Genetic association studies

Lancet

Volumn 366, Issue 9491, 2005, Pages 1121-1131

  Cordell, Heather J ^a   Clayton, David G ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENEALOGY; GENETIC ASSOCIATION; GENETIC EPIDEMIOLOGY; GENETIC EPISTASIS; GENETIC LINKAGE; GENETIC RISK; GENETIC SIMILARITY; GENETIC SUSCEPTIBILITY; GENOTYPE PHENOTYPE CORRELATION; HAPLOTYPE; HUMAN; HUMAN GENOME; LINKAGE ANALYSIS; PENETRANCE; PLEIOTROPY; PRIORITY JOURNAL; REVIEW; RISK ASSESSMENT; RISK FACTOR; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

EID: 25144501575     PISSN: 01406736     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0140-6736(05)67424-7     Document Type: Review

References (110)

1. K Livak, J Marmaro, J Todd Towards fully automated genome-wide polymorphism screening Nat Genet 9 1995 341 342
2. N Risch, K Merikangas The future of genetic studies of complex human diseases Science 273 1996 1516 1517
3. The International HapMap Consortium The International HapMap project Nature 426 2003 789 796
4. Hattersley AT, McCarthy MI. What makes a good genetic association study? Lancet (in press).
5. G Taubes Epidemiology faces its limits Science 269 1996 164 169
6. S Wacholder, N Rothman, N Caporaso Counterpoint: bias from population stratification is not a major threat to the validity of conclusions from epidemiological studies of common polymorphisms and cancer Cancer Epidemiol Biomarkers Prev 11 2002 513 520
7. J Ioannidis, T Trikalinos, E Ntzani, DG Contopoulos-Ioannidis Genetic associations in large versus small studies: an empirical assessment Lancet 361 2003 567 571
8. I Dahlman, IA Eaves, R Kosoy Parameters for reliable results in genetic association studies in common disease Nat Genet 30 2002 149 150
9. C Hoggart, E Parra, M Shriver Control of confounding of genetic associations in stratified populations Am J Hum Genet 72 2003 1492 1504
10. J Pritchard, N Rosenberg Use of unlinked genetic markers to detect population stratification in association studies Am J Hum Genet 65 1999 220 228
11. J Pritchard, M Stephens, N Rosenberg Association mapping in structured populations Am J Hum Genet 67 2000 170 181
12. G Satten, W Flanders, Q Yang Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model Am J Hum Genet 68 2001 466 477
13. B Devlin, K Roeder Genomic control for association studies Biometrics 55 1999 997 1004
14. SA Bacanu, B Devlin, K Roeder The power of genomic control Am J Hum Genet 66 2000 1933 1944
15. SA Bacanu, B Devlin, K Roeder Association studies for quantitative traits in structured populations Genet Epidemiol 22 2002 78 93
16. R Fisher The correlation between relatives on the supposition of Mendelian inheritance Trans R Soc Edin 52 1918 399 433
17. M Chiano, D Clayton Genotype relative risks under ordered restriction Genet Epidemiol 15 1998 135 146
18. S Wright The relative importance of heredity and environment in determining the piebald pattern of guinea-pigs Proc Natl Acad Sci USA 6 1920 320 322
19. N Breslow, N Day Statistical Methods in Cancer Research. Volume I - The Analysis of Case-Control Studies. IARC Scientific Publications 1980 IARC Lyon
20. D Clayton, M Hills Statistical Models in Epidemiology 1993 Oxford University Press Oxford
21. P Sasieni From genotypes to genes: doubling the sample size Biometrics 53 1997 1253 1261
22. W Bateson Mendel's principles of heredity 1909 Cambridge University Press Cambridge
23. P Phillips The language of gene interaction Genetics 149 1998 1167 1171
24. H Cordell, J Todd, N Hill Statistical modeling of interlocus interactions in a complex disease: Rejection of the multiplicative model of epistasis in type 1 diabetes Genetics 158 2001 357 367
25. H Cordell Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans Hum Mol Genet 11 2002 2463 2468
26. J Siemiatycki, D Thomas Biological models and statistical interactions: an example from multistage carcinogenesis Int J Epidemiol 10 1981 383 387
27. W Thompson Effect modification and the limits of biological inference from epidemiologic data J Clin Epidemiol 44 1991 221 232
