STrengthening the REporting of genetic association studies (STREGA)-an extension of the strobe statement

PLoS Medicine

Volumn 6, Issue 2, 2009, Pages 0151-0163

  Little, Julian ^a   Higgins, Julian P T ^b   Ioannidis, John P A ^c,d   Moher, David ^a   Gagnon, France ^e   Von Elm, Erik ^f,g   Khoury, Muin J ^h   Cohen, Barbara ⁱ   Davey Smith, George ^j   Grimshaw, Jeremy ^k   Scheet, Paul ^l   Gwinn, Marta ^h   Williamson, Robin E ^m   Zou, Guang Yong ^n,o   Hutchings, Kim ^b   Johnson, Candice Y ^b   Tait, Valerie ^b   Wiens, Miriam ^b   Golding, Jean ^p   Van Duijn, Cornelia ^q   McLaughlin, John ^r,s   Paterson, Andrew ^t   Wells, George ^a   Fortier, Isabel ^u   Freedman, Matthew ^v   Zecevic, Maja ^w   King, Richard ^x   Infante Rivard, Claire ^y   Stewart, Alex ^a   Birkett, Nick ^a   more..

^a UNIVERSITY OF OTTAWA   (Canada)

^b MRC BIOSTATISTICS UNIT   (United Kingdom)

^c UNIVERSITY OF IOANNINA   (Greece)

^d TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF TORONTO   (Canada)

^f UNIVERSITY OF BERN   (Switzerland)

^g UNIVERSITY OF FREIBURG   (Germany)

^h NATIONAL CENTER ON BIRTH DEFECTS AND DEVELOPMENTAL DISABILITIES   (United States)

ⁱ Public Library of Science ^*  (United States)

^j UNIVERSITY OF BRISTOL   (United Kingdom)

^k OTTAWA HOSPITAL RESEARCH INSTITUTE   (Canada)

^l UNIVERSITY OF TEXAS   (United States)

^m American Journal of Human Genetics   (United States)

ⁿ UNIVERSITY OF WESTERN ONTARIO   (Canada)

^o ROBARTS RESEARCH INSTITUTE   (Canada)

^p Paediatric and Perinatal Epidemiology   (United Kingdom)

^q European Journal of Epidemiology   (Netherlands)

^r CANCER CARE ONTARIO   (Canada)

^s MOUNT SINAI HOSPITAL   (Canada)

^t HOSPITAL FOR SICK CHILDREN   (Canada)

^u MCGILL UNIVERSITY   (Canada)

^v DANA FARBER CANCER INSTITUTE   (United States)

^w The Lancet   (United States)

^x Genetics in Medicine   (United States)

^y MCGILL UNIVERSITY   (Canada)

more..

Author keywords

Epidemiology; Gene disease associations; Gene environment interaction; Genetics; Genome wide association; Meta analysis; Reporting recommendations; Systematic review

Indexed keywords

GENETIC ASSOCIATION; GENOTYPE; HAPLOTYPE; HUMAN; HUMAN GENOME; MEDICAL DOCUMENTATION; MEDICAL RESEARCH; POPULATION RESEARCH; REVIEW; ARTICLE; DISEASES; GENETIC PREDISPOSITION; GENETICS; GENOMICS; PRACTICE GUIDELINE; PUBLICATION; STANDARD;

DISEASE; GENETIC PREDISPOSITION TO DISEASE; GENOMICS; GUIDELINES AS TOPIC; HUMANS; PERIODICALS AS TOPIC;

EID: 61449255938     PISSN: 15491277     EISSN: 15491676     Source Type: Journal    
DOI: 10.1371/journal.pmed.1000022     Document Type: Review

References (154)

