On combining triads and unrelated subjects data in candidate gene studies: An application to data on testicular cancer

Human Heredity

Volumn 67, Issue 2, 2009, Pages 88-103

  Hsu, Li ^a   Starr, Jacqueline R ^b,c   Zheng, Yingye ^a   Schwartz, Stephen M ^a,b  

^a USA   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c Landstuhl Regional Medical Center   (United States)

Author keywords

Family studies; Genetic association studies; Population based case control; Testicular cancer

Indexed keywords

ADULT; ARTICLE; CONTROLLED STUDY; ENVIRONMENTAL FACTOR; GENOTYPE ENVIRONMENT INTERACTION; HUMAN; MAJOR CLINICAL STUDY; MALE; METHODOLOGY; PARENT; POPULATION BASED CASE CONTROL STUDY; PROBABILITY; PROGENY; RISK FACTOR; SIMULATION; TESTIS CANCER;

COMPUTER SIMULATION; ENVIRONMENT; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MODELS, GENETIC; RESEARCH DESIGN; TESTICULAR NEOPLASMS;

EID: 57449104225     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000179557     Document Type: Article

References (54)

1. Allen-Brady K, Wong J, Camp NJ: PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size. BMC Bioinformatics 2006;7:209.
2. Allen AS, Rahouz PJ, Satten GA: Informative missingness in genetic association studies: case-parent designs. Am J Hum Genet 2003;72:671-680.
3. Allen AS, Satten GA: Inference on haplotype/disease association using parent-affected-child data: The projection conditional on parental haplotypes method. Genet Epidemiol 2007;31:211-223.
4. Allen AS, Satten GA, Tsiatis AA: Locally-efficient robust estimation of haplotype-disease association in family-based studies. Biometrika 2005;92:559-571.
5. Anderson JA: Separate sample logistic discrimination. Biometrika 1972;59:19-35.
6. Billingsley P: Convergence of Probability Measures, ed 2. New York, NY, J. Wiley & Sons, 1999.
7. Breslow NE, Day NE: Statistical Methods in Cancer Research (Vol. 1): The Analysis of Case-Control Studies. World Health Organization, 1980.
8. Chen YH: New approach to association testing in case-parent designs under informative parental missingness. Genet Epidemiol 2004;27:131-140.
9. Clayton DG: A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission. Am J Hum Genet 1999;62:950-961.
10. Clayton D, Jones H: Transmission disequilibrium tests for extended marker haplotypes. Am J Hum Genet 1999;65:1161-1169.
11. Cordell HJ, Barratt BJ, Clayton DG: Case/Pseudocontrol analysis in genetic association studies: a unified framework for detection of genotype and haplotype associations, gene-gene and geneenvironment interactions, and parent-of-origin effects. Genet Epidemiol 2004;26:167-185.
12. Croiseau P, Genin E, Cordell HJ: Dealing with missing data in family-based association studies: A multiple imputation approach. Hum Hered 2007;63:229-238.
13. Curtin K, Wong J, Allen-Brady K, Camp NJ: PedGenie: meta genetic association testing in mixed family and case-control designs. BMC Bioinformatics 2007;8:448.
14. Dempster AP, Laird NM, Rubin DB: Maximum Likelihood from Incomplete Data via the EM algorithm. J R Stat Soc B 1977;39:1-38.
15. Devlin B, Roeder K: Genomic Control for Association Studies. Biometrics 1999;55:997-1004.
16. Dieckmann KP, Pichlmeier U: The prevalence of familial testicular cancer. Cancer 1997;80:1954-1960.
17. Dudbridge F: UNPHASED User Guide. Technical Report 2006/5, Cambridge, UK, MRC Biostatistics Unit, 2006.
18. Epstein M, Veal C, Trembath R, Barker J, Li C, Satten G: Genetic association analysis using data from triads and unrelated subjects. Am J Hum Genet 2005;76:592-608.
19. Foutz RV: On the unique consistent solution to the likelihood equations. J Am Stat Ass 1977;72:147-148.
20. Hankey BF, Ries LA, Edwards BK: The surveillance, epidemiology, and end results program: a national resource. Cancer Epidemiol Biomarkers Prev 1999;8:1117-1121.
21. Harlow BL, Davis S: Two one-step methods for household screening and interviewing using random digit dialing. Am J Epidemiol 1988;127:857-863.
22. Hartge P, Brinton LA, Rosenthal JF, Cahill JI, Hoover RN, Waksberg J: Random digit dialing in selecting a population-based control group. Am J Epidemiol 1984;120:825-833.
23. Hopper JL, Bishop DT, Easton DF: Population-based family studies in genetic epidemiology. Lancet 2005;366:1397-406.
24. Kazeem GR, Farrall M: Integrating case-control and TDT studies. Ann Hum Genet 2005;69:329-335.
25. Kistner EO, Weinberg CR: A method for identifying genes related to a quantitative trait, incorporating multiple siblings and missing parents. Genet Epidemiol 2005;29:155-165.
