Skip to main content
Top
Published in: European Journal of Epidemiology 1/2009

Open Access 01-01-2009 | Genetic epidemiology

Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE statement

Authors: Julian Little, Julian P. T. Higgins, John P. A. Ioannidis, David Moher, France Gagnon, Erik von Elm, Muin J. Khoury, Barbara Cohen, George Davey-Smith, Jeremy Grimshaw, Paul Scheet, Marta Gwinn, Robin E. Williamson, Guang Yong Zou, Kim Hutchings, Candice Y. Johnson, Valerie Tait, Miriam Wiens, Jean Golding, Cornelia van Duijn, John McLaughlin, Andrew Paterson, George Wells, Isabel Fortier, Matthew Freedman, Maja Zecevic, Richard King, Claire Infante-Rivard, Alex Stewart, Nick Birkett

Published in: European Journal of Epidemiology | Issue 1/2009

Login to get access

Abstract

Making sense of rapidly evolving evidence on genetic associations is crucial to making genuine advances in human genomics and the eventual integration of this information in the practice of medicine and public health. Assessment of the strengths and weaknesses of this evidence, and hence the ability to synthesize it, has been limited by inadequate reporting of results. The STrengthening the REporting of Genetic Association studies (STREGA) initiative builds on the Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement and provides additions to 12 of the 22 items on the STROBE checklist. The additions concern population stratification, genotyping errors, modeling haplotype variation, Hardy–Weinberg equilibrium, replication, selection of participants, rationale for choice of genes and variants, treatment effects in studying quantitative traits, statistical methods, relatedness, reporting of descriptive and outcome data, and the volume of data issues that are important to consider in genetic association studies. The STREGA recommendations do not prescribe or dictate how a genetic association study should be designed but seek to enhance the transparency of its reporting, regardless of choices made during design, conduct, or analysis.
Literature
1.
go back to reference Khoury MJ, Little J, Burke W. Human genome epidemiology: scope and strategies. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology. New York: Oxford University Press; 2004. p. 3–16. Khoury MJ, Little J, Burke W. Human genome epidemiology: scope and strategies. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology. New York: Oxford University Press; 2004. p. 3–16.
2.
go back to reference Genomics Health and Society Working Group. Genomics, health and society. Emerging issues for public policy. Ottawa: Government of Canada Policy Research Initiative; 2004. Genomics Health and Society Working Group. Genomics, health and society. Emerging issues for public policy. Ottawa: Government of Canada Policy Research Initiative; 2004.
3.
go back to reference Lin BK, Clyne M, Walsh M, Gomez O, Yu W, Gwinn M, et al. Tracking the epidemiology of human genes in the literature: the HuGE published literature database. Am J Epidemiol. 2006;164:1–4.PubMedCrossRef Lin BK, Clyne M, Walsh M, Gomez O, Yu W, Gwinn M, et al. Tracking the epidemiology of human genes in the literature: the HuGE published literature database. Am J Epidemiol. 2006;164:1–4.PubMedCrossRef
5.
go back to reference Lawrence RW, Evans DM, Cardon LR. Prospects and pitfalls in whole genome association studies. Philos Trans R Soc Lond B Biol Sci. 2005;360:1589–95.PubMedCrossRef Lawrence RW, Evans DM, Cardon LR. Prospects and pitfalls in whole genome association studies. Philos Trans R Soc Lond B Biol Sci. 2005;360:1589–95.PubMedCrossRef
6.
go back to reference Thomas DC. Are we ready for genome-wide association studies? Cancer Epidemiol Biomarkers Prev. 2006;15:595–8.PubMedCrossRef Thomas DC. Are we ready for genome-wide association studies? Cancer Epidemiol Biomarkers Prev. 2006;15:595–8.PubMedCrossRef
7.
go back to reference Khoury MJ, Little J, Gwinn M, Ioannidis JP. On the synthesis and interpretation of consistent but weak gene-disease associations in the era of genome-wide association studies. Int J Epidemiol. 2007;36:439–45.PubMedCrossRef Khoury MJ, Little J, Gwinn M, Ioannidis JP. On the synthesis and interpretation of consistent but weak gene-disease associations in the era of genome-wide association studies. Int J Epidemiol. 2007;36:439–45.PubMedCrossRef
8.
go back to reference Little J, Khoury MJ, Bradley L, Clyne M, Gwinn M, Lin B, et al. The human genome project is complete. How do we develop a handle for the pump? Am J Epidemiol. 2003;157:667–73.PubMedCrossRef Little J, Khoury MJ, Bradley L, Clyne M, Gwinn M, Lin B, et al. The human genome project is complete. How do we develop a handle for the pump? Am J Epidemiol. 2003;157:667–73.PubMedCrossRef
9.
go back to reference Ioannidis JP, Bernstein J, Boffetta P, Danesh J, Dolan S, Hartge P, et al. A network of investigator networks in human genome epidemiology. Am J Epidemiol. 2005;162:302–4.PubMedCrossRef Ioannidis JP, Bernstein J, Boffetta P, Danesh J, Dolan S, Hartge P, et al. A network of investigator networks in human genome epidemiology. Am J Epidemiol. 2005;162:302–4.PubMedCrossRef
10.
go back to reference Ioannidis JP, Gwinn M, Little J, Higgins JP, Bernstein JL, Boffetta P, et al. A road map for efficient and reliable human genome epidemiology. Nat Genet. 2006;38:3–5.PubMedCrossRef Ioannidis JP, Gwinn M, Little J, Higgins JP, Bernstein JL, Boffetta P, et al. A road map for efficient and reliable human genome epidemiology. Nat Genet. 2006;38:3–5.PubMedCrossRef
11.
go back to reference von Elm E, Egger M. The scandal of poor epidemiological research. BMJ. 2004;329:868–9.CrossRef von Elm E, Egger M. The scandal of poor epidemiological research. BMJ. 2004;329:868–9.CrossRef
12.
go back to reference Nature Genetics. Freely associating (editorial). Nat Genet 1999;22:1–2. Nature Genetics. Freely associating (editorial). Nat Genet 1999;22:1–2.
13.
14.
go back to reference Weiss S. Association studies in asthma genetics. Am J Respir Crit Care Med. 2001;164:2014–5.PubMed Weiss S. Association studies in asthma genetics. Am J Respir Crit Care Med. 2001;164:2014–5.PubMed
15.
go back to reference Weiss ST, Silverman EK, Palmer LJ. Case-control association studies in pharmacogenetics. Pharmacogenomic J. 2001;1:157–8. Weiss ST, Silverman EK, Palmer LJ. Case-control association studies in pharmacogenetics. Pharmacogenomic J. 2001;1:157–8.
