A two-stage design for multiple testing in large-scale association studies

Journal of Human Genetics

Volumn 51, Issue 6, 2006, Pages 523-532

  Wen, Shu Hui ^a   Tzeng, Jung Ying ^b   Kao, Jau Tsuen ^c   Hsiao, Chuhsing Kate ^d  

^a TZU CHI UNIVERSITY   (Taiwan)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^d NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

Association studies; Cost effectiveness; False positive rate; Multiple testing; Two stage design

Indexed keywords

APOLIPOPROTEIN A1; APOLIPOPROTEIN A5; APOLIPOPROTEIN C3; LIPOPROTEIN LIPASE;

ARTICLE; BONFERRONI TEST; COST EFFECTIVENESS ANALYSIS; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC MARKER; GENOTYPE; HUMAN; HYPERTRIGLYCERIDEMIA; LABORATORY DIAGNOSIS; METHODOLOGY; PROBABILITY; SAMPLE SIZE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

COST-BENEFIT ANALYSIS; DATA INTERPRETATION, STATISTICAL; FALSE POSITIVE REACTIONS; GENETIC MARKERS; GENETIC TECHNIQUES; GENOTYPE; HUMANS; HYPERLIPOPROTEINEMIA TYPE IV; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33745475088     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10038-006-0393-6     Document Type: Article

References (31)

1. Allison DB, Coffey CS (2002) Two-stage testing in microarray analysis: what is gained? J Gerontol A Biol Sci Med Sci 57:B189-B192
2. Becker T, Knapp M (2004) Maximum-likelihood estimation of haplotype frequencies in nuclear families. Genet Epidemiol 27:21-32
3. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B Methodol 57:289-300
4. Benjamini Y, Yekutieli D (2001) The control of the false discovery rate in multiple testing under dependency. Ann Stat 29:1165-1188
5. Böddeker IR, Ziegler A (2001) Sequential designs for genetic epidemiological linkage or association studies a review of the literature. Biomed J 43:501-525
6. Collins A, Lonjou C, Morton NE (1999) Genetic epidemiology of single-nucleotide polymorphisms. Proc Natl Acad Sci USA 96:15173-15177
7. Dale RN (2004) A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am J Hum Genet 74:765-769
8. Dudoit S, Shaffer JP, Boldrick JC (2003) Multiple hypothesis testing in microarray experiments. Stat Sci 18:71-103
9. Elston RC, Guo X, Williams LV (1996) Two-stage global search designs for linkage analysis using pairs of affected relatives. Genet Epidemiol 13:535-558
10. Ge Y, Dudoit D, Speed TP (2003) Resampling-based multiple testing for microarray data analysis. Test 12:1-77
11. Guo X, Elston RC (2000) Two-stage global search designs for linkage analysis. I. Use of the mean statistic for affected sib pairs. Genet Epidemiol 18:97-110
12. Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T (2002) Gene-based SNP discovery as part of the Japanese millennium genome project: identification of 190,562 genetic variations in the human genome. J Hum Genet 47:605-610
13. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Benjamin W, Borg A, Trend J (2001) Gene-expression profiles in hereditary breast cancer. N Engl J Med 344:539-548
14. Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6:95-108
15. Hoh J, Wille A, Zee R, Cheng S, Reynolds R, Lindpaintner K, Ott J (2000) Selecting SNPs in two-stage analysis of disease association data: a model-free approach. Ann Hum Genet 64:413-417
16. Kao JT, Wen HC, Chien KL, Hsu HC, Lin SW (2003) A novel genetic variant in the apolipoprotein A5 gene is associated with hypertriglyceridemia. Hum Mol Genet 12:2533-2539
17. Miller RA, Galecki A, Shmookler-Reis RJ (2001) Interpretation, design, and analysis of gene array expression experiments. J Gerontol A Biol Sci Med Sci 56:B52-B57
18. Ohashi J, Tokunaga K (2001) The power of genome-wide association studies of complex disease genes: statistical limitations of indirect approaches using SNP markers. J Hum Genet 46:478-482
19. Ott J, Hoh J (2001) Statistical multilocus methods for disequilibrium analysis in complex traits. Hum Mutat 17:285-288
20. Ozaki K, Ohnishi Y, Iida A, Sekine A, Yamada R, Tsunoda T, Sato H, Sato H, Hori M, Nakamura Y, Tanaka T (2002) Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction. Nat Genet 32:650-654
21. Reich DE, Gabriel SB, Altshuler D (2003) Quality and completeness of SNP databases. Nat Genet 33:457-458
22. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516-1517
23. Saito A, Kamatani N (2002) Strategies for genome-wide association studies: optimization of study designs by the stepwise focusing method. J Hum Genet 47:360-365
24. Satagopan JM, Elston RC (2003) Optimal two-stage genotyping in population-based association studies. Genet Epidemiol 25:149-157
25. Satagopan JM, Verbel DA, Venkatraman ES, Offit KE, Begg CB (2002) Two-stage designs for gene-disease association studies. Biometrics 58:163-170
26. Satagopan JM, Venkatraman ES, Begg CB (2004) Two-stage designs for gene-disease association studies with sample size constraints. Biometrics 60:589-597
27. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440-9445
28. Thomas D, Xie R, Gebregziabher M (2004) Two-stage sampling designs for gene association studies. Genet Epidemiol 27:401-414
29. Tsai CA, Hsueh H, Chen JJ (2003) Estimation of false discovery rates in multiple testing: application to gene microarray data. Biometrics 59:1071-1081
30. van den Oord EJCG, Sullivan PF (2003a) A framework for controlling false discovery rates and minimizing the amount of genotyping in the search for disease mutations. Hum Hered 56:188-199
31. van den Oord EJCG, Sullivan PF (2003b) False discoveries and models for gene discovery. Trends Genet 19:537-542