A family-based likelihood ratio test for general pedigree structures that allows for genotyping error and missing data

Human Heredity

Volumn 66, Issue 2, 2008, Pages 99-110

  Yang, Yang ^a   Wise, Carol A ^b,c,d   Gordon, Derek ^e   Finch, Stephen J ^a  

^a Stony Brook University   (United States)

^b TEXAS SCOTTISH RITE HOSPITAL FOR CHILDREN   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^d UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^e RUTGERS UNIVERSITY   (United States)

Author keywords

Family based association study; Genetic association studies; Missing data; TDT like tests

Indexed keywords

ARTICLE; CHI SQUARE DISTRIBUTION; FAMILY; GENE LOCUS; GENOTYPE; HUMAN; IDIOPATHIC SCOLIOSIS; MAJOR CLINICAL STUDY; NULL HYPOTHESIS; PARENT; PEDIGREE; SIMULATION; STATISTICAL ANALYSIS; STATISTICAL MODEL; TRANSMISSION DISEQUILIBRIUM TEST;

CHILD; CHROMOSOME MAPPING; COMPUTER SIMULATION; DNA HELICASES; DNA-BINDING PROTEINS; GENETIC DISEASES, INBORN; GENETIC TECHNIQUES; GENOTYPE; HUMANS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; NUCLEAR FAMILY; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; SCOLIOSIS;

EID: 41649115381     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000119109     Document Type: Article

References (38)

