- Genome-wide association
Non-replication and inconsistency had been common features in the search for common variants of candidate genes affecting the risk of complex diseases. They may continue to require attention in the current era, when massive hypothesis-free testing of genetic variants is feasible. An empirical evaluation of the early experience with genome-wide association (GWA) studies suggests several examples where proposed associations have failed to be replicated by subsequent investigations. Non-replication and inconsistency is defined here in the framework of cumulative meta-analysis. Ideally, associations exist, GWA finds them, and subsequent investigations should replicate them. However, a number of other possibilities need to be considered. No common genetic variants may associate with the phenotype of interest and GWA may find nothing; or associations may exist, but GWA may miss them. Associations that do not exist may be falsely selected by the GWA and subsequent studies may appropriately refute them or falsely replicate them. Finally, GWA may find true associations that are nevertheless falsely non-replicated in the subsequent studies; or associations may be genuinely inconsistent across study populations. A list of options is presented for consideration in each of these scenarios.
Copyright © 2007 S. Karger AG, Basel
- Carlson CS, Eberle MA, Kruglyak L, Nickerson DA: Mapping complex disease loci in whole-genome association studies. Nature 2004;429:446–452.
- Thomas DC, Haile RW, Duggan D: Recent developments in genomewide association scans: A workshop summary and review. Am J Hum Genet 2005;77:337–345.
- Wang WY, Barratt BJ, Clayton DG, Todd JA: Genome-wide association studies: Theoretical and practical concerns. Nat Rev Genet 2005;6:109–118.
- Hirschhorn JN, Daly MJ: Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 2005;6:95–108.
- Thomas DC: Are we ready for genome-wide association studies? Cancer Epidemiol Biomarkers Prev 2006;15:595–598.
- Marchini J, Donnelly P, Cardon LR: Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005;37:413–417.
- Wang H, Thomas DC, Pe’er I, Stram DO: Optimal two-stage genotyping designs for genome-wide association scans. Genet Epidemiol 2006;30:356–368.
- Thomas D, Xie R, Gebregziabher M: Two-stage sampling designs for gene association studies. Genet Epidemiol 2004;27:401–414.
- Kuchiba A, Tanaka NY, Ohashi Y: Optimum two-stage designs in case-control association studies using false discovery rate. J Hum Genet 2006;51:1046–1054.
- Skol AD, Scott LJ, Abecasis GR, Boehnke M: Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nat Genet 2006;38:209–213.
- Todd JA: Statistical false positive or true disease pathway? Nat Genet 2006;38:731–733.
- Ioannidis JP, Ntzani EE, Trikalinos TA, Contopoulos-Ioannidis DG: Replication validity of genetic association studies. Nat Genet 2001;29:306–309.
- Wacholder S, Chanock S, Garcia-Closas M, El Ghormli L, Rothman N: Assessing the probability that a positive report is false: An approach for molecular epidemiology studies. J Natl Cancer Inst 2004;96:434–442.
- Ioannidis JP: Genetic associations: False or true? Trends Mol Med 2003;9:135–138.
- Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J: Complement factor H polymorphism in age-related macular degeneration. Science 2005;308:385–389.
- Herbert A, Gerry NP, McQueen MB, Heid IM, Pfeufer A, Illig T, Wichmann HE, Meitinger T, Hunter D, Hu FB, Colditz G, Hinney A, Hebebrand J, Koberwitz K, Zhu X, Cooper R, Ardlie K, Lyon H, Hirschhorn JN, Laird NM, Lenburg ME, Lange C, Christman MF: A common genetic variant is associated with adult and childhood obesity. Science 2006;312:279–283.
- Maraganore DM, de Andrade M, Lesnick TG, Strain KJ, Farrer MJ, Rocca WA, Pant PV, Frazer KA, Cox DR, Ballinger DG: High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet 2005;77:685–693.
- Ozaki K, Ohnishi Y, Iida A, Skine A, Yamada R, Tsunoda T, Sato H, Sato H, Hori M, Nakamura Y, et al: Functional SNPs in the lymphotoxin- gene that are associated with susceptibility to myocardial infarction. Nat Genet 2002;32:650–654.
