, Lindblad, U, Lindgren, CM, McCann, OT, Mohlke, KL, Morris, AD, Naitza, S, Orruù, M, Palmer, CN, Pouta, A, Randall, J, Rathmann, W, Saramies, J, Scheet, P, Scott, LJ, Scuteri, A, Sharp, S, Sijbrands, E, Smit, JH, Song, K, Steinthorsdottir, V, Stringham, HM, Tuomi, T, Tuomilehto, J, Uitterlinden, AG, Voight, BF, Waterworth, D, Wichmann, HE, Willemsen, G, Witteman, JC, Yuan, X, Zhao, JH, Zeggini, E, Schlessinger, D, Sandhu, M, Boomsma, DI, Uda, M, Spector, TD, Penninx, BW, Altshuler, D, Vollenweider, P, Jarvelin, MR, Lakatta, E, Waeber, G, Fox, CS, Peltonen, L, Groop, LC, Mooser, V, Cupples, LA, Thorsteinsdottir, U, Boehnke, M, Barroso, I, Van Duijn, C, Dupuis, J, Watanabe, RM, Stefansson, K, McCarthy, MI, Wareham, NJ, Meigs, JB, Abecasis, GR. Variants in MTNR1B influence fasting glucose levels. Nat Genet. 2009; 41: 77-81 [OpenAIRE] [PubMed]

Raychaudhuri, S, Remmers, EF, Lee, AT, Hackett, R, Guiducci, C, Burtt, NP, Gianniny, L, Korma, BD, Padyukov, L, Kurreeman, FA, Chang, M, Catanese, JJ, Ding, B, Wong, S, van der Helm-van Mil, AH, Neale, BM, Coblyn, J, Cui, J, Tak, PP, Wolbink, GJ, Crusius, JB, van der Horst-Bruinsma, IE, Criswell, LA, Amos, CI, Seldin, MF, Kastner, DL, Ardlie, KG, Alfredsson, L, Costenbader, KH, Altshuler, D, Huizinga, TW, Shadick, NA, Weinblatt, ME, de Vries, N, Worthington, J, Seielstad, M, Toes, RE, Karlson, EW, Begovich, AB, Klareskog, L, Gregersen, PK, Daly, MJ, Plenge, RM. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat Genet. 2008; 40: 1216-1223 [OpenAIRE] [PubMed]

A haplotype map of the human genome. Nature. 2005; 437: 1299-1320 [OpenAIRE] [PubMed]

Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007; 447: 661-678 [OpenAIRE] [PubMed]

20 references, page 1 of 2
Powered by OpenAIRE Open Research Graph
Any information missing or wrong?Report an Issue
publication . Article . Other literature type . 2010

An evaluation of statistical approaches to rare variant analysis in genetic association studies.

Morris, Andrew P.; Zeggini, Eleftheria;