1. Spielman RS, McGinnis RE, Ewens WJ: Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 1993;52:506-516.
2. Schaid DJ: General score tests for associations of genetic markers with disease using cases and their parents. Genet Epidemiol 1996;13:423-449.
3. Schaid DJ, Sommer SS: Comparison of statistics for candidate-gene association studies using cases and parents. Am J Hum Genet 1994;55:402-409.
4. Spielman RS, Ewens WJ: The TDT and other family-based tests for linkage disequilibrium and association. Am J Hum Genet 1996;59:983-989.
5. Spielman RS, Ewens WJ: A sibship test for linkage in the presence of association: the sib transmission/disequilibrium test. Am J Hum Genet 1998;62:450-458.
6. Martin ER, Kaplan NL, Weir BS: Tests for linkage and association in nuclear families. Am J Hum Genet 1997;61:439-448.
7. Horvath S, Xu X, Laird NM: The family based association test method: strategies for studying general genotype - phenotype associations. Eur J Hum Genet 2001;9:301-306.
8. Allison DB: Transmission-disequilibrium tests for quantitative traits. Am J Hum Genet 1997;60:676-690.
9. Rabinowitz D: A transmission disequilibrium test for quantitative trait loci. Hum Hered 1997;47:342-350.
10. Sun F, Flanders WD, Yang Q, Khoury MJ: Transmission disequilibrium test (TDT) when only one parent is available: The 1-TDT. Am J Epidemiol 1999;150:97-104.
11. Cheng KF, Chen JH: A simple and robust TDT-type test against genotyping error with error rates varying across families. Hum Hered 2007;64:114-122.
12. Gordon D, Haynes C, Johnnidis C, Patel SB, Bowcock AM, Ott J: A transmission disequilibrium test for general pedigrees that is robust to the presence of random genotyping errors and any number of untyped parents. Eur J Hum Genet 2004;12:752-761.
13. Gordon D, Heath SC, Liu X, Ott J: A transmission/disequilibrium test that allows for genotyping errors in the analysis of singlenucleotide polymorphism data. Am J Hum Genet 2001;69:371-380.
14. Laird NM, Lange C: Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 2006;7:385-394.
15. Lange K, Sinsheimer JS, Sobel E: Association testing with Mendel. Genet Epidemiol 2005;29:36-50.
16. Guo CY, Lunetta KL, DeStefano AL, Ordovas JM, Cupples LA: Informative-transmission disequilibrium test (i-TDT): Combined linkage and association mapping that includes unaffected offspring as well as affected offspring. Genet Epidemiol 2007;31:115-133.
17. Huang J, Jiang Y: The score statistic of the LD-lod analysis: detecting linkage adaptive to linkage disequilibrium. Hum Hered 2001;52:83-98.
18. Laird NM, Horvath S, Xu X: Implementing a unified approach to family-based tests of association. Genet Epidemiol 2000;19(suppl 1):S36-S42.
19. Morris RW, Kaplan NL: Testing for association with a case-parents design in the presence of genotyping errors. Genet Epidemiol 2004;26:142-154.
20. Bernardinelli L, Berzuini C, Seaman S, Holmans P: Bayesian trio models for association in the presence of genotyping errors. Genet Epidemiol 2004;26:70-80.
21. Gao X, Gordon D, Zhang D, Browne R, Helms C, Gillum J, Weber S, Devroy S, Swaney S, Dobbs M, Morcuende J, Sheffield V, Lovett M, Bowcock A, Herring J, Wise C: CHD7 gene polymorphisms are associated with susceptibility to idiopathic scoliosis. Am J Hum Genet 2007;80:957-965.
22. Little RJA, Rubin DB: Statistical Analysis with Missing Data. New York, John Wiley, 1987.
23. Tu IP, Balise RR, Whittemore AS: Detection of disease genes by use of family data. II. Application to nuclear families. Am J Hum Genet 2000;66:1341-1350.
24. Whittemore AS, Tu IP: Detection of disease genes by use of family data. I. Likelihood-based theory. Am J Hum Genet 2000;66:1328-1340.
25. Demenais FM, Elston RC: A general transmission probability model for pedigree data. Hum Hered 1981;31:93-99.
26. Schafer JL, Graham JW: Missing data: Our view of the state of the art. Psychol Meth 2002;7:147-177.
27. Gordon D, Ott J: Assessment and management of single nucleotide polymorphism genotype errors in genetic association analysis. Pac Symp Biocomput 2001:18-29.
28. Douglas JA, Skol AD, Boehnke M: Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data. Am J Hum Genet 2002;70:487-495.
29. Ehm MG, Kimmel M, Cottingham RW Jr: Error detection for genetic data, using likelihood methods. Am J Hum Genet 1996;58:225-234.
30. Chanock SJ, Manolio T, Boehnke M, Boerwinkle E, Hunter DJ, Thomas G, Hirschhorn JN, Abecasis G, Altshuler D, Bailey-Wilson JE, Brooks LD, Cardon LR, Daly M, Donnelly P, Fraumeni JF Jr, Freimer NB, Gerhard DS, Gunter C, Guttmacher AE, Guyer MS, Harris EL, Hoh J, Hoover R, Kong CA, Merikangas KR, Morton CC, Palmer LJ, Phimister EG, Rice JP, Roberts J, Rotimi C, Tucker MA, Vogan KJ, Wacholder S, Wijsman EM, Winn DM, Collins FS: Replicating genotype-phenotype associations. Nature 2007;447:655-660.
31. Powell M, Dorai-Raj S: Powell's UObyQA algorithm. 2006: http://cran.r-project.org/doc/packages/powell.pdf.
32. Weeks DE, Ott J, M. LG: SLINK: A general simulation program for linkage analysis. Am J Hum Genet 1990;47(suppl):A204.
33. Kolmogoroff A: Confidence limits for an unknown distribution function. Ann Math Stat 1941;12:461-463.
34. Smirnoff N: On the estimation of the discrepancy between empirical curves of distribution for two independent samples. Bulletin de l Universite de Moscou, Serie internationale (Mathematiques) 1939;2:3-14.
35. Abel L, Muller-Myhsok B: Maximum-likelihood expression of the transmission/disequilibrium test and power considerations. Am J Hum Genet 1998;63:664-667.
36. Siegmund KD, Gauderman WJ: Association tests in nuclear families. Hum Hered 2001;52:66-76.
37. Dempster AP, Laird NM, Rubin DB: Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc B 1977;39:1-38.
38. Weeks DE. http://cran.r-project.org/doc/packages/powerpkg.pdf