1. Khoury MJ, Little J, Burke W (2004) Human genome epidemiology: Scope and strategies. Khoury MJ, Little J, Burke W, editors. In: Human genome epidemiology: A scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press. pp. 3-16.
2. Genomics, Health and Society Working Group (2004) Genomics, health and society. Emerging issues for public policy. Ottawa: Government of Canada Policy Research Initiative.
3. Lin BK, Clyne M, Walsh M, Gomez O, Yu W, et al. (2006) Tracking the epidemiology of human genes in the literature: The HuGE published literature database. Am J Epidemiol 164: 1-4.
4. Yu W, Yesupriya A, Clyne M, Wulf A, Gwinn M, et al. (2008) HuGE Literature Finder. HuGE Navigator. Available: http://www.hugenavigator.net/ HuGENavigator/searchSummary.do?firstQuery=Gene- disease+association&publitSearchType=now&whichContinue= firststart&check=n&dbType=publit&Mysubmit=go. Accessed 15 December 2008.
5. Lawrence RW, Evans DM, Cardon LR (2005) Prospects and pitfalls in whole genome association studies. Philos Trans R Soc Lond B Biol Sci 360: 1589-1595.
6. Thomas DC (2006) Are we ready for genome-wide association studies? Cancer Epidemiol Biomarkers Prev 15: 595-598.
7. Khoury MJ, Little J, Gwinn M, Ioannidis JP (2007) On the synthesis and interpretation of consistent but weak gene-disease associations in the era of genome-wide association studies. Int J Epidemiol 36: 439-445.
8. Little J, Khoury MJ, Bradley L, Clyne M, Gwinn M, et al. (2003) The human genome project is complete. How do we develop a handle for the pump? Am J Epidemiol 157: 667-673.
9. Ioannidis JP, Bernstein J, Boffetta P, Danesh J, Dolan S, et al. (2005) A network of investigator networks in human genome epidemiology. Am J Epidemiol 162: 302-304.
10. Ioannidis JP, Gwinn M, Little J, Higgins JP, Bernstein JL, et al. (2006) A road map for efficient and reliable human genome epidemiology. Nat Genet 38: 3-5.
11. von Elm E, Egger M (2004) The scandal of poor epidemiological research. BMJ 329: 868-869.
12. [Anonymous] (1999) Freely associating (editorial). Nat Genet 22:1-2.
13. Cardon L, Bell J (2001) Association study designs for complex diseases. Nat Rev Genet 2: 91-99.
14. Weiss S (2001) Association studies in asthma genetics. Am J Respir Crit Care Med 164: 2014-2015.
15. Weiss ST, Silverman EK, Palmer LJ (2001) Case-control association studies in pharmacogenetics. Pharmacogenomics J 1: 157-158.
16. Cooper DN, Nussbaum RL, Krawczak M (2002) Proposed guidelines for papers describing DNA polymorphism-disease associations. Hum Genet 110: 208.
17. Hegele R (2002) SNP judgements and freedom of association. Arterioscler Thromb Vasc Biol 22: 1058-1061.
18. Little J, Bradley L, Bray MS, Clyne M, Dorman J, et al. (2002) Reporting, appraising, and integrating data on genotype prevalence and gene-disease associations. Am J Epidemiol 156: 300-310.
19. Romero R, Kuivaniemi H, Tromp G, Olson JM (2002) The design, execution, and interpretation of genetic association studies to decipher complex diseases. Am J Obstet Gynecol 187: 1299-1312.
20. Colhoun HM, McKeigue PM, Davey Smith G (2003) Problems of reporting genetic associations with complex outcomes. Lancet 361: 865-872.
21. van Duijn CM, Porta M (2003) Good prospects for genetic and molecular epidemiologic studies in the European Journal of Epidemiology. Eur J Epidemiol 18: 285-286.
22. Crossman D, Watkins H (2004) Jesting Pilate, genetic case-control association studies, and Heart. Heart 90: 831-832.
23. Huizinga TW, Pisetsky DS, Kimberly RP (2004) Associations, populations, and the truth: Recommendations for genetic association studies in arthritis & rheumatism. Arthritis Rheum 50: 2066-2071.
24. Little J (2004) Reporting and review of human genome epidemiology studies. Khoury MJ, Little J, Burke W, editors. In: Human genome epidemiology: A scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press. pp. 168-192.
25. Rebbeck TR, Martinez ME, Sellers TA, Shields PG, Wild CP, et al. (2004) Genetic variation and cancer: Improving the environment for publication of association studies. Cancer Epidemiol Biomarkers Prev 13: 1985-1986.