- Yang Z, Camp NJ, Sun H, Tong Z, Gibbs D, Cameron DJ, Chen H, Zhao Y, Pearson E, Li X, Chien J, Dewan A, Harmon J, Bernstein PS, Shridhar V, Zabriskie NA, Hoh J, Howes K, Zhang K: A variant of the HTRA1 gene increases susceptibility to age-related macular degeneration. Science 2006;314:992–993.
- Arking DE, Pfeufer A, Post W, Kao WH, Newton-Cheh C, Ikeda M, West K, Kashuk C, Akyol M, Perz S, Jalilzadeh S, Illig T, Gieger C, Guo CY, Larson MG, Wichmann HE, Marban E, O’Donnell CJ, Hirschhorn JN, Kaab S, Spooner PM, Meitinger T, Chakravarti A: A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization. Nat Genet 2006;38:644–651.
- Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, Daly MJ, Steinhart AH, Abraham C, Regueiro M, Griffiths A, Dassopoulos T, Bitton A, Yang H, Targan S, Datta LW, Kistner EO, Schumm LP, Lee AT, Gregersen PK, Barmada MM, Rotter JI, Nicolae DL, Cho JH: A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 2006;314:1461–1463.
- Conley YP, Jakobsdottir J, Mah T, Weeks DE, Klein R, Kuller L, Ferrell RE, Gorin MB: CFH, ELOVL4, PLEKHA1 and LOC387715 genes and susceptibility to age-related maculopathy: AREDS and CHS cohorts and meta-analyses. Hum Mol Genet 2006;15:3206–3218.
- Despriet DD, Klaver CC, Witteman JC, Bergen AA, Kardys I, de Maat MP, Boekhoorn SS, Vingerling JR, Hofman A, Oostra BA, Uitterlinden AG, Stijnen T, van Duijn CM, de Jong PT: Complement factor H polymorphism, complement activators, and risk of age-related macular degeneration. JAMA 2006;296:301–309.
- Uka J, Tamura H, Kobayashi T, Yamane K, Kawakami H, Minamoto A, Mishima HK: No association of complement factor H gene polymorphism and age-related macular degeneration in the Japanese population. Retina 2006;26:985–987.
- Gotoh N, Yamada R, Hiratani H, Renault V, Kuroiwa S, Monet M, Toyoda S, Chida S, Mandai M, Otani A, Yoshimura N, Matsuda F: No association between complement factor H gene polymorphism and exudative age-related macular degeneration in Japanese. Hum Genet 2006;120:139–143.
- Rosskopf D, Bornhorst A, Rimmbach C, Schwahn C, Kayser A, Kruger A, Tessmann G, Geissler I, Kroemer HK, Volzke H: Comment on ‘A common genetic variant is associated with adult and childhood obesity’. Science 2007;315:187.
- Loos RJ, Barroso I, O’rahilly S, Wareham NJ: Comment on ‘A common genetic variant is associated with adult and childhood obesity’. Science 2007;315:187.
- Dina C, Meyre D, Samson C, Tichet J, Marre M, Jouret B, Charles MA, Balkau B, Froguel P: Comment on ‘A common genetic variant is associated with adult and childhood obesity’. Science 2007;315:187.
- Elbaz A, Nelson LM, Payami H, Ioannidis JP, Fiske BK, Annesi G, Carmine Belin A, Factor SA, Ferrarese C, Hadjigeorgiou GM, Higgins DS, Kawakami H, Kruger R, Marder KS, Mayeux RP, Mellick GD, Nutt JG, Ritz B, Samii A, Tanner CM, Van Broeckhoven C, Van Den Eeden SK, Wirdefeldt K, Zabetian CP, Dehem M, Montimurro JS, Southwick A, Myers RM, Trikalinos TA: Lack of replication of thirteen single-nucleotide polymorphisms implicated in Parkinson’s disease: a large-scale international study. Lancet Neurol 2006;5:917–923.
- Clarke R, Xu P, Bennett D, Lewington S, Zondervan K, Parish S, Palmer A, Clark S, Cardon L, Peto R, Lathrop M, Collins R: Lymphotoxin-alpha gene and risk of myocardial infarction in 6,928 cases and 2,712 controls in the ISIS case-control study. PLoS Genet 2006;2:e107.