28. M Khoury, D Wagener Epidemiological evaluation of the use of genetics to improve the predictive value of disease risk factors Am J Hum Genet 56 1995 835 844
29. O Shpilberg, J Dorman, M Ferrel The next stage: molecular epidemiology J Clin Epidemiol 50 1997 635 638
30. M Khoury Genetic and epidemiological approaches to the search for gene-environment interaction: the case of osteoporosis Am J Epidemiol 147 1998 1 2
31. D Clayton, P McKeigue Epidemiological methods for studying genes and environmental factors in complex diseases Lancet 358 2001 1357 1360
32. J Hoh, J Ott Mathematical multi-locus approaches to localizing complex human trait genes Nat Rev Genet 4 2003 701 709
33. J Moore The ubiquitous nature of epistasis in determining susceptibility to common human diseases Hum Hered 56 2003 73 82
34. R Culverhouse, B Suarez, J Lin A perspective on epistasis: limits of models displaying no main effects Am J Hum Genet 70 2001 461 471
35. J Marchini, P Donnelly, L Cardon Genome-wide strategies for detecting multiple loci that influence complex diseases Nat Genet 37 2005 413 417
36. J Sonquist, J Morgan The detection of interaction effects. volume Monograph 35 of Survey Research Center, Institute of Social Research 1964 University of Michigan Ann Arbor
37. AJ Jeffreys, C May Intense and highly localized gene conversion activity in human meiotic crossover hot spots Nat Genet 36 2004 151 156
38. B Devlin, N Risch A comparison of linkage disequilibrium measures for fine-scale mapping Genomics 29 1995 311 322
39. R Lewontin The interaction of selection and linkage I. General considerations Genetics 49 1964 49 67
40. N Morton, W Zhang, P Taillon-Miller The optimal measure of allelic association Proc Natl Acad Sci US 98 2001 5217 5221
41. PC Sham, SS Cherny, S Purcell Power of linkage versus association analysis of quantitative traits, by use of variance-components models, for sibship data Am J Hum Genet 66 2000 1616 1630
42. M Daly, J Rioux, S Schaffer High-resolution haplotype structure in the human genome Nat Genet 29 2001 229 232
43. K Ardlie, L Kruglyak, M Seielstad Patterns of linkage disequilibrium in the human genome Nat Rev Genet 3 2002 299 309
44. J Wall, J Pritchard Haplotype blocks and linkage disequilibrium in the human genome Nat Rev Genet 4 2003 587 597
45. AJ Jeffreys, L Kauppi, H Neumann Intensely punctate meiotic recombination in the class II region of the major histocompatibilty complex Nat Genet 29 2001 217 222
46. G Johnson, L Esposito, B Barratt Haplotype tagging for the identification of common disease genes Nat Genet 29 2001 233 237
47. D Stram, C Haiman, D Altshuler Choosing haplotype tagging SNPs based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the multiethnic cohort study Hum Hered 55 2003 27 36
48. JM Chapman, JD Cooper, JA Todd Detecting disease associations due to linkage disequilibrium using haplotype tags: a class of tests and the determinants of statistical power Hum Hered 56 2003 18 31
49. MC Byng, JC Whittaker, AP Cuthbert SNP subset selection for genetic association studies Ann Hum Genet 67 2003 543 556
50. CS Carlson, MA Eberle, MJ Rieder Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium Am J Hum Genet 74 2004 106 120
51. D Clayton, J Chapman, J Cooper The use of unphased multilocus genotype data in indirect association studies Genet Epidemiol 27 2004 415 428
52. N Breslow, N Day Statistical Methods in Cancer Research. Volume II: The Design and Analysis of Cohort Studies. IARC Scientific Publications 1987 IARC Lyon
53. C Falk, P Rubinstein Haplotype relative risks: an easy and reliable way to construct a proper control sample for risk calculations Ann Hum Genet 51 1987 227 233
54. D Schaid, S Sommer Genotype relative risks: methods for design and analysis of candidate-gene association studies Am J Hum Genet 53 1993 1114 1126
55. C Weinberg Studying parents and grandparents to assess genetic contributions to early-onset disease Am J Hum Genet 72 2003 438 447