26. Tan N, MulleyJ, Berkovic S (2004) Association studies in epilepsy: "The truth is out there". Epilepsia 45: 1429-1442.
27. [Anonymous] (2005) Framework for a fully powered risk engine. Nat Genet 37: 1153.
28. Ehm MG, Nelson MR, Spurr NK (2005) Guidelines for conducting and reporting whole genome/large-scale association studies. Hum Mol Genet 14: 2485-2488.
29. Freimer NB, Sabatti C (2005) Guidelines for association studies in human molecular genetics. Hum Mol Genet 14: 2481-2483.
30. Hattersley AT, McCarthy MI (2005) What makes a good genetic association study? Lancet 366: 1315-1323.
31. Manly K (2005) Reliability of statistical associations between genes and disease. Immunogenetics 57: 549-558.
32. Shen H, Liu Y, Liu P, Recker R, Deng H (2005) Nonreplication in genetic studies of complex diseases-Lessons learned from studies of osteoporosis and tentative remedies. J Bone Miner Res 20: 365-376.
33. Vitali S, Randolph A (2005) Assessing the quality of case-control association studies on the genetic basis of sepsis. Pediatr Crit Care Med 6:S74-S77.
34. Wedzicha JA, Hall IP (2005) Publishing genetic association studies in Thorax. Thorax 60: 357.
35. Hall IP, Blakey JD (2005) Genetic association studies in Thorax. Thorax 60: 357-359.
36. DeLisi LE, Faraone SV (2006) 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 141: 319-322.
37. Saito YA, Talley NJ, de Andrade M, Petersen GM (2006) Case-control genetic association studies in gastrointestinal disease: Review and recommendations. Am J Gastroenterol 101: 1379-1389.
38. Uhlig K, Menon V, Schmid CH (2007) Recommendations for reporting of clinical research studies. Am J Kidney Dis 49: 3-7.
39. NCI-NHGRI Working Group on Replication in Association Studies, Chanock SJ, Manolio T, Boehnke M, Boerwinkle E, et al. (2007) Replicating genotype-phenotype associations. Nature 447: 655-660.
40. Begg CB (2005) Reflections on publication criteria for genetic association studies. Cancer Epidemiol Biomarkers Prev 14: 1364-1365.
41. Byrnes G, Gurrin L, Dowty J, Hopper JL (2005) Publication policy or publication bias? Cancer Epidemiol Biomarkers Prev 14: 1363.
42. Pharoah PD, Dunning AM, Ponder BA, Easton DF (2005) The reliable identification of disease-gene associations. Cancer Epidemiol Biomarkers Prev 14: 1362.
43. Wacholder S (2005) Publication environment and broad investigation of the genome. Cancer Epidemiol Biomarkers Prev 14: 1361.
44. Whittemore AS (2005) Genetic association studies: Time for a new paradigm? Cancer Epidemiol Biomarkers Prev 14: 1359-1360.
45. Bogardus ST, Jr., Concato J, Feinstein AR (1999) Clinical epidemiological quality in molecular genetic research. The need for methodological standards. JAMA 281: 1919-1926.
46. Peters DL, Barber RC, Flood EM, Garner HR, O'Keefe GE (2003) Methodologic quality and genotyping reproducibility in studies of tum or necrosis factor -308 G->A single nucleotide polymorphism and bacterial sepsis: Implications for studies of complex traits. Crit Care Med 31: 1691-1696.
47. Clark MF, Baudouin SV (2006) A systematic review of the quality of genetic association studies in human sepsis. Intensive Care Med 32: 1706-1712.
48. Lee W, Bindman J, Ford T, Glozier N, Moran P, et al. (2007) Bias in psychiatric case-control studies: Literature survey. Br J Psychiatry 190: 204-209.
49. Yesupriya A, Evangelou E, Kavvoura FK, Patsopoulos NA, Clyne M, et al. (2008) Reporting of human genome epidemiology (HuGE) association studies: An empirical assessment. BMC Med Res Methodol 8: 31.
50. Reid MC, Lachs MS, Feinstein AR (1995) Use of methodological standards in diagnostic test research. Getting better but still not good. JAMA 274:645-651.
51. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, et al. (2001) Minimum information about a microarray experiment (MIAME)-Toward standards for microarray data. Nat Genet 29: 356-371.
52. Pocock SJ, Collier TJ, Dandreo KJ, de Stavola BL, Goldman MB, et al. (2004) Issues in the reporting of epidemiological studies: A survey of recent practice. BMJ 329: 883.