16.
go back to reference Cooper DN, Nussbaum RL, Krawczak M. Proposed guidelines for papers describing DNA polymorphism–disease associations. Hum Genet. 2002;110:208. Cooper DN, Nussbaum RL, Krawczak M. Proposed guidelines for papers describing DNA polymorphism–disease associations. Hum Genet. 2002;110:208.
17.
go back to reference Hegele R. SNP judgements and freedom of association. Arterioscler Thromb Vasc Biol. 2002;22:1058–61.PubMedCrossRef Hegele R. SNP judgements and freedom of association. Arterioscler Thromb Vasc Biol. 2002;22:1058–61.PubMedCrossRef
18.
go back to reference Little J, Bradley L, Bray MS, Clyne M, Dorman J, Ellsworth DL, et al. Reporting, appraising, and integrating data on genotype prevalence and gene-disease associations. Am J Epidemiol. 2002;156:300–10.PubMed Little J, Bradley L, Bray MS, Clyne M, Dorman J, Ellsworth DL, et al. Reporting, appraising, and integrating data on genotype prevalence and gene-disease associations. Am J Epidemiol. 2002;156:300–10.PubMed
19.
go back to reference Romero R, Kuivaniemi H, Tromp G, Olson JM. The design, execution, and interpretation of genetic association studies to decipher complex diseases. Am J Obstet Gynecol. 2002;187:1299–312.PubMedCrossRef Romero R, Kuivaniemi H, Tromp G, Olson JM. The design, execution, and interpretation of genetic association studies to decipher complex diseases. Am J Obstet Gynecol. 2002;187:1299–312.PubMedCrossRef
20.
go back to reference Colhoun HM, McKeigue PM, Davey Smith G. Problems of reporting genetic associations with complex outcomes. Lancet. 2003;361:865–72.PubMedCrossRef Colhoun HM, McKeigue PM, Davey Smith G. Problems of reporting genetic associations with complex outcomes. Lancet. 2003;361:865–72.PubMedCrossRef
21.
go back to reference van Duijn CM, Porta M. Good prospects for genetic and molecular epidemiologic studies in the European journal of epidemiology. Eur J Epidemiol. 2003;18:285–6.PubMedCrossRef van Duijn CM, Porta M. Good prospects for genetic and molecular epidemiologic studies in the European journal of epidemiology. Eur J Epidemiol. 2003;18:285–6.PubMedCrossRef
22.
go back to reference Crossman D, Watkins H. Jesting Pilate, genetic case-control association studies, and heart. Heart. 2004;90:831–2.PubMedCrossRef Crossman D, Watkins H. Jesting Pilate, genetic case-control association studies, and heart. Heart. 2004;90:831–2.PubMedCrossRef
23.
go back to reference Huizinga TW, Pisetsky DS, Kimberly RP. Associations, populations, and the truth: recommendations for genetic association studies in arthritis & rheumatism. Arthritis Rheum. 2004;50:2066–71.PubMedCrossRef Huizinga TW, Pisetsky DS, Kimberly RP. Associations, populations, and the truth: recommendations for genetic association studies in arthritis & rheumatism. Arthritis Rheum. 2004;50:2066–71.PubMedCrossRef
24.
go back to reference Little J. Reporting and review of human genome epidemiology studies. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology: a scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press; 2004. p. 168–92. Little J. Reporting and review of human genome epidemiology studies. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology: a scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press; 2004. p. 168–92.
25.
go back to reference Rebbeck TR, Martinez ME, Sellers TA, Shields PG, Wild CP, Potter JD. Genetic variation and cancer: improving the environment for publication of association studies. Cancer Epidemiol Biomarkers Prev. 2004;13:1985–6.PubMed Rebbeck TR, Martinez ME, Sellers TA, Shields PG, Wild CP, Potter JD. Genetic variation and cancer: improving the environment for publication of association studies. Cancer Epidemiol Biomarkers Prev. 2004;13:1985–6.PubMed
26.
go back to reference Tan N, Mulley J, Berkovic S. Association studies in epilepsy: “the truth is out there”. Epilepsia. 2004;45:1429–42.PubMedCrossRef Tan N, Mulley J, Berkovic S. Association studies in epilepsy: “the truth is out there”. Epilepsia. 2004;45:1429–42.PubMedCrossRef
27.
go back to reference Anonymous. Framework for a fully powered risk engine. Nat Genet 2005;37:1153. Anonymous. Framework for a fully powered risk engine. Nat Genet 2005;37:1153.
28.
go back to reference Ehm MG, Nelson MR, Spurr NK. Guidelines for conducting and reporting whole genome/large-scale association studies. Hum Mol Genet. 2005;14:2485–8.PubMedCrossRef Ehm MG, Nelson MR, Spurr NK. Guidelines for conducting and reporting whole genome/large-scale association studies. Hum Mol Genet. 2005;14:2485–8.PubMedCrossRef
29.
go back to reference Freimer NB, Sabatti C. Guidelines for association studies in human molecular genetics. Hum Mol Genet. 2005;14:2481–3.PubMedCrossRef Freimer NB, Sabatti C. Guidelines for association studies in human molecular genetics. Hum Mol Genet. 2005;14:2481–3.PubMedCrossRef
30.
go back to reference Hattersley AT, McCarthy MI. What makes a good genetic association study? Lancet. 2005;366:1315–23.PubMedCrossRef Hattersley AT, McCarthy MI. What makes a good genetic association study? Lancet. 2005;366:1315–23.PubMedCrossRef
31.
go back to reference Manly K. Reliability of statistical associations between genes and disease. Immunogenetics. 2005;57:549–58.PubMedCrossRef Manly K. Reliability of statistical associations between genes and disease. Immunogenetics. 2005;57:549–58.PubMedCrossRef
32.
go back to reference Shen H, Liu Y, Liu P, Recker R, Deng H. Nonreplication in genetic studies of complex diseases—lessons learned from studies of osteoporosis and tentative remedies. J Bone Miner Res. 2005;20:365–76.PubMedCrossRef Shen H, Liu Y, Liu P, Recker R, Deng H. Nonreplication in genetic studies of complex diseases—lessons learned from studies of osteoporosis and tentative remedies. J Bone Miner Res. 2005;20:365–76.PubMedCrossRef
33.
go back to reference Vitali S, Randolph A. Assessing the quality of case-control association studies on the genetic basis of sepsis. Pediatr Crit Care Med. 2005;6:S74–7.PubMedCrossRef Vitali S, Randolph A. Assessing the quality of case-control association studies on the genetic basis of sepsis. Pediatr Crit Care Med. 2005;6:S74–7.PubMedCrossRef
34.
go back to reference Wedzicha JA, Hall IP. Publising genetic association studies in Thorax. Thorax. 2005;60:357.CrossRef Wedzicha JA, Hall IP. Publising genetic association studies in Thorax. Thorax. 2005;60:357.CrossRef
36.
go back to reference DeLisi LE, Faraone SV. When is a “positive” association truly a “positive” in psychiatric genetics? A commentary based on issues debated at the World Congress of Psychiatric Genetics, Boston, October 12–18, 2005. Am J Med Genet B Neuropsychiatr Genet. 2006;141:319–22. DeLisi LE, Faraone SV. When is a “positive” association truly a “positive” in psychiatric genetics? A commentary based on issues debated at the World Congress of Psychiatric Genetics, Boston, October 12–18, 2005. Am J Med Genet B Neuropsychiatr Genet. 2006;141:319–22.