- Sutton AJ, Abrams KR, Jones DR, Sheldon TA, Song F: Methods for Meta-Analysis in Medical Research. New York, Wiley, 2000, pp 205–228.
- Sterne JA, Davey Smith G: Sifting the evidence-what’s wrong with significance tests? BMJ 2001;322:226–231.
- Lau J, Ioannidis JP, Schmid CH: Quantitative synthesis in systematic reviews. Ann Intern Med 1997;127:820–826.
- Higgins JP, Thompson SG, Deeks JJ, Altman DG: Measuring inconsistency in meta-analyses. BMJ 2003;327:557–560.
- Hemminki K, Lorenzo Bermejo J, Forsti A: The balance between heritable and environmental aetiology of human disease. Nat Rev Genet 2006;7:958–965.
- King MC, Marks JH, Mandell JB; New York Breast Cancer Study Group: Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2. Science 2003;302:643–646.
- Easton DF, Hopper JL, Thomas DC, Antoniou A, Pharoah PD, Whittemore AS, Haile RW: Breast cancer risks for BRCA1/2 carriers. Science 2004;306:2187–2191.
- Wacholder S, Struewing JP, Hartge P, Greene MH, Tucker MA: Breast cancer risks for BRCA1/2 carriers. Science 2004;306:2187–2191.
- Breast Cancer Association Consortium. Commonly studied single-nucleotide polymorphisms and breast cancer: Results from the Breast Cancer Association Consortium. J Natl Cancer Inst 2006;98:1382–1396.
- Ioannidis JP: Common genetic variants for breast cancer: 32 largely refuted candidates and larger prospects. J Natl Cancer Inst 2006;98:1350–1353.
- Ralston SH, de Crombrugghe B: Genetic regulation of bone mass and susceptibility to osteoporosis. Genes Dev 2006;20:2492–2506.
- Barrett JC, Cardon LR: Evaluating coverage of genome-wide association studies. Nat Genet 2006;38:659–662.
- Jorgenson E, Witte JS: Coverage and power in genomewide association studies. Am J Hum Genet 2006;78:884–888.
- Service S, DeYoung J, Karayiorgou M, Roos JL, Pretorious H, Bedoya G, Ospina J, Ruiz-Linares A, Macedo A, Palha JA, Heutink P, Aulchenko Y, Oostra B, van Duijn C, Jarvelin MR, Varilo T, Peddle L, Rahman P, Piras G, Monne M, Murray S, Galver L, Peltonen L, Sabatti C, Collins A, Freimer N: Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. Nat Genet 2006;38:556–560.
- Ioannidis JP, Trikalinos TA, Khoury MJ: Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases. Am J Epidemiol 2006;164:609–614.
- Kelsey JL, Whittemore AS, Evans AS, Thompson WD: Methods in observational epidemiology, 2nd Edition, Oxford University Press, 1996.
- Welcome Trust Case Control Consortium. Accessible at: http://www.wtccc.org.uk/.
- Pompanon F, Bonin A, Bellemain E, Taberlet P: Genotyping errors: causes, consequences and solutions. Nat Rev Genet 2005;6:847–859.
- Kang SJ, Finch SJ, Haynes C, Gordon D: Quantifying the percent increase in minimum sample size for SNP genotyping errors in genetic model-based association studies. Hum Hered 2004;58:139–144.
- Edwards BJ, Haynes C, Levenstien MA, Finch SJ, Gordon D: Power and sample size calculations in the presence of phenotype errors for case/control genetic association studies. BMC Genet 2005;6:18.
- Zheng G, Tian X: The impact of diagnostic error on testing genetic association in case-control studies. Stat Med 2005;24:869–882.
- Wong MY, Day NE, Luan JA, Wareham NJ: Estimation of magnitude in gene-environment interactions in the presence of measurement error. Stat Med 2004;23:987–998.
- Gorroochurn P, Hodge SE, Heiman G, Greenberg DA: Effect of population stratification on case-control association studies. II. False-positive rates and their limiting behavior as number of subpopulations increases. Hum Hered 2004;58:40–48.
