The Maximum-Likelihood-Binomial method revisited: A robust approach for model-free linkage analysis of quantitative traits in large sibships

Genetic Epidemiology

Volumn 35, Issue 1, 2011, Pages 46-56

  Cobat, Aurelie ^a,b,c   Abel, Laurent ^a,b,d   Alcaïs, Alexandre ^a,b,d  

^a IMAGINE INSTITUTE   (France)

^b UNIVERSITÉ PARIS DESCARTES   (France)

^c HÔPITAL NECKER ENFANTS MALADES   (France)

^d ROCKEFELLER UNIVERSITY   (United States)

Author keywords

Binomial distribution; Leprosy; Likelihood; Linkage analysis; Quantitative trait locus; Sibships

Indexed keywords

BCG VACCINE; MYCOBACTERIUM VACCINE;

ALLELE; ARTICLE; CHROMOSOME; CLINICAL ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETIC MODEL; HUMAN; LEPROMIN TEST; LEPROSY; MAXIMUM LIKELIHOOD METHOD; PHENOTYPE; QUANTITATIVE ANALYSIS; QUANTITATIVE TRAIT; QUANTITATIVE TRAIT LOCUS; SAMPLE SIZE; SIMULATION;

ALLELES; BINOMIAL DISTRIBUTION; ENDOPHENOTYPES; GENETIC LINKAGE; GENOTYPE; HUMANS; LEPROSY; LIKELIHOOD FUNCTIONS; QUANTITATIVE TRAIT LOCI; SIBLINGS;

EID: 78650347553     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20548     Document Type: Article

References (38)

1. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. 2002. Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97-101.
2. Abel L, Muller-Myhsok B. 1998. Robustness and power of the maximum-likelihood-binomial and maximum-likelihood-score methods, in multipoint linkage analysis of affected-sibship data. Am J Hum Genet 63:638-647.
3. Abel L, Alcais A, Mallet A. 1998. Comparison of four sib-pair linkage methods for analyzing sibships with more than two affecteds: interest of the binomial maximum likelihood approach. Genet Epidemiol 15:371-390.
4. Alcais A, Abel L. 1999. Maximum-Likelihood-Binomial method for genetic model-free linkage analysis of quantitative traits in sibships. Genet Epidemiol 17:102-117.
5. Alcais A, Abel L. 2000. Robustness of the Maximum-Likelihood-Binomial approach for linkage analysis of quantitaive trait loci with non-normal phenotypic data. GeneScreen 1:47-50.
6. Alcais A, Sanchez FO, Thuc NV, Lap VD, Oberti J, Lagrange PH, Schurr E, Abel L. 2000. Granulomatous reaction to intradermal injection of lepromin (Mitsuda reaction) is linked to the human NRAMP1 gene in Vietnamese leprosy sibships. J Infect Dis 181:302-308.
7. Allison DB, Neale MC, Zannolli R, Schork NJ, Amos CI, Blangero J. 1999. Testing the robustness of the likelihood-ratio test in a variance-component quantitative-trait loci-mapping procedure. Am J Hum Genet 65:531-544.
8. Almasy L, Blangero J. 1998. Multipoint quantitative-trait linkage analysis in general pedigrees. Am J Hum Genet 62:1198-1211.
9. Almasy L, Blangero J. 2009. Human QTL linkage mapping. Genetica 136:333-340.
10. Amos CI. 1994. Robust variance-components approach for assessing genetic linkage in pedigrees. Am J Hum Genet 54:535-543.
11. Amos CI, de Andrade M. 2001. Genetic linkage methods for quantitative traits. Stat Methods Med Res 10:3-25.
12. Bhattacharjee S, Kuo CL, Mukhopadhyay N, Brock GN, Weeks DE, Feingold E. 2008. Robust score statistics for QTL linkage analysis. Am J Hum Genet 82:567-582.
13. Bouzigon E, Ulgen A, Dizier MH, Siroux V, Lathrop M, Kauffmann F, Pin I, Demenais F. 2007. Evidence for a pleiotropic QTL on chromosome 5q13 influencing both time to asthma onset and asthma score in French EGEA families. Hum Genet 121:711-719.
14. Chen WM, Broman KW, Liang KY. 2004. Quantitative trait linkage analysis by generalized estimating equations: unification of variance components and Haseman-Elston regression. Genet Epidemiol 26:265-272.
15. Cobat A, Gallant CJ, Simkin L, Black GF, Stanley K, Hughes J, Doherty TM, Hanekom WA, Eley B, Jaïs JP, Boland-Auge A, van Helden P, Casanova JL, Abel L, Hoal EG, Schurr E, Alcaïs A. 2009. Two loci control tuberculin skin test reactivity in an area hyperendemic for tuberculosis. J Exp Med 206:2583-2591.
16. Cuenco KT, Szatkiewicz JP, Feingold E. 2003. Recent advances in human quantitative-trait-locus mapping: comparison of methods for selected sibling pairs. Am J Hum Genet 73:863-873.
17. Feingold E. 2002. Regression-based quantitative-trait-locus mapping in the 21st century. Am J Hum Genet 71:217-222.
18. Gallant CJ, Cobat A, Simkin L, Black GF, Stanley K, Hughes J, Doherty TM, Hanekom WA, Eley B, Beyers N, Jaïs JP, van Helden P, Abel L, Alcaïs A, Hoal EG, Schurr E. 2010. Tuberculin skin test and in-vitro assays provide complementary measures of anti-mycobacterial immunity in children and adolescents. Chest 137:1071-1077.
19. Goldgar DE. 1990. Multipoint analysis of human quantitative genetic variation. Am J Hum Genet 47:957-967.
20. Gu C, Todorov A, Rao DC. 1996. Combining extremely concordant sibpairs with extremely discordant sibpairs provides a cost effective way to linkage analysis of quantitative trait loci. Genet Epidemiol 13:513-533.
21. Haseman JK, Elston RC. 1972. The investigation of linkage between a quantitative trait and a marker locus. Behav Genet 2:3-19.
22. Jamieson SE, Miller EN, Black GF, Peacock CS, Cordell HJ, Howson JM, Shaw MA, Burgner D, Xu W, Lins-Lainson Z, Shaw JJ, Ramos F, Silveira F, Blackwell JM. 2004. Evidence for a cluster of genes on chromosome 17q11-q21 controlling susceptibility to tuberculosis and leprosy in Brazilians. Genes Immun 5:46-57.
23. Kleensang A, Franke D, Alcais A, Abel L, Muller-Myhsok B, Ziegler A. 2010. An extensive comparison of quantitative trait Loci mapping methods. Hum Hered 69:202-211.
24. Knoblauch H, Muller-Myhsok B, Busjahn A, Ben Avi L, Bähring S, Baron H, Heath SC, Uhlmann R, Faulhaber HD, Shpitzen S, Aydin A, Reshef A, Rosenthal M, Eliav O, Mühl A, Lowe A, Schurr D, Harats D, Jeschke E, Friedlander Y, Schuster H, Luft FC, Leitersdorf E. 2000. A cholesterol-lowering gene maps to chromosome 13q. Am J Hum Genet 66:157-166.
25. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES. 1996. Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 58:1347-1363.
26. Lander E, Kruglyak L. 1995. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11:241-247.
27. Lebrec J, Putter H, Houwelingen JC. 2004. Score test for detecting linkage to complex traits in selected samples. Genet Epidemiol 27:97-108.
28. Majumder PP, Pal N. 1987. Nonrandom segregation: uniformly most powerful test and related considerations. Genet Epidemiol 4:277-287.
29. Morton NE, MacLean CJ. 1974. Analysis of family resemblance. 3. Complex segregation of quantitative traits. Am J Hum Genet 26:489-503.
30. Peng J, Siegmund D. 2006. QTL mapping under ascertainment. Ann Hum Genet 70:867-881.
31. Ranque B, Alcais A, Thuc NV, Woynard S, Thai VH, Huong NT, Ba NN, Khoa PX, Schurr E, Abel L. 2005. A recessive major gene controls the mitsuda reaction in a region endemic for leprosy. J Infect Dis 192:1475-1482.
32. Ranque B, Alter A, Mira M, Thuc NV, Thai VH, Huong NT, Ba NN, Khoa PX, Schurr E, Abel L, Alcaïs A. 2007. Genomewide linkage analysis of the granulomatous mitsuda reaction implicates chromosomal regions 2q35 and 17q21. J Infect Dis 196:1248-1252.
33. Risch N, Zhang H. 1995. Extreme discordant sib pairs for mapping quantitative trait loci in humans. Science 268:1584-1589.
34. Sham PC, Purcell S. 2001. Equivalence between Haseman-Elston and variance-components linkage analyses for sib pairs. Am J Hum Genet 68:1527-1532.
35. Sham PC, Purcell S, Cherny SS, Abecasis GR. 2002. Powerful regression-based quantitative-trait linkage analysis of general pedigrees. Am J Hum Genet 71:238-253.
36. Szatkiewicz JP, Cuenco KT, Feingold E. 2003. Recent advances in human quantitative-trait-locus mapping: comparison of methods for discordant sibling pairs. Am J Hum Genet 73:874-885.
37. Vincent Q, Alcais A, Alter A, Schurr E, Abel L. 2006. Quantifying genomic imprinting in the presence of linkage. Biometrics 62:1071-1080.
38. Wang K, Huang J. 2002. A score-statistic approach for the mapping of quantitative-trait loci with sibships of arbitrary size. Am J Hum Genet 70:412-424.