37.
go back to reference Saito YA, Talley NJ, de Andrade M, Petersen GM. Case-control genetic association studies in gastrointestinal disease: review and recommendations. Am J Gastroenterol. 2006;101:1379–89.PubMedCrossRef Saito YA, Talley NJ, de Andrade M, Petersen GM. Case-control genetic association studies in gastrointestinal disease: review and recommendations. Am J Gastroenterol. 2006;101:1379–89.PubMedCrossRef
38.
go back to reference Uhlig K, Menon V, Schmid CH. Recommendations for reporting of clinical research studies. Am J Kidney Dis. 2007;49:3–7.PubMedCrossRef Uhlig K, Menon V, Schmid CH. Recommendations for reporting of clinical research studies. Am J Kidney Dis. 2007;49:3–7.PubMedCrossRef
39.
go back to reference NCI-NHGRI Working Group on Replication in Association Studies, Chanock SJ, Manolio T, Boehnke M, Boerwinkle E, Hunter DJ, et al. Replicating genotype–phenotype associations. Nature. 2007;447:655–60.PubMedCrossRef NCI-NHGRI Working Group on Replication in Association Studies, Chanock SJ, Manolio T, Boehnke M, Boerwinkle E, Hunter DJ, et al. Replicating genotype–phenotype associations. Nature. 2007;447:655–60.PubMedCrossRef
40.
go back to reference Begg CB. Reflections on publication criteria for genetic association studies. Cancer Epidemiol Biomarkers Prev. 2005;14:1364–5.PubMedCrossRef Begg CB. Reflections on publication criteria for genetic association studies. Cancer Epidemiol Biomarkers Prev. 2005;14:1364–5.PubMedCrossRef
41.
go back to reference Byrnes G, Gurrin L, Dowty J, Hopper JL. Publication policy or publication bias? Cancer Epidemiol Biomarkers Prev. 2005;14:1363.PubMedCrossRef Byrnes G, Gurrin L, Dowty J, Hopper JL. Publication policy or publication bias? Cancer Epidemiol Biomarkers Prev. 2005;14:1363.PubMedCrossRef
42.
go back to reference Pharoah PD, Dunning AM, Ponder BA, Easton DF. The reliable identification of disease–gene associations. Cancer Epidemiol Biomarkers Prev. 2005;14:1362.PubMedCrossRef Pharoah PD, Dunning AM, Ponder BA, Easton DF. The reliable identification of disease–gene associations. Cancer Epidemiol Biomarkers Prev. 2005;14:1362.PubMedCrossRef
43.
go back to reference Wacholder S. Publication environment and broad investigation of the genome. Cancer Epidemiol Biomarkers Prev. 2005;14:1361.PubMedCrossRef Wacholder S. Publication environment and broad investigation of the genome. Cancer Epidemiol Biomarkers Prev. 2005;14:1361.PubMedCrossRef
44.
go back to reference Whittemore AS. Genetic association studies: time for a new paradigm? Cancer Epidemiol Biomarkers Prev. 2005;14:1359–60.PubMedCrossRef Whittemore AS. Genetic association studies: time for a new paradigm? Cancer Epidemiol Biomarkers Prev. 2005;14:1359–60.PubMedCrossRef
45.
go back to reference Bogardus ST Jr, Concato J, Feinstein AR. Clinical epidemiological quality in molecular genetic research. The need for methodological standards. JAMA. 1999;281:1919–26.PubMedCrossRef Bogardus ST Jr, Concato J, Feinstein AR. Clinical epidemiological quality in molecular genetic research. The need for methodological standards. JAMA. 1999;281:1919–26.PubMedCrossRef
46.
go back to reference Peters DL, Barber RC, Flood EM, Garner HR, O’Keefe GE. Methodologic quality and genotyping reproducibility in studies of tumor necrosis factor -308 G–> A. A single nucleotide polymorphism and bacterial sepsis: implications for studies of complex traits. Crit Care Med. 2003;31:1691–6.PubMedCrossRef Peters DL, Barber RC, Flood EM, Garner HR, O’Keefe GE. Methodologic quality and genotyping reproducibility in studies of tumor necrosis factor -308 G–> A. A single nucleotide polymorphism and bacterial sepsis: implications for studies of complex traits. Crit Care Med. 2003;31:1691–6.PubMedCrossRef
47.
go back to reference Clark MF, Baudouin SV. A systematic review of the quality of genetic association studies in human sepsis. Intensive Care Med. 2006;32:1706–12.PubMedCrossRef Clark MF, Baudouin SV. A systematic review of the quality of genetic association studies in human sepsis. Intensive Care Med. 2006;32:1706–12.PubMedCrossRef
48.
go back to reference Lee W, Bindman J, Ford T, Glozier N, Moran P, Stewart R, et al. Bias in psychiatric case-control studies: literature survey. Br J Psychiatry. 2007;190:204–9.PubMedCrossRef Lee W, Bindman J, Ford T, Glozier N, Moran P, Stewart R, et al. Bias in psychiatric case-control studies: literature survey. Br J Psychiatry. 2007;190:204–9.PubMedCrossRef
49.
go back to reference Yesupriya A, Evangelou E, Kavvoura FK, Patsopoulos NA, Clyne M, Walsh M, et al. Reporting of human genome epidemiology (HuGE) association studies: an empirical assessment. BMC Med Res Methodol. 2008;8:31.PubMedCrossRef Yesupriya A, Evangelou E, Kavvoura FK, Patsopoulos NA, Clyne M, Walsh M, et al. Reporting of human genome epidemiology (HuGE) association studies: an empirical assessment. BMC Med Res Methodol. 2008;8:31.PubMedCrossRef
50.
go back to reference Reid MC, Lachs MS, Feinstein AR. Use of methodological standards in diagnostic test research. Getting better but still not good. JAMA. 1995;274:645–51.PubMedCrossRef Reid MC, Lachs MS, Feinstein AR. Use of methodological standards in diagnostic test research. Getting better but still not good. JAMA. 1995;274:645–51.PubMedCrossRef
51.
go back to reference Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat Genet. 2001;29:356–71.CrossRef Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, et al. Minimum information about a microarray experiment (MIAME)—toward standards for microarray data. Nat Genet. 2001;29:356–71.CrossRef
52.