- Berger M, Stassen HH, Kohler K, Krane V, Monks D, Wanner C, Hoffmann K, Hoffmann MM, Zimmer M, Bickeboller H, Lindner TH: Hidden population substructures in an apparently homogeneous population bias association studies. Eur J Hum Genet 2006;14:236–244.
- Marchini J, Cardon LR, Phillips MS, Donnelly P: The effects of human population structure on large genetic association studies. Nat Genet 2004;36:512–517.
- Heiman GA, Hodge SE, Gorroochurn P, Zhang J, Greenberg DA: Effect of population stratification on case-control association studies. I. Elevation in false positive rates and comparison to confounding risk ratios (a simulation study). Hum Hered 2004;58:30–39.
- Evangelou E, Trikalinos TA, Salanti G, Ioannidis JP: Family-based versus unrelated case-control designs for genetic associations. PLoS Genet 2006;2:e123.
- Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, Smink LJ, Lam AC, Ovington NR, Stevens HE, Nutland S, Howson JM, Faham M, Moorhead M, Jones HB, Falkowski M, Hardenbol P, Willis TD, Todd JA: Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 2005;37:1243–1246.
- Devlin B, Roeder K, Wasserman L: Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 2001;60:155–166.
- Kohler K, Bickeboller H: Case-control association tests correcting for population stratification. Ann Hum Genet 2006;70:98–115.
- Hinds DA, Stokowski RP, Patil N, Konvicka K, Kershenobich D, Cox DR, Ballinger DG: Matching strategies for genetic association studies in structured populations. Am J Hum Genet 2004;74:317–325.
- Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D: Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006;38:904–909.
- Ioannidis JP: Why most published research findings are false. PLoS Med 2005;2:e124.
- Benjamini Y, Hochberg Y: Controlling the false discovery rate – a practical and powerful approach to multiple testing. J R Stat Soc B 1995;57:289–300.
- Pounds S, Cheng C: Improving false discovery rate estimation. Bioinformatics 2004;20:1737–1745.
- van den Oord EJ, Sullivan PF: False discoveries and models for gene discovery. Trends Genet 2003;19:537–542.
- Zehetmayer S, Bauer P, Posch M: Two-stage designs for experiments with a large number of hypotheses. Bioinformatics 2005;21:3771–3777.
- Cordell HJ, Clayton DG: Genetic association studies. Lancet 2005;366:1121–1131.
- Ioannidis JP, Gwinn M, Little J, Higgins JP, Bernstein JL, Boffetta P, Bondy M, Bray MS, Brenchley PE, Buffler PA, Casas JP, Chokkalingam A, Danesh J, Smith GD, Dolan S, Duncan R, Gruis NA, Hartge P, Hashibe M, Hunter DJ, Jarvelin MR, Malmer B, Maraganore DM, Newton-Bishop JA, O’Brien TR, Petersen G, Riboli E, Salanti G, Seminara D, Smeeth L, Taioli E, Timpson N, Uitterlinden AG, Vineis P, Wareham N, Winn DM, Zimmern R, Khoury MJ; Human Genome Epidemiology Network and the Network of Investigator Networks. A road map for efficient and reliable human genome epidemiology. Nat Genet 2006;38:3–5.
- Little J, Bradley L, Bray MS, Clyne M, Dorman J, Ellsworth DL, Hanson J, Khoury M, Lau J, O’Brien TR, Rothman N, Stroup D, Taioli E, Thomas D, Vainio H, Wacholder S, Weinberg C: Reporting, appraising, and integrating data on genotype prevalence and gene-disease associations. Am J Epidemiol 2002;156:300–310.
- Salanti G, Amountza G, Ntzani EE, Ioannidis JP: Hardy-Weinberg equilibrium in genetic association studies: An empirical evaluation of reporting, deviations, and power. Eur J Hum Genet 2005;13:840–848.
- Maraganore DM, de Andrade M, Elbaz A, Farrer MJ, Ioannidis JP, Kruger R, Rocca WA, Schneider NK, Lesnick TG, Lincoln SJ, Hulihan MM, Aasly JO, Ashizawa T, Chartier-Harlin MC, Checkoway H, Ferrarese C, Hadjigeorgiou G, Hattori N, Kawakami H, Lambert JC, Lynch T, Mellick GD, Papapetropoulos S, Parsian A, Quattrone A, Riess O, Tan EK, Van Broeckhoven C: Collaborative analysis of alpha-synuclein gene promoter variability and Parkinson disease. JAMA 2006;296:661–670.