53. Altman D, Moher D (2005) Developing guidelines for reporting healthcare research: Scientific rationale and procedures. Med Clin (Barc) 125: 8-13.
54. Gluud LL (2006) Bias in clinical intervention research. Am J Epidemiol 163: 493-501.
55. von Elm E, Altman DG, Egger M, Pocock SJ, Gotzsche PC, et al. (2007) The strengthening the reporting of observational studies in epidemiology (STROBE) statement: Guidelines for reporting observational studies. PLoS Med 4: e296. doi:10.1371/journal.pmed.0040296
56. Vandenbroucke JP, von Elm E, Altman DG, Gotzsche PC, Mulrow CD, et al. (2007) Strengthening the reporting of observational studies in epidemiology (STROBE): Explanation and elaboration. Ann Intern Med 147: W163-W194.
57. Little J, Higgins JPT, editors (2006) The HuGENet™ HuGE Review Handbook, version 1.0. Available: http://www.hugenet.ca. Accessed 28 February 2006.
58. Higgins JP, Little J, Ioannidis JP, Bray MS, Manolio TA, et al. (2007) Turning the pump handle: Evolving methods for integrating the evidence on gene-disease association. Am J Epidemiol 166: 863-866.
59. Altman DG, Schulz KF, Moher D, Egger M, Davidoff F, et al. (2001) The revised CONSORT statement for reporting randomized trials: Explanation and elaboration. Ann Intern Med 134: 663-694.
60. Moher D, Schultz KF, Altman D (2001) The CONSORT statement: Revised recommendations for improving the quality of reports of parallel-group randomized trials. JAMA 285: 1987-1991.
61. Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: Causes, consequences and solutions. Nat Rev Genet 6: 847-859.
62. Akey JM, Zhang K, Xiong M, Doris P, Jin L (2001) The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. Am J Hum Genet 68: 1447-1456.
63. Dequeker E, Ramsden S, Grody WW, Stenzel TT, Barton DE (2001) Quality control in molecular genetic testing. Nat Rev Genet 2: 717-723.
64. Mitchell AA, Cutler DJ, Chakravarti A (2003) Undetected genotyping errors cause apparent overtransmission of common alleles in the transmission/ disequilibrium test. Am J Hum Genet 72: 598-610.
65. Rothman N, Stewart WF, Caporaso NE, Hayes RB (1993) Misclassification of genetic susceptibility biomarkers: Implications for case-control studies and cross-population comparisons. Cancer Epidemiol Biomarkers Prev 2:299-303.
66. Garcia-Closas M, Wacholder S, Caporaso N, Rothman N (2004) Inference issues in cohort and case-control studies of genetic effects and gene-environment interactions. Khoury MJ, Little J, Burke W, editors. In: Human genome epidemiology: A scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press. pp. 127-144.
67. Wong MY, Day NE, Luan JA, Wareham NJ (2004) Estimation of magnitude in gene-environment interactions in the presence of measurement error. Stat Med 23: 987-998.
68. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, et al. (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37: 1243-1246.
69. Knowler WC, Williams RC, Pettitt DJ, Steinberg AG (1988) Gm3;5,13,14 and type 2 diabetes mellitus: An association in American Indians with genetic admixture. Am J Human Genet 43: 520-526.
70. Gelernter J, Goldman D, Risch N (1993) The A1 allele at the D2 dopamine receptor gene and alcoholism: A reappraisal. JAMA 269: 1673-1677.
71. Kittles RA, Chen W, Panguluri RK, Ahaghotu C, Jackson A, et al. (2002) CYP3A4-V and prostate cancer in African Americans: Causal or confounding association because of population stratification? Hum Genet 110: 553-560.
72. Thomas DC, Witte JS (2002) Point: Population stratification: A problem for case control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 11: 505-512.
73. Wacholder S, Chatterjee N, Hartge P (2002) Joint effects of genes and environment distorted by selection biases: Implications for hospital-based case-control studies. Cancer Epidemiol Biomarkers Prev 11: 885-889.
74. Cardon LR, Palmer LJ (2003) Population stratification and spurious allelic association. Lancet 361: 598-604.
75. Wacholder S, Rothman N, Caporaso N (2000) Population stratification in epidemiologic studies of common genetic variants and cancer: Quantification of bias. J Natl Cancer Inst 92: 1151-1158.