56. LR Cardon, LJ Palmer Population stratification and spurious allelic association Lancet 361 2003 598 604
57. C Weinberg, A Wilcox, R Lie A log-linear approach to case-parent-triad data: assessing effects of disease genes that act either directly or through maternal effects and that may be subject to parental imprinting Am J Hum Genet 62 1998 969 978
58. C Weinberg Methods for detection of parent-of-origin effects in genetic studies of case-parents triads Am Hum Genet 65 1999 229 235
59. J Sinsheimer, C Palmer, J Woodward Detecting genotype combinations that increase risk for disease: maternal-fetal genotype incompatibility test Genet Epidemiol 24 2003 1 13
60. H Cordell, B Barratt, D Clayton Case/pseudo-control analysis in genetic association studies: a unified framework for detection of genotype and haplotype associations, gene-gene and gene-environment interactions and parent-of-origin effects Genet Epidemiol 26 2004 167 185
61. P Sham, J Bader, I Craig DNA pooling: a tool for large-scale association studies Nat Rev Genet 3 2002 862 871
62. J Satagopan, R Elston Optimal two-stage genotyping in population-based association studies Genet Epidemiol 25 2003 149 157
63. C Lowe, J Cooper, J Chapman Cost-effective analysis of candidate genes using htSNPs: a staged approach Genes Immun 5 2004 301 305
64. NJ Camp Genomewide transmission/disequilibrium testing: consideration of the genotypic relative risks at disease loci Am J Hum Genet 61 1997 1424 1430
65. N Camp Genomewide transmission/disequilibrium testing: a correction Am J Hum Genet 64 1999 1485 1487
66. W Gauderman Sample size calculations for matched case-control studies of gene-environment interaction Stat Med 21 2002 35 50
67. W Gauderman Sample size requirements for association studies of gene-gene interaction Am J Epidemiol 155 2002 478 484
68. S Purcell, S Cherny, P Sham Genetic power calculator: design of linkage and association genetic mapping studies of complex traits Bioinformatics 19 2003 149 150
69. C Saunders, D Bishop, J Barrett Power and sample size calculations for studies of gene-gene and gene-environment interactions Genet Epidemiol 23 2002 302 303
70. C Saunders, D Bishop, J Barrett Sample size calculations for main effects and interactions in case-control studies using Stata's nchi2 and npnchi2 functions Stata J 3 2003 47 56
71. M Knapp A note on power approximations for the transmission/ disequilibrium test Am J Hum Genet 64 1999 861 870
72. R McGinnis General equations for Pt, Ps, and the power of the TDT and the affected-sib-pair test Am J Hum Genet 67 2000 1340 1347
73. R McGinnis, S Shifman, A Darvasi Power and efficiency of the TDT and case-control design for association scans Behav Genet 32 2002 135 144
74. W Chen, H Deng A general and accurate approach for computing the statistical power of the transmission disequilibrium test for complex disease genes Genet Epidemiol 21 2001 53 67
75. P McCullagh, J Nelder Generalized Linear Models 1989 Chapman & Hall London
76. R Spielman, R McGinnis, W Ewens Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus Am J Hum Genet 52 1993 506 516
77. D Clayton A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission Am J Hum Genet 65 1999 1170 1177
78. F Dudbridge, B Koeleman, J Todd Unbiased application of the transmission/disequilibrium test to multilocus haplotypes Am J Hum Genet 66 2000 2009 2012
79. D Schaid General score tests for associations of genetic markers with disease using cases and their parents Genet Epidemiol 13 1996 423 449
80. H Cordell, D Clayton A unified stepwise regression procedure for evaluating the relative effects of polymorphisms within a gene using case/control or family data: application to HLA in type 1 diabetes Am J Hum Genet 70 2002 124 141
81. E Martin, S Monks, L Warren A test for linkage and association in general pedigrees: the pedigree disequilibrium test Am J Hu Genet 67 2000 146 154
