An extension of the transmission disequilibrium test incorporating imprinting

Genetics

Volumn 175, Issue 3, 2007, Pages 1489-1504

  Hu, Yue Qing ^a,b   Zhou, Ji Yuan ^a,c   Fung, Wing K ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b SOUTHEAST UNIVERSITY   (China)

^c HUAIHUA UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; GENE EXPRESSION; GENE LINKAGE DISEQUILIBRIUM; GENETIC RECOMBINATION; GENOME IMPRINTING; HETEROZYGOSITY; PRIORITY JOURNAL; SIMULATION;

ANIMALS; COMPUTER SIMULATION; FEMALE; GENOMIC IMPRINTING; HUMANS; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; MALE; MODELS, GENETIC; SEX FACTORS;

MAMMALIA;

EID: 34249018224     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.058461     Document Type: Article

References (35)

1. AINSCOUGH, J. F. X., and M. A. SURANI, 1996 Organization and control of imprinted genes: the common features, pp. 173-194 in Epigenetic Mechanisms of Gene Regulation, edited by V. E. A. RUSSO, R. A. MARTIENSSEN and A. D. RIGGS. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
2. BARTOLOMEI, M. S., and S. M. TILGHMAN, 1997 Genomic imprinting in mammals. Annu. Rev. Genet. 31: 493-525.
3. BENNETT, S. T., J. A. TODD, D. M. WATERWORTH, S. FRANKS and M. I. MCCARTHY, 1997 Association of insulin gene VNTR polymorphism with polycystic ovary syndrome. Lancet 349: 1771-1772.
4. BROMAN, K. W., J. C. MURRAY, V. C. SHEFFIELD, R. L. WHITE and J. L. WEBER, 1998 Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am. J. Hum. Genet. 63: 861-869.
5. DENG, H. W., and W. M. CHEN, 2001 The power of the transmission disequilibrium test (TDT) with both case-parent and control-parent trios. Genet. Res. 78: 289-302.
6. FALLS, J. G., D. J. PULFORD, A. A. WYLIE and R. L. JIRTLE, 1999 Genomic imprinting: implications for human disease. Am. J. Pathol. 154: 635-647.
7. FANN, C. S. J., and J. OTT, 1995 Parsimonious estimation of sex-specific map distances by stepwise maximum likelihood regression. Genomics 29: 571-575.
8. HALDANE, J. B. S., 1922 Sex ratio and unisexual sterility in hybrid animals. J. Genet. 12: 101-109.
9. HALL, J. G., 1990 Genomic imprinting: review and relevance to human diseases. Am. J. Hum. Genet. 46: 857-873.
10. HANSON, R. L., S. KOBES, R. S. LINDSAY and W. C. KNOWLER, 2001 Assessment of parent-of-origin effects in linkage analysis of quantitative traits. Am. J. Hum. Genet. 68: 951-962.
11. HOLMANS, P., 1993 Asymptotic properties of affected sib-pair linkage analysis. Am. J. Hum. Genet. 52: 362-374.
12. KNAPP, M.,1999 A note on power approximations for the transmission/ disequilibrium test. Am. J. Hum. Genet. 64: 1177-1185.
13. KNAPP, M., and K. STRAUCH, 2004 Affected-sib-pair test for linkage based on constraints for identical-by-descent distributions corresponding to disease models with imprinting. Genet. Epidemiol. 26: 273-285.
14. MORISON, I. M., C. J. PATON and S. D. CLEVERLEY, 2001 The imprinted gene and parent-of-origin effect database. Nucleic Acids Res. 29: 275-276.
15. OTT, J., 1999 Analysis of Human Genetic Linkage. Johns Hopkins University Press, Baltimore/London.
16. PFEIFER, K., 2000 Mechanisms of genomic imprinting. Am. J. Hum. Genet. 67: 777-787.
17. RAO, C. R., 1973 Linear Statistical Inference and Its Applications, Ed. 2. Wiley, New York.
18. REIK, W., and J. WALTER, 2001 Genomic imprinting: parental influence on the genome. Nat. Rev. Genet. 2: 21-32.
19. RISCH, N., and K. MERIKANGAS, 1996 The future of genetic studies of complex human diseases. Science 273: 1516-1517.
20. SEBASTIANI, P., M. M. ABAD, G. ALPARGU and M. F. RAMONI, 2004 Robust transmission/disequilibrium test for incomplete family genotypes. Genetics 168: 2329-2337.
21. SHETE, S., and C. I. AMOS, 2002 Testing for genetic linkage in families by a variance-components approach in the presence of genomic imprinting. Am. J. Hum. Genet. 70: 751-757.
22. SHETE, S., X. ZHOU and C. I. AMOS, 2003 Genomic imprinting and linkage test for quantitative-trait loci in extended pedigrees. Am. J. Hum. Genet. 73: 933-938.
23. SMALLEY, S. L., 1993 Sex-specific recombination frequencies: A consequence of imprinting? Am. J. Hum. Genet. 52: 210-212.
24. SPIELMAN, R. S., and W. J. EWENS, 1998 A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am. J. Hum. Genet. 62: 450-458.
25. SPIELMAN, R. S., R. E. MCGINNIS and W. J. EWENS, 1993 Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am. J. Hum. Genet. 52: 506-516.
26. STRAUCH, K., 2005 Gene mapping, imprinting and epigenetics, pp. 379-388 in Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, Vol. 1, edited by L. B. JORDE, P. F. R. LITTLE, M. J. DUNN and S. SUBRAMANIAM. John Wiley & Sons, Chichester, UK.
27. STRAUCH, K., and M. P. BAUR, 2005 Parent-of-origin, imprinting, mitochondrial, and X-linked effects in traits related to alcohol dependence: presentation group 18 of genetic analysis workshop 14. Genet. Epidemiol. 29(Suppl.): S125-S132.
28. STRAUCH, K., R. FIMMERS, T. KURZ, K. A. DEICHMANN, T. F. WIENKER et al., 2000 Parametric and nonparametric multipoint linkage analysis with imprinting and two-locus-trait models: application to mite sensitization. Am. J. Hum. Genet. 66: 1945-1957.
29. SUN, F. Z., W. D. FLANDERS, Q. H. YANG and M. J. KHOURY, 1999 Transmission disequilibrium test (TDT) when only one parent is available: the 1-TDT. Am. J. Epidemiol. 150: 97-104.
30. WEINBERG, C. R., 1999 Methods for detection of parent-of-origin effects in genetic studies of case-parents triads. Am. J. Hum. Genet. 65: 229-235.
31. WEINBERG, C. R., A. J. WILCOX and R. T. LIE, 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.
32. WILKINS, J. F., and D. HAIG, 2003 What good is genomic imprinting: the function of parent-specific gene expression. Nat. Rev. Genet. 4: 359-368.
33. WU, C. C., S. SHETE and C. I. AMOS, 2005 Linkage analysis of affected sib pairs allowing for parent-of-origin effects. Ann. Hum. Genet. 69: 113-126.
34. XIONG, M. M., and S. W. GUO, 1998 The power of linkage detection by the transmission disequilibrium tests. Hum. Hered. 48: 295-312.
35. ZHOU, J. Y., Y. Q. HU and W. K. FUNG, 2007 A simple method for detection of imprinting effects based on case-parents trios. Heredity 98: 85-91.