76. Ardlie KG, Lunetta KL, Seielstad M (2002) Testing for population subdivision and association in four case-control studies. Am J Human Genet 71: 304-311.
77. Edland SD, Slager S, Farrer M (2004) Genetic association studies in Alzheimer's disease research: Challenges and opportunities. Stat Med 23: 169-178.
78. Millikan RC (2001) Re: Population stratification in epidemiologic studies of common genetic variants and cancer: Quantification of bias. J Natl Cancer Inst 93: 156-157.
79. Wang Y, Localio R, Rebbeck TR (2004) Evaluating bias due to population stratification in case-control association studies of admixed populations. Genet Epidemiol 27: 14-20.
80. Ioannidis JP, Ntzani EE, Trikalinos TA (2004) 'Racial' differences in genetic effects for complex diseases. Nat Genet 36: 1312-1318.
81. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36: 512-517.
82. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, et al. (2004) Assessing the impact of population stratification on genetic association studies. Nat Genet 36: 388-393.
83. Khlat M, Cazes MH, Genin E, Guiguet M (2004) Robustness of case-control studies of genetic factors to population stratification: Magnitude of bias and type I error. Cancer Epidemiol Biomarkers Prev 13: 1660-1664.
84. Balding DJ (2006) A tutorial on statistical methods for population association studies. Nat Rev Genet 7: 781-791.
85. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.
86. Ioannidis JP (2007) Non-replication and inconsistency in the genome-wide association setting. Hum Hered 64: 203-213.
87. Parkes M, Barrett JC, Prescott NJ, Tremelling M, Anderson CA, et al. (2007) Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat Genet 39: 830-832.
88. Todd JA, Walker NM, Cooper JD, Smyth DJ, Downes K, et al. (2007) Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. Nat Genet 39: 857-864.
89. Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, et al. (2007) Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 316: 1336-1341.
90. 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, et al. (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 316: 1331-1336.
91. Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, et al. (2007) A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 316: 1341-1345.
92. Helgadottir A, Thorleifsson G, Manolescu A, Gretarsdottir S, Blondal T, et al. (2007) A common variant on chromosome 9p21 affects the risk of myocardial infarction. Science 316: 1491-1493.
93. McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, et al. (2007) A common allele on chromosome 9 associated with coronary heart disease. Science 316: 1488-1491.
94. Easton DF, Pooley KA, Dunning AM, Pharoah PD, Thompson D, et al. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447: 1087-1093.
95. Hunter DJ, Kraft P, Jacobs KB, Cox DG, Yeager M, et al. (2007) A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39: 870-874.
96. Stacey SN, Manolescu A, Sulem P, Rafnar T, Gudmundsson J, et al. (2007) Common variants on chromosomes 2q35 and 16q12 confer susceptibility to estrogen receptor-positive breast cancer. Nat Genet 39: 865-869.
97. Gudmundsson J, Sulem P, Steinthorsdottir V, Bergthorsson JT, Thorleifsson G, et al. (2007) Two variants on chromosome 17 confer prostate cancer risk, and the one in TCF2 protects against type 2 diabetes. Nat Genet 39: 977-983.
98. Haiman CA, Patterson N, Freedman ML, Myers SR, Pike MC, et al. (2007) Multiple regions within 8q24 independently affect risk for prostate cancer. Nat Genet 39: 638-644.
99. Yeager M, Orr N, Hayes RB, Jacobs KB, Kraft P, et al. (2007) Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. Nat Genet 39: 645-649.
100. Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, et al. (2007) Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet 39: 989-994.
101. Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, et al. (2007) A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet 39: 984-988.
