Using case-parent triads to estimate relative risks associated with a candidate haplotype

Annals of Human Genetics

Volumn 73, Issue 3, 2009, Pages 346-359

  Shi, Min ^a   Umbach, David M ^a   Weinberg, Clarice R ^a  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

Author keywords

Candidate haplotype; Expectation maximization algorithm; Hardy Weinberg equilibrium; Log linear model; Maternal genetic effects; Phase ambiguity; Yin Yang haplotypes

Indexed keywords

INTERFERON REGULATORY FACTOR 6;

ARTICLE; CLEFT FACE; GENE FREQUENCY; GENE MAPPING; GENETIC ALGORITHM; GENETIC RISK; GENOTYPE; HAPLOTYPE; HUMAN; LOGLINEAR MODEL; MAJOR CLINICAL STUDY; MATHEMATICAL COMPUTING; MATING TYPE; MOTHER CHILD RELATION; PRIORITY JOURNAL; PROGENY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

FEMALE; GENETICS, POPULATION; HAPLOTYPES; HUMANS; INTERFERON REGULATORY FACTORS; MALE; MODELS, GENETIC; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK;

EID: 65449146360     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2009.00515.x     Document Type: Article

References (20)

1. Abecasis, G. R., Cherny, S. S., Cookson, W. O. & Cardon, L. R. (2002) Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30, 97-101.
2. Abecasis, G. R. & Wigginton, J. E. (2005) Handling marker-marker linkage disequilibrium: Pedigree analysis with clustered markers. Am J Hum Genet 77, 754-767.
3. Allen, A. S. & Satten, G. A. (2007) Inference on haplotype/disease association using parent-affected-child data: The projection conditional on parental haplotypes method. Genet Epidemiol 31, 211-223.
4. Carayol, J., Philippi, A. & Tores, F. (2006) Estimating haplotype relative risks in complex disease from unphased SNPs data in families using a likelihood adjusted for ascertainment. Genet Epidemiol 30, 666-676.
5. Cordell, H. J. (2004) Properties of case/pseudocontrol analysis for genetic association studies: Effects of recombination, ascertainment, and multiple affected offspring. Genet Epidemiol 26, 186-205.
6. Cordell, H. J., Barratt, B. J. & Clayton, D. G. (2004) Case/ pseudocontrol 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, 167-185.
7. Dempster, A. P., Laird, N. M. & Rubin, D. B. (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc. Series B Methodol 39, 1-38.
8. Dudbridge, F. (2008) Likelihood-based association analysis for nuclear families and unrelated subjects with missing genotype data. Hum Hered 66, 87-98.
9. Gjessing, H. K. & Lie, R. T. (2006) Case-parent triads: Estimating single- and double-dose effects of fetal and maternal disease gene haplotypes. Ann Hum Genet 70, 382-396.
10. Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z. S., Munro, H. M., Abecasis, G. R. & Donnelly, P. (2006) A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78, 437-450.
11. Schaid, D. J. (2004) Linkage disequilibrium testing when linkage phase is unknown. Genetics 166, 505-512.
12. Shi, M., Umbach, D. M. & Weinberg, C. R. (2007) Identification of risk-related haplotypes with the use of multiple SNPs from nuclear families. Am J Hum Genet 81, 53-66.
13. Venzon, D. J. & Moolgavkar, S. H. (1988) A method for computing profile-likelihood-based confidence intervals. Appl Stat 37, 87-94.
14. Wacholder, S., Rothman, N. & Caporaso, N. (2002) 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, 513-520.
15. Weinberg, C. R., Wilcox, A. J. & Lie, R. T. (1998) 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, 969-978.
16. Wilcox, A. J., Weinberg, C. R. & Lie, R. T. (1998) Distinguishing the effects of maternal and offspring genes through studies of "case-parent triads". Am J Epidemiol 148, 893-901.
17. Zhang, J., Rowe, W. L., Clark, A. G. & Buetow, K. H. (2003) Genomewide distribution of high-frequency, completely mismatching SNP haplotype pairs observed to be common across human populations. Am J Hum Genet 73, 1073-1081.
18. Zhang, K., Sun, F. & Zhao, H. (2005) HAPLORE: A program for haplotype reconstruction in general pedigrees without recombination. Bioinformatics 21, 90-103.
19. Zhang, K. & Zhao, H. (2006) A comparison of several methods for haplotype frequency estimation and haplotype reconstruction for tightly linked markers from general pedigrees. Genet Epidemiol 30, 423-437.
20. Zucchero, T. M., Cooper, M. E., Maher, B. S., Daack-Hirsch, S., Nepomuceno, B., Ribeiro, L., Caprau, D., Christensen, K., Suzuki, Y., Machida, J., Natsume, N., Yoshiura, K., Vieira, A. R., Orioli, I. M., Castilla, E. E., Moreno, L., Arcos-Burgos, M., Lidral, A. C., Field, L. L., Liu, Y. E., Ray, A., Goldstein, T. H., Schultz, R. E., Shi, M., Johnson, M. K., Kondo, S., Schutte, B. C., Marazita, M. L. & Murray, J. C. (2004) Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate. N Engl J Med 351, 769-780.