- Ioannidis JP, Trikalinos TA, Ntzani EE, Contopoulos-Ioannidis DG: Genetic associations in large versus small studies: an empirical assessment. Lancet 2003;361:567–571.
- International HapMap Consortium. A haplotype map of the human genome. Nature 2005;437:1299–1320.
- Hinds DA, Stuve LL, Nilsen GB, Halperin E, Eskin E, Ballinger DG, Frazer KA, Cox DR: Whole-genome patterns of common DNA variation in three human populations. Science 2005;307:1072–1079.
- Hunter DJ: Gene-environment interactions in human diseases. Nat Rev Genet 2005;6:287–298.
- Yang Q, Khoury MJ, Sun F, Flanders WD: Case-only design to measure gene-gene interaction. Epidemiology 1999;10:167–170.
- Garcia-Closas M, Malats N, Silverman D, Dosemeci M, Kogevinas M, Hein DW, Tardon A, Serra C, Carrato A, Garcia-Closas R, Lloreta J, Castano-Vinyals G, Yeager M, Welch R, Chanock S, Chatterjee N, Wacholder S, Samanic C, Tora M, Fernandez F, Real FX, Rothman N: NAT2 slow acetylation, GSTM1 null genotype, and risk of bladder cancer: Results from the Spanish Bladder Cancer Study and meta-analyses. Lancet. 2005;366:649–659.
- Zhong W, Sternberg PW: Genome-wide prediction of C. elegans genetic interactions. Science 2006;311:1481–1484.
- Engels EA, Schmid CH, Terrin N, Olkin I, Lau J: Heterogeneity and statistical significance in meta-analysis: an empirical study of 125 meta-analyses. Stat Med 2000;19:1707–1728.
- Greenland S: Tests for interaction in epidemiologic studies: A review and a study of power. Stat Med 1983;2:243–251.
- Fan C, Oh DS, Wessels L, Weigelt B, Nuyten DS, Nobel AB, van’t Veer LJ, Perou CM: Concordance among gene-expression-based predictors for breast cancer. N Engl J Med 2006;355:560–569.
- Pan Z, Trikalinos TA, Kavvoura FK, Lau J, Ioannidis JP: Local literature bias in genetic epidemiology: An empirical evaluation of the Chinese literature. PLoS Med 2005;2:e334.
- Calnan M, Smith GD, Sterne JA: The publication process itself was the major cause of publication bias in genetic epidemiology. J Clin Epidemiol 2006;59:1312–1318.
- Kavvoura FK, Liberopoulos G, Ioannidis JP: Selection in reported epidemiological risks: An empirical assessment. PLoS Med 2007;4:e79.
- Ioannidis JP: Journals should publish all ‘null’ results and should sparingly publish ‘positive’ results. Cancer Epidemiol Biomarkers Prev 2006;15:186.
- Evangelou E, Maraganore DM, Ioannidis JP: Meta-analysis in genome-wide association datasets: Strategies and application in Parkinson disease. PLoS ONE. 2007 Feb 7;2:e196.
Prof. John P.A. Ioannidis, Chairman
Department of Hygiene and Epidemiology
University of Ioannina School of Medicine
GR–45110 Ioannina (Greece)
Tel. +30 265 109 7807, Fax +30 265 109 7867, E-Mail email@example.com
Received: February 5, 2007
Accepted after revision: April 4, 2007
Published online: June 6, 2007
Number of Print Pages : 11
Number of Figures : 2, Number of Tables : 3, Number of References : 87
Human Heredity (International Journal of Human and Medical Genetics)
Vol. 64, No. 4, Year 2007 (Cover Date: July 2007)
Journal Editor: Devoto, M. (Philadelphia, Pa.)
ISSN: 0001–5652 (print), 1423–0062 (Online)
For additional information: http://www.karger.com/HHE
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher or, in the case of photocopying, direct payment of a specified fee to the Copyright Clearance Center.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in goverment regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.