102. Haiman CA, Le Marchand L, Yamamoto J, Stram DO, Sheng X, et al. (2007) A common genetic risk factor for colorectal and prostate cancer. Nature Genetics 39: 954-956.
103. Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, et al. (2007) Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet 39: 596-604.
104. Libioulle C, Louis E, Hansoul S, Sandor C, Farnir F, et al. (2007) Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4. PLoS Genet 3: e58. doi:10.1371/journal.pgen.0030058
105. Duerr RH, Taylor KD, Brant SR, Rioux JD, Silverberg MS, et al. (2006) A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science 314: 1461-1463.
106. Zhao LP, Li SS, Khalid N (2003) A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet 72: 1231-1250.
107. International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
108. Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
109. Qin ZS, Niu T, Liu JS (2002) Partition-ligation-expectation-maximization algorithm for haplotype inference with single-nucleotide polymorphisms. Am J Hum Genet 71: 1242-1247.
110. Scheet P, Stephens M (2006) A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78: 629-644.
111. Browning SR (2008) Missing data imputation and haplotype phase inference for genome-wide association studies. Hum Genet 124: 439-450.
112. Huang Q, Fu YX, Boerwinkle E (2003) Comparison of strategies for selecting single nucleotide polymorphisms for case/control association studies. Hum Genet 113: 253-257.
113. Kamatani N, Sekine A, Kitamoto T, Iida A, Saito S, et al. (2004) 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 75: 190-203.
114. Zhang W, Collins A, Morton NE (2004) Does haplotype diversity predict power for association mapping of disease susceptibility? Hum Genet 115: 157-164.
115. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, et al. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analysis using linkage disequilibrium. Am J Hum Genet 74: 106-120.
116. van Hylckama Vlieg A, Sandkuijl LA, Rosendaal FR, Bertina RM, Vos HL (2004) Candidate gene approach in association studies: Would the factor V leiden mutation have been found by this approach? Eur J Hum Genet 12: 478-482.
117. Greenspan G, Geiger D (2004) Model-based inference of haplotype block variation. J Comput Biol 11: 493-504.
118. Kimmel G, Shamir R (2005) GERBIL: Genotype resolution and block identification using likelihood. Proc Natl Acad Sci USA 102: 158-162.
119. Cardon LR, Abecasis GR (2003) Using haplotype blocks to map human complex triat loci. Trends Genet 19: 135-140.
120. Ke X, Hunt S, Tapper W, Lawrence R, Stavrides G, et al. (2004) The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum Mol Genet 13: 577-588.
121. Servin B, Stephens M (2007) Imputation-based analysis of association studies: Candidate regions and quantitative traits. PLoS Genet 3: e114. doi:10.1371/journal.pgen.0030114
122. Marchini J, Howie B, Myers S, McVean G, Donnelly P (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 39: 906-913.
123. Hardy GH (1908) Mendelian proportions in a mixed population. Science 28: 49-50.
124. Weinberg W (1908) Über den nachweis der vererbung beim menschen. Jahrhefte Des Vereines Für Vaterländische Naturkunde in Württemberg 64: 368-382.
125. Minelli C, Thompson JR, Abrams KR, Thakkinstian A, Attia J (2008) How should we use information about HWE in the meta-analyses of genetic association studies? Int J Epidemiol 37: 136-146.
126. Xu J, Turner A, Little J, Bleecker ER, Meyers DA (2002) Positive results in association studies are associated with departure from Hardy-Weinberg equilibrium: Hint for genotyping error? Hum Genet 111: 573-574.
127. Hosking L, Lumsden S, Lewis K, Yeo A, McCarthy L, et al. (2004) Detection of genotyping errors by Hardy-Weinberg equilibrium testing. Eur J Hum Genet 12: 395-399.
128. Salanti G, Amountza G, Ntzani EE, Ioannidis JP (2005) Hardy-Weinberg equilibrium in genetic association studies: An empirical evaluation of reporting, deviations, and power. Eur J Hum Genet 13: 840-848.
129. Pearson TA, Manolio TA (2008) How to interpret a genome-wide association study. JAMA 299: 1335-1344.
130. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, et al. (2008) Genome-wide association studies for complex traits: Consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369.
131. Zou GY, Donner A (2006) The merits of testing Hardy-Weinberg equilibrium in the analysis of unmatched case-control data: A cautionary note. Ann Hum Genet 70: 923-933.
132. Shoemaker J, Painter I, Weir BS (1998) A Bayesian characterization of Hardy-Weinberg disequilibrium. Genetics 149: 2079-2088.
133. Ayres KL, Balding DJ (1998) Measuring departures from Hardy-Weinberg: A Markov chain Monte Carlo method for estimating the inbreeding coefficient. Heredity 80: 769-777.
134. Trikalinos TA, Salanti G, Khoury MJ, Ioannidis JP (2006) Impact of violations and deviations in Hardy-Weinberg equilibrium on postulated gene-disease associations. Am J Epidemiol 163: 300-309.
135. Davidoff F, Batalden P, Stevens D, Ogrinc G, Mooney S, et al. (2008) Publication guidelines for improvement studies in health care: Evolution of the SQUIRE project. Ann Intern Med 149: 670-676.
136. Steinberg K, Gallagher M (2004) Assessing genotypes in human genome epidemiology studies. Khoury MJ, Little J, Burke W, editors. In: Human genome epidemiology: A scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press. pp. 79-91.
137. Plagnol V, Cooper JD, Todd JA, Clayton DG (2007) A method to address differential bias in genotyping in large-scale association studies. PLoS Genet 3: e74. doi:10.1371/journal.pgen.0030074
138. Winker MA (2006) Race and ethnicity in medical research: Requirements meet reality. J Law Med Ethics 34: 520-5, 480.
139. Scuteri A, Sanna S, Chen WM, Uda M, Albai G, et al. (2007) Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet 3: e115. doi:10.1371/journal. pgen.0030115
140. Chan AW, Hrobjartsson A, Haahr MT, Gotzsche PC, Altman DG (2004) Empirical evidence for selective reporting of outcomes in randomized trials: Comparison of protocols to published articles. JAMA 291: 2457-2465.
141. Chan AW, Krleza-Jeric K, Schmid I, Altman DG (2004) Outcome reporting bias in randomized trials funded by the Canadian Institutes of Health Research. CMAJ 171: 735-740.
142. Chan AW, Altman DG (2005) Identifying outcome reporting bias in randomised trials on PubMed: Review of publications and survey of authors. BMJ 330: 753.
143. Contopoulos-Ioannidis DG, Alexiou GA, Gouvias TC, Ioannidis JP (2006) An empirical evaluation of multifarious outcomes in pharmacogenetics: Beta-2 adrenoceptor gene polymorphisms in asthma treatment. Pharmacogenet Genomics 16: 705-711.
144. Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, et al. (2002) Guidelines for human gene nomenclature. Genomics 79: 464-470.
145. Wain HM, Lush M, Ducluzeau F, Povey S (2002) Genew: The human gene nomenclature database. Nucleic Acids Res 30: 169-171.
146. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, et al. (2001) dbSNP: The NCBI database of genetic variation. Nucleic Acids Res 29: 308-311.
147. Antonarakis SE (1998) Recommendations for a nomenclature system for human gene mutations. nomenclature working group. Hum Mutat 11: 1-3.
148. den Dunnen JT, Antonarakis SE (2000) Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Hum Mutat 15: 7-12.
149. Tobin MD, Sheehan NA, Scurrah KJ, Burton PR (2005) Adjusting for treatment effects in studies of quantitative traits: Antihypertensive therapy and systolic blood pressure. Stat Med 24: 2911-2935.
150. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152: 1753-1766.
151. Slager SL, Schaid DJ (2001) Evaluation of candidate genes in case-control studies: A statistical method to account for related subjects. Am J Hum Genet 68: 1457-1462.
152. Voight BF, Pritchard JK (2005) Confounding from cryptic relatedness in case-control association studies. PLoS Genet 1: e32. doi:10.1371/journal. pgen.0010032
153. Homer N, Szelinger S, Redman M, Duggan D, Tembe W, et al. (2008) Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays. PLoS Genet 4: e1000167. doi:10.1371/journal. pgen.1000167
154. Zerhouni EA, Nabel EG (2008) Protecting aggregate genomic data. Science 322: 44.