go back to reference Pocock SJ, Collier TJ, Dandreo KJ, de Stavola BL, Goldman MB, Kalish LA, et al. Issues in the reporting of epidemiological studies: a survey of recent practice. BMJ. 2004;329:883.PubMedCrossRef Pocock SJ, Collier TJ, Dandreo KJ, de Stavola BL, Goldman MB, Kalish LA, et al. Issues in the reporting of epidemiological studies: a survey of recent practice. BMJ. 2004;329:883.PubMedCrossRef
53.
go back to reference Altman D, Moher D. Developing guidelines for reporting healthcare research: scientific rationale and procedures. Med Clin (Barc). 2005;125:8–13.CrossRef Altman D, Moher D. Developing guidelines for reporting healthcare research: scientific rationale and procedures. Med Clin (Barc). 2005;125:8–13.CrossRef
55.
go back to reference von Elm E, Altman DG, Egger M, Pocock SJ, Gotzsche PC, Vandenbroucke JP, et al. The strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies. PLoS Med. 2007;4:e296.CrossRef von Elm E, Altman DG, Egger M, Pocock SJ, Gotzsche PC, Vandenbroucke JP, et al. The strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies. PLoS Med. 2007;4:e296.CrossRef
56.
go back to reference Vandenbroucke JP, von Elm E, Altman DG, Gotzsche PC, Mulrow CD, Pocock SJ, et al. Strengthening the reporting of observational studies in epidemiology (STROBE): explanation and elaboration. Ann Intern Med. 2007;147:W163–94.PubMed Vandenbroucke JP, von Elm E, Altman DG, Gotzsche PC, Mulrow CD, Pocock SJ, et al. Strengthening the reporting of observational studies in epidemiology (STROBE): explanation and elaboration. Ann Intern Med. 2007;147:W163–94.PubMed
58.
go back to reference Higgins JP, Little J, Ioannidis JP, Bray MS, Manolio TA, Smeeth L, et al. Turning the pump handle: evolving methods for integrating the evidence on gene–disease association. Am J Epidemiol. 2007;166:863–6.PubMedCrossRef Higgins JP, Little J, Ioannidis JP, Bray MS, Manolio TA, Smeeth L, et al. Turning the pump handle: evolving methods for integrating the evidence on gene–disease association. Am J Epidemiol. 2007;166:863–6.PubMedCrossRef
59.
go back to reference Altman DG, Schulz KF, Moher D, Egger M, Davidoff F, Elbourne D, et al. The revised CONSORT statement for reporting randomized trials: explanation and elaboration. Ann Intern Med. 2001;134:663–94.PubMed Altman DG, Schulz KF, Moher D, Egger M, Davidoff F, Elbourne D, et al. The revised CONSORT statement for reporting randomized trials: explanation and elaboration. Ann Intern Med. 2001;134:663–94.PubMed
60.
go back to reference Moher D, Schultz KF, Altman D. The CONSORT statement: revised recommendations for improving the quality of reports of parallel-group randomized trials. JAMA. 2001;285:1987–91.PubMedCrossRef Moher D, Schultz KF, Altman D. The CONSORT statement: revised recommendations for improving the quality of reports of parallel-group randomized trials. JAMA. 2001;285:1987–91.PubMedCrossRef
61.
go back to reference Pompanon F, Bonin A, Bellemain E, Taberlet P. Genotyping errors: causes, consequences and solutions. Nat Rev Genet. 2005;6:847–59.PubMedCrossRef Pompanon F, Bonin A, Bellemain E, Taberlet P. Genotyping errors: causes, consequences and solutions. Nat Rev Genet. 2005;6:847–59.PubMedCrossRef
62.
go back to reference Akey JM, Zhang K, Xiong M, Doris P, Jin L. The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. Am J Hum Genet. 2001;68:1447–56.PubMedCrossRef Akey JM, Zhang K, Xiong M, Doris P, Jin L. The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. Am J Hum Genet. 2001;68:1447–56.PubMedCrossRef
63.
go back to reference Dequeker E, Ramsden S, Grody WW, Stenzel TT, Barton DE. Quality control in molecular genetic testing. Nat Rev Genet. 2001;2:717–23.PubMedCrossRef Dequeker E, Ramsden S, Grody WW, Stenzel TT, Barton DE. Quality control in molecular genetic testing. Nat Rev Genet. 2001;2:717–23.PubMedCrossRef
64.
go back to reference Mitchell AA, Cutler DJ, Chakravarti A. Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test. Am J Hum Genet. 2003;72:598–610.PubMedCrossRef Mitchell AA, Cutler DJ, Chakravarti A. Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/disequilibrium test. Am J Hum Genet. 2003;72:598–610.PubMedCrossRef
65.
go back to reference Rothman N, Stewart WF, Caporaso NE, Hayes RB. Misclassification of genetic susceptibility biomarkers: implications for case-control studies and cross-population comparisons. Cancer Epidemiol Biomarkers Prev. 1993;2:299–303.PubMed Rothman N, Stewart WF, Caporaso NE, Hayes RB. Misclassification of genetic susceptibility biomarkers: implications for case-control studies and cross-population comparisons. Cancer Epidemiol Biomarkers Prev. 1993;2:299–303.PubMed
66.
go back to reference Garcia-Closas M, Wacholder S, Caporaso N, Rothman N. Inference issues in cohort and case-control studies of genetic effects and gene-environment interactions. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology: a scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press; 2004. p. 127–44. Garcia-Closas M, Wacholder S, Caporaso N, Rothman N. Inference issues in cohort and case-control studies of genetic effects and gene-environment interactions. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology: a scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press; 2004. p. 127–44.
67.
go back to reference Wong MY, Day NE, Luan JA, Wareham NJ. Estimation of magnitude in gene–environment interactions in the presence of measurement error. Stat Med. 2004;23:987–98.PubMedCrossRef Wong MY, Day NE, Luan JA, Wareham NJ. Estimation of magnitude in gene–environment interactions in the presence of measurement error. Stat Med. 2004;23:987–98.PubMedCrossRef
68.
go back to reference Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, et al. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet. 2005;37:1243–6.PubMedCrossRef Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, et al. Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet. 2005;37:1243–6.PubMedCrossRef
69.
go back to reference Knowler WC, Williams RC, Pettitt DJ, Steinberg AG. Gm3;5, 13, 14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. Am J Human Genet. 1988;43:520–6. Knowler WC, Williams RC, Pettitt DJ, Steinberg AG. Gm3;5, 13, 14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. Am J Human Genet. 1988;43:520–6.