26. Kraft P, Thomas DC: Bias and efficiency in family-based gene-characterization studies: conditional, prospective, retrospective, and joint likelihoods. Am J Hum Genet 2000;66:1119-1131.
27. Laird NM, Lange C: Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 2006;7:385-394.
28. Langholz B, Borgan Ø: Counter-matching: A stratified nested case-control sampling method. Biometrika 1995;82:69-79.
29. Lin DY, Zeng D, Millikan R: Maximum likelihood estimation of haplotype effects and haplotype-environment interactions in association studies. Genet Epidemiol 2005;29:299-312.
30. Little RJA, Rubin D: Statistical Analysis with Missing Data, ed 2. Chichester, John Wiley, 2002.
31. Nagelkerke NJ, Hoebee B, Teunis P, Kimman TG: Combining the transmission disequilibrium test and case-control methodology using generalized logistic regression. Eur J Hum Genet 2004;12:964-970.
32. Newcomb PA, Baron J, Cotterchio M, Gallinger S, Grove J, Haile R, Hall D, Hopper JL, Jass J, Le Marchand L, Limburg P, Lindor N, Potter JD, Templeton AS, Thibodeau S, Seminara D: Colon Cancer Family Registry: an international resource for studies of the genetic epidemiology of colon cancer. Cancer Epidemiol Biomarkers Prev 2007;16:2331-2343.
33. Prentice RL, Pyke R: Logistic disease incidence models and case-control studies. Biometrika 1979;66:403-411.
34. Pritchard JK, Rosenberg NA: Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 1999;65:220-228.
35. R Development Core Team: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, 2006. ISBN 3-900051-07-0, url: http://www.R-project.org.
36. Rabinowitz D, Laird N: A unified approach to adjusting association tests for population admixture with arbitrary pedigree structure and arbitrary missing marker information. Hum Hered 2000;50:211-223.
37. Rabinowitz D: Adjusting for population heterogeneity and misspecified haplotype frequencies when testing nonparametric null hypotheses in statistical genetics. J Am Stat Assoc 2002;97:742-758.
38. Richiardi L, Pettersson A, Akre O: Genetic and environmental risk factors for testicular cancer. Int J Androl 2007 (OnlineEarly Articles) doi:10.1111/j.1365-2605.2007.00760.x
39. Rubin DB: Multiple imputation for nonresponse in surveys. New York, J Wiley & Sons, 1987.
40. Satten GA, Flanders WD, Yang Q: Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet 2001;68:466-477.
41. Schaid DJ: General score tests for associations of genetic markers with disease using cases and their parents. Genet Epidemiol 1996;13:423-449.
42. Self SG, Longton G, Kopecky KJ, et al: On estimating HLA/disease association with application to a study of aplastic anemia. Biometrics 1991;47:53-61.
43. Starr JR, Chen C, Doody DR, Hsu L, Ricks S, Weiss NS, Schwartz SM: Risk of testicular germ cell cancer in relation to variation in maternal and offspring cytochrome p450 genes involved in catechol estrogen metabolism. Cancer Epidemiol Biomarkers Prev 2005;14:2183-2190.
44. Swerdlow AJ: Testicular cancer: epidemiology and molecular endocrinology;in Henderson BE, Ponder B, Ross RK (eds): Hormones, Genes, and Cancer. New York, Oxford University Press, 2003.
45. Thomas DC: Statistical Methods in Genetic Epidemiology. New York, Oxford University Press, 2004.
46. Thomas DC, Witte JS: Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev 2002;11:505-512.
47. Weinberg CR: Allowing for missing parents in genetic studies of case-parent triads. Am J Hum Genet 1999;64:1186-1193.
48. Weinberg CR, Umbach DM: A hybrid design for studying genetic influences on risk of diseases with onset early in life. Am J Hum Genet 2005;77:627-636.
49. Whittemore AS: Logistic regression of family data from case-control studies. Biometrika 1995;82:57-64.
50. Whittemore AS: Estimating genetic association parameters from family data. Biometrika 2004;91:219-225.
51. Witte JS, Gauderman WJ, Thomas D: Asymptotic bias and efficiency in case-control studies of candidate genes and gene-environment interactions: Basic family designs. Am J Epidemiol 1999;149:693-705.
52. Zavos C, Andreadis C, Diamantopoulos N, Mouratidou D: A hypothesis on the role of insulin-like growth factor I in testicular germ cell tumours. Med Hypotheses 2004;63:511-514.
53. Zhang S, Zhu X, Zhao H: On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol 2003;24:44-56.
54. Zhao LP, Li S, Khalid N: Assessing haplotype-based association with multiple SNPs in case-control studies. Am J Hum Genet 2003;72:1231-1250.