82. F Dudbridge Pedigree disequilibrium tests for multilocus haplotypes Genet Epidemiol 25 2003 115 121
83. N Laird, S Horvath, X Xu Implementing a unified approach to family based tests of association Genet Epidemiol 19 suppl 1 2000 S36 S42
84. S Lake, D Blacker, N Laird Family-based tests of association in the presence of linkage Am J Hum Genet 67 2000 1515 1525
85. K Lunetta, S Faraone, J Biederman Family-based tests of association and linkage that use unaffected sibs, covariates, and interactions Am J Hum Genet 66 2000 605 614
86. S Horvath, X Xu, N Laird The family based association test method: strategies for studying general genotype-phenotype associations Eur J Hum Genet 9 2001 301 306
87. G Abecasis, L Cardon, W Cookson A general test of association for quantitative traits in nuclear families Am J Hum Genet 66 2000 279 292
88. G Abecasis, W Cookson, L Cardon Pedigree tests of transmission disequilibrium Eur J Hum Genet 8 2000 545 551
89. A Darvasi, M Soller Selective DNA pooling for determination of linkage between a molecular markers and a quantitative trait locus Genetics 138 1994 1365 1373
90. L Barcellos, W Klitz, L Field Association mapping of disease loci, by use of a pooled DNA genomic screen Am J Hum Genet 61 1997 734 747
91. J Bader, A Bansal, P Sham Efficient SNP-based tests of association for quantitative phenotypes using pooled DNA GeneScreen 1 2001 143 150
92. H Seltman, K Roeder, B Devlin Transmission/disequilibrium test meets measured haplotype analysis: family-based association analysis guided by evolution of haplotypes Am J Hum Genet 68 2001 1250 1263
93. H Hotelling The generalization of Student's ratio Ann Math Stat 2 1931 360 378
94. R Fan, M Knapp Genome association studies of complex diseases by case-control designs Am J Hum Genet 72 2003 850 868
95. S Lin, A Chakravarti, DJ Cutler Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies Nat Genet 35 2004 1181 1188
96. M Stephens, N Smith, P Donnelly A new statistical method for haplotype reconstruction from population data Am J Hum Genet 68 2001 978 989
97. D Fallin, N Schork Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data Am J Hum Genet 67 2000 947 959
98. D Clayton SNPHAP, a program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects http://www-gene.cimr.cam.ac.uk/clayton/software/ (accessed Aug 4, 2005)
99. J O'Connell Zero-recombinant haplotyping: application of fine mapping usings SNPs Genet Epidemiol 19 2000 S64 S70
100. M Epstein, G Satten Inference on haplotype effects in case-control studies using unphased genotype data Am J Hum Genet 73 2003 1316 1329
101. S Michalatos-Beloin, S Tishkoff, K Bentley Molecular haplotyping of genetic markers 10 kb apart by allele-specific long-range PCR Nucleic Acids Res 24 1996 4841 4843
102. Y Eitan, Y Kashi Direct micro-haplotyping by multiple double PCR amplifications of specific alleles (MD-PASA) Nucleic Acids Res 30 2002 e62
103. W Piegorsch, C Weinberg, J Taylor Non-hierarchical logistic models and case-only designs for assessing susceptibility in population-based case-control studies Stat Med 13 1994 153 162
104. C Weinberg, D Umbach Choosing a retrospective design to assess joint genetic and environmental contributions to risk Am J Epidemiol 152 2000 197 203
105. S Wacholder, S Chanock, M Garcia-Closas, L El Ghormli, N Rothman Assessing the probability that a positive report is false: an approach for molecular epidemiology studies J Natl Cancer Inst 96 2004 434 442
106. D Thomas, D Clayton Betting odds and genetic associations J Natl Cancer Inst 96 2004 421 423
107. B Efron, R Tibshirani Empirical Bayes methods and false discovery rates for microarrays Genet Epidemiol 23 2002 70 86
108. J Storey, R Tibshirani Statistical significance for genomewide studies Proc Natl Acad Sci US A 100 2003 9440 9445
109. C Sabatti, S Service, N Freimer False discovery rate in linkage and association genome screens for complex disorders Genetics 164 2003 829 833
110. Smith G Davey, S Ebrahim Mendelian randomisation Int J Epidemiol 32 2003 1 22