70.
go back to reference Gelernter J, Goldman D, Risch N. The A1 allele at the D2 dopamine receptor gene and alcoholism: a reappraisal. JAMA. 1993;269:1673–7.PubMedCrossRef Gelernter J, Goldman D, Risch N. The A1 allele at the D2 dopamine receptor gene and alcoholism: a reappraisal. JAMA. 1993;269:1673–7.PubMedCrossRef
71.
go back to reference Kittles RA, Chen W, Panguluri RK, Ahaghotu C, Jackson A, Adebamowo CA, et al. CYP3A4-V and prostate cancer in African Americans: causal or confounding association because of population stratification? Hum Genet. 2002;110:553–60.PubMedCrossRef Kittles RA, Chen W, Panguluri RK, Ahaghotu C, Jackson A, Adebamowo CA, et al. CYP3A4-V and prostate cancer in African Americans: causal or confounding association because of population stratification? Hum Genet. 2002;110:553–60.PubMedCrossRef
72.
go back to reference Thomas DC, Witte JS. Point: population stratification: a problem for case control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev. 2002;11:505–12.PubMed Thomas DC, Witte JS. Point: population stratification: a problem for case control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev. 2002;11:505–12.PubMed
73.
go back to reference Wacholder S, Chatterjee N, Hartge P. Joint effects of genes and environment distorted by selection biases: implications for hospital-based case-control studies. Cancer Epidemiol Biomarkers Prev. 2002;11:885–9.PubMed Wacholder S, Chatterjee N, Hartge P. Joint effects of genes and environment distorted by selection biases: implications for hospital-based case-control studies. Cancer Epidemiol Biomarkers Prev. 2002;11:885–9.PubMed
74.
go back to reference Cardon LR, Palmer LJ. Population stratification and spurious allelic association. Lancet. 2003;361:598–604.PubMedCrossRef Cardon LR, Palmer LJ. Population stratification and spurious allelic association. Lancet. 2003;361:598–604.PubMedCrossRef
75.
go back to reference Wacholder S, Rothman N, Caporaso N. Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. J Natl Cancer Inst. 2000;92:1151–8.PubMedCrossRef Wacholder S, Rothman N, Caporaso N. Population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. J Natl Cancer Inst. 2000;92:1151–8.PubMedCrossRef
76.
go back to reference Ardlie KG, Lunetta KL, Seielstad M. Testing for population subdivision and association in four case-control studies. Am J Human Genet. 2002;71:304–11.CrossRef Ardlie KG, Lunetta KL, Seielstad M. Testing for population subdivision and association in four case-control studies. Am J Human Genet. 2002;71:304–11.CrossRef
77.
go back to reference Edland SD, Slager S, Farrer M. Genetic association studies in Alzheimer’s disease research: challenges and opportunities. Stat Med. 2004;23:169–78.PubMedCrossRef Edland SD, Slager S, Farrer M. Genetic association studies in Alzheimer’s disease research: challenges and opportunities. Stat Med. 2004;23:169–78.PubMedCrossRef
78.
go back to reference Millikan RC. Re: population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. J Natl Cancer Inst. 2001;93:156–7.PubMedCrossRef Millikan RC. Re: population stratification in epidemiologic studies of common genetic variants and cancer: quantification of bias. J Natl Cancer Inst. 2001;93:156–7.PubMedCrossRef
79.
go back to reference Wang Y, Localio R, Rebbeck TR. Evaluating bias due to population stratification in case-control association studies of admixed populations. Genet Epidemiol. 2004;27:14–20.PubMedCrossRef Wang Y, Localio R, Rebbeck TR. Evaluating bias due to population stratification in case-control association studies of admixed populations. Genet Epidemiol. 2004;27:14–20.PubMedCrossRef
80.
go back to reference Ioannidis JP, Ntzani EE, Trikalinos TA. ‘Racial’ differences in genetic effects for complex diseases. Nat Genet. 2004;36:1312–8.PubMedCrossRef Ioannidis JP, Ntzani EE, Trikalinos TA. ‘Racial’ differences in genetic effects for complex diseases. Nat Genet. 2004;36:1312–8.PubMedCrossRef
81.
go back to reference Marchini J, Cardon LR, Phillips MS, Donnelly P. The effects of human population structure on large genetic association studies. Nat Genet. 2004;36:512–7.PubMedCrossRef Marchini J, Cardon LR, Phillips MS, Donnelly P. The effects of human population structure on large genetic association studies. Nat Genet. 2004;36:512–7.PubMedCrossRef
82.
go back to reference Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, Patterson N, et al. Assessing the impact of population stratification on genetic association studies. Nat Genet. 2004;36:388–93.PubMedCrossRef Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, Patterson N, et al. Assessing the impact of population stratification on genetic association studies. Nat Genet. 2004;36:388–93.PubMedCrossRef
83.
go back to reference Khlat M, Cazes MH, Genin E, Guiguet M. Robustness of case-control studies of genetic factors to population stratification: magnitude of bias and type I error. Cancer Epidemiol Biomarkers Prev. 2004;13:1660–4.PubMed Khlat M, Cazes MH, Genin E, Guiguet M. Robustness of case-control studies of genetic factors to population stratification: magnitude of bias and type I error. Cancer Epidemiol Biomarkers Prev. 2004;13:1660–4.PubMed
84.
go back to reference Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet. 2006;7:781–91.PubMedCrossRef Balding DJ. A tutorial on statistical methods for population association studies. Nat Rev Genet. 2006;7:781–91.PubMedCrossRef
85.
go back to reference Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3, 000 shared controls. Nature. 2007;447:661–78.CrossRef Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3, 000 shared controls. Nature. 2007;447:661–78.CrossRef
86.
go back to reference Ioannidis JP. Non-replication and inconsistency in the genome-wide association setting. Hum Hered. 2007;64:203–13.PubMedCrossRef Ioannidis JP. Non-replication and inconsistency in the genome-wide association setting. Hum Hered. 2007;64:203–13.PubMedCrossRef
87.
go back to reference Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA, et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn’s disease susceptibility. Nat Genet. 2007;39:830–2.PubMedCrossRef Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, Fisher SA, et al. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn’s disease susceptibility. Nat Genet. 2007;39:830–2.PubMedCrossRef
88.
go back to reference Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, et al. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet. 2007;39:857–64.PubMedCrossRef Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, Plagnol V, et al. Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet. 2007;39:857–64.PubMedCrossRef
89.
go back to reference Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, Lango H, et al. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science. 2007;316:1336–41.PubMedCrossRef Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, Lango H, et al. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science. 2007;316:1336–41.PubMedCrossRef
90.
go back to reference Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research, Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PI, et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science. 2007;316:1331–6.PubMedCrossRef Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical Research, Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker PI, et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science. 2007;316:1331–6.PubMedCrossRef
91.
go back to reference Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science. 2007;316:1341–5.PubMedCrossRef Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL, et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science. 2007;316:1341–5.PubMedCrossRef
92.
go back to reference Helgadottir A, Thorleifsson G, Manolescu A, Gretarsdottir S, Blondal T, Jonasdottir A, et al. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science. 2007;316:1491–3.PubMedCrossRef Helgadottir A, Thorleifsson G, Manolescu A, Gretarsdottir S, Blondal T, Jonasdottir A, et al. A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science. 2007;316:1491–3.PubMedCrossRef
93.
go back to reference McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, et al. A common allele on chromosome 9 associated with coronary heart disease. Science. 2007;316:1488–91.PubMedCrossRef McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, et al. A common allele on chromosome 9 associated with coronary heart disease. Science. 2007;316:1488–91.PubMedCrossRef
94.
go back to reference Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007;447:1087–93.PubMedCrossRef Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, Ballinger DG, et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature. 2007;447:1087–93.PubMedCrossRef
95.
go back to reference Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet. 2007;39:870–4.PubMedCrossRef Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, Hankinson SE, et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet. 2007;39:870–4.PubMedCrossRef
96.
go back to reference Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson SA, et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet. 2007;39:865–9.PubMedCrossRef Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, Gudjonsson SA, et al. Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet. 2007;39:865–9.PubMedCrossRef
97.
go back to reference Gudmundsson J, Sulem P, Steinthorsdottir V, Bergthorsson JT, Thorleifsson G, Manolescu A, et al. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet. 2007;39:977–83.PubMedCrossRef Gudmundsson J, Sulem P, Steinthorsdottir V, Bergthorsson JT, Thorleifsson G, Manolescu A, et al. Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet. 2007;39:977–83.PubMedCrossRef
98.
go back to reference Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, Waliszewska A, et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet. 2007;39:638–44.PubMedCrossRef Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, Waliszewska A, et al. Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet. 2007;39:638–44.PubMedCrossRef
99.
go back to reference Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet. 2007;39:645–9.PubMedCrossRef Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, Wacholder S, et al. Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet. 2007;39:645–9.PubMedCrossRef
100.
go back to reference Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, Farrington SM, et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet. 2007;39:989–94.PubMedCrossRef Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, Farrington SM, et al. Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet. 2007;39:989–94.PubMedCrossRef
101.
go back to reference Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, Spain S, et al. A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet. 2007;39:984–8.PubMedCrossRef Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, Spain S, et al. A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet. 2007;39:984–8.PubMedCrossRef
102.
go back to reference Haiman CA, Le Marchand L, Yamamoto J, Stram DO, Sheng X, Kolonel LN, et al. A common genetic risk factor for colorectal and prostate cancer. Nat Genet. 2007;39:954–6.PubMedCrossRef Haiman CA, Le Marchand L, Yamamoto J, Stram DO, Sheng X, Kolonel LN, et al. A common genetic risk factor for colorectal and prostate cancer. Nat Genet. 2007;39:954–6.PubMedCrossRef
103.
go back to reference Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A, et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet. 2007;39:596–604.PubMedCrossRef Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A, et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet. 2007;39:596–604.PubMedCrossRef
104.
go back to reference Libioulle C, Louis E, Hansoul S, Sandor C, Farnir F, Franchimont D, et al. Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet. 2007;3:e58.PubMedCrossRef Libioulle C, Louis E, Hansoul S, Sandor C, Farnir F, Franchimont D, et al. Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet. 2007;3:e58.PubMedCrossRef
105.
go back to reference Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, Daly MJ, et al. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science. 2006;314:1461–3.PubMedCrossRef Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, Daly MJ, et al. A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science. 2006;314:1461–3.PubMedCrossRef
106.
go back to reference Zhao LP, Li SS, Khalid N. A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet. 2003;72:1231–50.PubMedCrossRef Zhao LP, Li SS, Khalid N. A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet. 2003;72:1231–50.PubMedCrossRef
107.
go back to reference International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007;449:851–61.PubMedCrossRef International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007;449:851–61.PubMedCrossRef
108.
go back to reference Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 2001;68:978–89.PubMedCrossRef Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 2001;68:978–89.PubMedCrossRef
109.
go back to reference Qin ZS, Niu T, Liu JS. Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet. 2002;71:1242–7.PubMedCrossRef Qin ZS, Niu T, Liu JS. Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet. 2002;71:1242–7.PubMedCrossRef
110.
go back to reference Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006;78:629–44.PubMedCrossRef Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet. 2006;78:629–44.PubMedCrossRef
111.
go back to reference Browning SR. Missing data imputation and haplotype phase inference for genome-wide association studies. Hum Genet. 2008;124:439–50.PubMedCrossRef Browning SR. Missing data imputation and haplotype phase inference for genome-wide association studies. Hum Genet. 2008;124:439–50.PubMedCrossRef
112.
go back to reference Huang Q, Fu YX, Boerwinkle E. Comparison of strategies for selecting single nucleotide polymorphisms for case/control association studies. Hum Genet. 2003;113:253–7.PubMedCrossRef Huang Q, Fu YX, Boerwinkle E. Comparison of strategies for selecting single nucleotide polymorphisms for case/control association studies. Hum Genet. 2003;113:253–7.PubMedCrossRef
113.
go back to reference Kamatani N, Sekine A, Kitamoto T, Iida A, Saito S, Kogame A, et al. Large-scale single-nucleotide polymorphism (SNP) and haplotype analyses, using dense SNP maps, of 199 drug-related genes in 752 subjects: the analysis of the association between uncommon SNPs within haplotype blocks and the haplotypes constructed with haplotype-tagging SNPs. Am J Hum Genet. 2004;75:190–203.PubMedCrossRef Kamatani N, Sekine A, Kitamoto T, Iida A, Saito S, Kogame A, et al. Large-scale single-nucleotide polymorphism (SNP) and haplotype analyses, using dense SNP maps, of 199 drug-related genes in 752 subjects: the analysis of the association between uncommon SNPs within haplotype blocks and the haplotypes constructed with haplotype-tagging SNPs. Am J Hum Genet. 2004;75:190–203.PubMedCrossRef
114.
go back to reference Zhang W, Collins A, Morton NE. Does haplotype diversity predict power for association mapping of disease susceptibility? Hum Genet. 2004;115:157–64.PubMedCrossRef Zhang W, Collins A, Morton NE. Does haplotype diversity predict power for association mapping of disease susceptibility? Hum Genet. 2004;115:157–64.PubMedCrossRef
115.
go back to reference Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. Selecting a maximally informative set of single-nucleotide polymorphisms for association analysis using linkage disequilibrium. Am J Hum Genet. 2004;74:106–20.PubMedCrossRef Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. Selecting a maximally informative set of single-nucleotide polymorphisms for association analysis using linkage disequilibrium. Am J Hum Genet. 2004;74:106–20.PubMedCrossRef
116.
go back to reference a Vlieg A, Sandkuijl LA, Rosendaal FR, Bertina RM, Vos HL. Candidate gene approach in association studies: would the factor V Leiden mutation have been found by this approach? Eur J Hum Genet. 2004;12:478–82.CrossRef a Vlieg A, Sandkuijl LA, Rosendaal FR, Bertina RM, Vos HL. Candidate gene approach in association studies: would the factor V Leiden mutation have been found by this approach? Eur J Hum Genet. 2004;12:478–82.CrossRef
117.
go back to reference Greenspan G, Geiger D. Model-based inference of haplotype block variation. J Comput Biol. 2004;11:493–504.PubMedCrossRef Greenspan G, Geiger D. Model-based inference of haplotype block variation. J Comput Biol. 2004;11:493–504.PubMedCrossRef
118.
go back to reference Kimmel G, Shamir R. GERBIL: genotype resolution and block identification using likelihood. ProcNatl Acad Sci USA. 2005;102:158–62.CrossRef Kimmel G, Shamir R. GERBIL: genotype resolution and block identification using likelihood. ProcNatl Acad Sci USA. 2005;102:158–62.CrossRef
119.
go back to reference Cardon LR, Abecasis GR. Using haplotype blocks to map human complex triat loci. Trends Genet. 2003;19:135–40.PubMedCrossRef Cardon LR, Abecasis GR. Using haplotype blocks to map human complex triat loci. Trends Genet. 2003;19:135–40.PubMedCrossRef
120.
go back to reference Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, et al. The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet. 2004;13:577–88.PubMedCrossRef Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, Ghori J, et al. The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet. 2004;13:577–88.PubMedCrossRef
121.
go back to reference Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 2007;3:e114.PubMedCrossRef Servin B, Stephens M. Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet. 2007;3:e114.PubMedCrossRef
122.
go back to reference Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007;39:906–13.PubMedCrossRef Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 2007;39:906–13.PubMedCrossRef
124.
go back to reference Weinberg W. Über den Nachweis der Vererbung beim Menschen. Jahrhefte des Vereines für Vaterländische Naturkunde in Württemberg. 1908;64:368–82. Weinberg W. Über den Nachweis der Vererbung beim Menschen. Jahrhefte des Vereines für Vaterländische Naturkunde in Württemberg. 1908;64:368–82.
125.
go back to reference Minelli C, Thompson JR, Abrams KR, Thakkinstian A, Attia J. How should we use information about HWE in the meta-analyses of genetic association studies? Int J Epidemiol. 2008;37:136–46.PubMedCrossRef Minelli C, Thompson JR, Abrams KR, Thakkinstian A, Attia J. How should we use information about HWE in the meta-analyses of genetic association studies? Int J Epidemiol. 2008;37:136–46.PubMedCrossRef
126.
go back to reference Xu J, Turner A, Little J, Bleecker ER, Meyers DA. Positive results in association studies are associated with departure from Hardy–Weinberg equilibrium: hint for genotyping error? Hum Genet. 2002;111:573–4.PubMedCrossRef Xu J, Turner A, Little J, Bleecker ER, Meyers DA. Positive results in association studies are associated with departure from Hardy–Weinberg equilibrium: hint for genotyping error? Hum Genet. 2002;111:573–4.PubMedCrossRef
127.
go back to reference Hosking L, Lumsden S, Lewis K, Yeo A, McCarthy L, Bansal A, et al. Detection of genotyping errors by Hardy–Weinberg equilibrium testing. Eur J Hum Genet. 2004;12:395–9.PubMedCrossRef Hosking L, Lumsden S, Lewis K, Yeo A, McCarthy L, Bansal A, et al. Detection of genotyping errors by Hardy–Weinberg equilibrium testing. Eur J Hum Genet. 2004;12:395–9.PubMedCrossRef
128.
go back to reference 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;13:840–8.PubMedCrossRef 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;13:840–8.PubMedCrossRef
129.
go back to reference Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA. 2008;299:1335–44.PubMedCrossRef Pearson TA, Manolio TA. How to interpret a genome-wide association study. JAMA. 2008;299:1335–44.PubMedCrossRef
130.
go back to reference McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008;9:356–69.PubMedCrossRef McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008;9:356–69.PubMedCrossRef
131.
go back to reference Zou GY, Donner A. The merits of testing Hardy–Weinberg equilibrium in the analysis of unmatched case-control data: a cautionary note. Ann Hum Genet. 2006;70:923–33.PubMedCrossRef Zou GY, Donner A. The merits of testing Hardy–Weinberg equilibrium in the analysis of unmatched case-control data: a cautionary note. Ann Hum Genet. 2006;70:923–33.PubMedCrossRef
132.
go back to reference Shoemaker J, Painter I, Weir BS. A Bayesian characterization of Hardy–Weinberg disequilibrium. Genetics. 1998;149:2079–88.PubMed Shoemaker J, Painter I, Weir BS. A Bayesian characterization of Hardy–Weinberg disequilibrium. Genetics. 1998;149:2079–88.PubMed
133.
go back to reference Ayres KL, Balding DJ. Measuring departures from Hardy–Weinberg: a Markov chain Monte Carlo method for estimating the inbreeding coefficient. Heredity. 1998;80(Pt 6):769–77.PubMedCrossRef Ayres KL, Balding DJ. Measuring departures from Hardy–Weinberg: a Markov chain Monte Carlo method for estimating the inbreeding coefficient. Heredity. 1998;80(Pt 6):769–77.PubMedCrossRef
134.
go back to reference Trikalinos TA, Salanti G, Khoury MJ, Ioannidis JP. Impact of violations and deviations in Hardy–Weinberg equilibrium on postulated gene-disease associations. Am J Epidemiol. 2006;163:300–9.PubMedCrossRef Trikalinos TA, Salanti G, Khoury MJ, Ioannidis JP. Impact of violations and deviations in Hardy–Weinberg equilibrium on postulated gene-disease associations. Am J Epidemiol. 2006;163:300–9.PubMedCrossRef
135.
go back to reference Davidoff F, Batalden P, Stevens D, Ogrinc G, Mooney S. SQUIRE Development Group. Publication guidelines for improvement studies in health care: evolution of the SQUIRE project. Ann Intern Med. 2008;149:670–6.PubMed Davidoff F, Batalden P, Stevens D, Ogrinc G, Mooney S. SQUIRE Development Group. Publication guidelines for improvement studies in health care: evolution of the SQUIRE project. Ann Intern Med. 2008;149:670–6.PubMed
136.
go back to reference Steinberg K, Gallagher M. Assessing genotypes in human genome epidemiology studies. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology: a scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press; 2004. p. 79–91. Steinberg K, Gallagher M. Assessing genotypes in human genome epidemiology studies. In: Khoury MJ, Little J, Burke W, editors. Human genome epidemiology: a scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press; 2004. p. 79–91.
137.
go back to reference Plagnol V, Cooper JD, Todd JA, Clayton DG. A method to address differential bias in genotyping in large-scale association studies. PLoS Genet. 2007;3:e74.PubMedCrossRef Plagnol V, Cooper JD, Todd JA, Clayton DG. A method to address differential bias in genotyping in large-scale association studies. PLoS Genet. 2007;3:e74.PubMedCrossRef
138.
go back to reference Winker MA. Race and ethnicity in medical research: requirements meet reality. J Law Med Ethics. 2006;34:520,5,480.CrossRef Winker MA. Race and ethnicity in medical research: requirements meet reality. J Law Med Ethics. 2006;34:520,5,480.CrossRef
139.
go back to reference Scuteri A, Sanna S, Chen WM, Uda M, Albai G, Strait J, et al. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet. 2007;3:e115.PubMedCrossRef Scuteri A, Sanna S, Chen WM, Uda M, Albai G, Strait J, et al. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet. 2007;3:e115.PubMedCrossRef
140.
go back to reference Chan AW, Hrobjartsson A, Haahr MT, Gotzsche PC, Altman DG. Empirical evidence for selective reporting of outcomes in randomized trials: comparison of protocols to published articles. JAMA. 2004;291:2457–65.PubMedCrossRef Chan AW, Hrobjartsson A, Haahr MT, Gotzsche PC, Altman DG. Empirical evidence for selective reporting of outcomes in randomized trials: comparison of protocols to published articles. JAMA. 2004;291:2457–65.PubMedCrossRef
141.
go back to reference Chan AW, Krleza-Jeric K, Schmid I, Altman DG. Outcome reporting bias in randomized trials funded by the Canadian Institutes of Health Research. CMAJ. 2004;171:735–40.PubMed Chan AW, Krleza-Jeric K, Schmid I, Altman DG. Outcome reporting bias in randomized trials funded by the Canadian Institutes of Health Research. CMAJ. 2004;171:735–40.PubMed
142.
go back to reference Chan AW, Altman DG. Identifying outcome reporting bias in randomised trials on PubMed: review of publications and survey of authors. BMJ. 2005;330:753.PubMedCrossRef Chan AW, Altman DG. Identifying outcome reporting bias in randomised trials on PubMed: review of publications and survey of authors. BMJ. 2005;330:753.PubMedCrossRef
143.
go back to reference Contopoulos-Ioannidis DG, Alexiou GA, Gouvias TC, Ioannidis JP. An empirical evaluation of multifarious outcomes in pharmacogenetics: beta-2 adrenoceptor gene polymorphisms in asthma treatment. Pharmacogenet Genomics. 2006;16:705–11.PubMedCrossRef Contopoulos-Ioannidis DG, Alexiou GA, Gouvias TC, Ioannidis JP. An empirical evaluation of multifarious outcomes in pharmacogenetics: beta-2 adrenoceptor gene polymorphisms in asthma treatment. Pharmacogenet Genomics. 2006;16:705–11.PubMedCrossRef
144.
go back to reference Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S. Guidelines for human gene nomenclature. Genomics. 2002;79:464–70.PubMedCrossRef Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S. Guidelines for human gene nomenclature. Genomics. 2002;79:464–70.PubMedCrossRef
145.
go back to reference Wain HM, Lush M, Ducluzeau F, Povey S. Genew: the human gene nomenclature database. Nucleic Acids Res. 2002;30:169–71.PubMedCrossRef Wain HM, Lush M, Ducluzeau F, Povey S. Genew: the human gene nomenclature database. Nucleic Acids Res. 2002;30:169–71.PubMedCrossRef
146.
go back to reference Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–11.PubMedCrossRef Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–11.PubMedCrossRef
147.
go back to reference Antonarakis SE. Recommendations for a nomenclature system for human gene mutations. Nomenclature Working Group. Hum Mutat. 1998;11:1–3.PubMedCrossRef Antonarakis SE. Recommendations for a nomenclature system for human gene mutations. Nomenclature Working Group. Hum Mutat. 1998;11:1–3.PubMedCrossRef
148.
go back to reference den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat. 2000;15:7–12.CrossRef den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat. 2000;15:7–12.CrossRef
149.
go back to reference Tobin MD, Sheehan NA, Scurrah KJ, Burton PR. Adjusting for treatment effects in studies of quantitative traits: antihypertensive therapy and systolic blood pressure. Stat Med. 2005;24:2911–35.PubMedCrossRef Tobin MD, Sheehan NA, Scurrah KJ, Burton PR. Adjusting for treatment effects in studies of quantitative traits: antihypertensive therapy and systolic blood pressure. Stat Med. 2005;24:2911–35.PubMedCrossRef
150.
go back to reference Lynch M, Ritland K. Estimation of pairwise relatedness with molecular markers. Genetics. 1999;152:1753–66.PubMed Lynch M, Ritland K. Estimation of pairwise relatedness with molecular markers. Genetics. 1999;152:1753–66.PubMed
151.
go back to reference Slager SL, Schaid DJ. Evaluation of candidate genes in case-control studies: a statistical method to account for related subjects. Am J Hum Genet. 2001;68:1457–62.PubMedCrossRef Slager SL, Schaid DJ. Evaluation of candidate genes in case-control studies: a statistical method to account for related subjects. Am J Hum Genet. 2001;68:1457–62.PubMedCrossRef
152.
go back to reference Voight BF, Pritchard JK. Confounding from cryptic relatedness in case-control association studies. PLoS Genet. 2005;1:e32.PubMedCrossRef Voight BF, Pritchard JK. Confounding from cryptic relatedness in case-control association studies. PLoS Genet. 2005;1:e32.PubMedCrossRef
153.
go back to reference Homer N, Szelinger S, Redman M, Duggan D, Tembe W, Muehling J, et al. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet. 2008;4:e1000167.PubMedCrossRef Homer N, Szelinger S, Redman M, Duggan D, Tembe W, Muehling J, et al. Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet. 2008;4:e1000167.PubMedCrossRef
Metadata
Title
Strengthening the reporting of genetic association studies (STREGA): an extension of the STROBE statement
Authors
Julian Little
Julian P. T. Higgins
John P. A. Ioannidis
David Moher
France Gagnon
Erik von Elm
Muin J. Khoury
Barbara Cohen
George Davey-Smith
Jeremy Grimshaw
Paul Scheet
Marta Gwinn
Robin E. Williamson
Guang Yong Zou
Kim Hutchings
Candice Y. Johnson
Valerie Tait
Miriam Wiens
Jean Golding
Cornelia van Duijn
John McLaughlin
Andrew Paterson
George Wells
Isabel Fortier
Matthew Freedman
Maja Zecevic
Richard King
Claire Infante-Rivard
Alex Stewart
Nick Birkett
Publication date
01-01-2009
Publisher
Springer Netherlands
Published in
European Journal of Epidemiology / Issue 1/2009
Print ISSN: 0393-2990
Electronic ISSN: 1573-7284
DOI
https://doi.org/10.1007/s10654-008-9302-y

Other articles of this Issue 1/2009

European Journal of Epidemiology 1/2009 Go to the issue