On the use of haplotype phylogeny to detect disease susceptibility loci

BMC Genetics

Volumn 6, Issue , 2005, Pages

  Bardel, Claire ^a   Danjean, Vincent ^b   Hugot, Jean Pierre ^c,d   Darlu, Pierre ^a   Génin, Emmanuelle ^a  

^a INSERM   (France)

^b UNIVERSITÉ BORDEAUX 1   (France)

^c HÔPITAL ROBERT DEBRÉ   (France)

^d Fondation Jean Dausset   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; NOD2 PROTEIN, HUMAN; SIGNAL PEPTIDE;

ARTICLE; CLADISTICS; COMPUTER MODEL; CONTROLLED STUDY; CROHN DISEASE; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCATION; GENE LOCUS; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC MODEL; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HAPLOTYPE; INTERMETHOD COMPARISON; MOLECULAR PHYLOGENY; PHYLOGENETIC TREE; PROBABILITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; GENETIC POLYMORPHISM; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; HUMAN; METHODOLOGY; MUTATION; PHYLOGENY;

CROHN DISEASE; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; HAPLOTYPES; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; LINKAGE DISEQUILIBRIUM; MUTATION; NOD2 SIGNALING ADAPTOR PROTEIN; PHYLOGENY; POLYMORPHISM, GENETIC;

EID: 25444512399     PISSN: 14712156     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2156-6-24     Document Type: Article

References (44)

1. Collins FS: Preparing health professionals for the genetic revolution. Jama 1997, 278:1285-1286.
2. Collins FS, Brooks LD, Chakravarti A: A DNA polymorphism discovery resource for research on human genetic variation. Genome Res 1998, 8:1229-1231.
3. Schork NJ, Fallin D, Lanchbury S: Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet 2000, 58:250-264.
4. Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, Ehm MG: Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 2002, 53:79-91.
5. Akey J, Jin L, Xiong M: Haplotypes vs single marker linkage disequilibrium tests: what do we gain? European J of Hum Genet 2001, 9:291-300.
6. Douglas JA, Boehnke M, Guillanders E, Trent JM, Gruber SB: Experimentally-derived haplotyes substantially increase the efficiency of linkage disequilibrium studies. Nat Genet 2001, 28:361-364.
7. Fallin D, Cohen A, Essioux L, Chumakov I, Blumenfeld M, Cohen D, Schork NJ: Genetic analysis of case/control data using estimated haplotype frequencies: application to APOE locus variation and Alzheimer's Disease. Genome Res 2001, 11:143-151.
8. Tiret L, Amouyel P, Rakotovao R, Cambien F, Ducimetière P: Testing for association between disease and linked marker loci: a log-linear-mode analysis. Am J Hum Genet 1991, 48:926-934.
9. Nielsen DM, Ehm MG, Zaykin DV, Weir BS: Effect of two- and three-locus linkage disequilibrium on the power to detect marker/phenotype association. Genetics 2004, 168:1029-1040.
10. Zhao JH, Curtis D, Sham PC: Model-free analysis and permutation tests for allelic associations. Hum Hered 2000, 50:133-139.
11. Templeton AR, Boerwinkle E, Sing CF: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics 1987, 117:343-351.
12. Schierup MH, Hein J: Consequences of recombination on traditional phylogenetic analysis. Genetics 2000, 156:879-891.
13. Gabriel SB, Scaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyamo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D: The structure of haplotype blocks in the human genome. Science 2002, 296:2225-2229.
14. Templeton AR, Sing CF, Kessling A, Humphries S: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations. Genetics 1988, 120:1145-1154.
15. Templeton AR, Crandall KA, Sing CF: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 1992, 132:619-633.
16. Templeton AR, Sing CF: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analysis with cladogram uncertainty and recombination. Genetics 1993, 134:659-669.
17. Templeton AR: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. analysis of case/control sampling designs: Alzheimer's disease and the Apolipoprotein E locus. Genetics 1995, 140:403-409.
18. Haviland MB, Kessling AM, Davignon J, Sing CF: Cladistic analysis of the Apolipoprotein AI-CIII-AIV gene cluster using a healthy French Canadian sample. I. Haploid analysis. Ann Hum Genet 1995, 59:211-231.
19. Keavney B, McKenzie CA, Connell JMC, Julier C, Ratcliffe PJ, Sobel E, Lathrop M, Farrall M: Measured haplotype analysis of the angiotensin-I converting enzyme gene. Hum Mol Genet 1998, 7(11):1745-1751.
20. Zhu X, Cooper RS, Chen G, Luke A, Eltson R: Localization of the Q1 mutation by cladistic analysis. Genet Epidemiol 2001, 21(Suppl.1):S594-S599.
21. Wang GQ, Pietro MD, Roeder K, Heng CK, Bunker CH, Hamman RF, Kamboh MI: Cladistic analysis of human Apolipoprotein A4 polymorphisms in relation to quantitative plasma lipid risk factors of coronary heart disease. Ann of Hum Genet 2003, 67:107-124.
22. Kittles RA, Long JC, Bergen AW, Eggert M, Virkkunen M, Linnoila M, Goldman D: Cladistic association analysis of Y chromosome effects on alcohol dependence and related personality traits. Proc Natl Acad Sci 1999, 96:4204-4209.
23. Lobos EA, Todd RD: Cladistic analysis of disease association with tyroxine hydroxylase: Application to manic-depressive disease and alcoholism. Am J Med Genet 1997, 74:289-295.
24. Lobos E, Todd RD: Association analysis in an evolutionary context: cladistic analysis of the DRD2 locus to test for association with alcoholism. Am J Med Genet 1998, 81:411-419.
25. Darlu P, Génin E: Cladistic analysis of haplotypes as an attempt to detect disease susceptibility. Genet Epidemiol 2001, 21(Suppl.1):S602-S607.
26. Heng CK, Low PS: Cladistic analysis: its application in association studies of complex diseases. Ann Acad Med Singapore 2000, 29:313-321.
27. Seltman H, Roeder K, Devlin B: Transmission/Disequilibrium test meets measured haplotype analysis: family-based association analysis guided by evolution of haplotypes. Am J Hum Genet 2001, 68:1250-1263.
28. Seltman H, Roeder K, Devlin B: Evolutionary-based association using haplotype data. Genet Epidemiol 2003, 25:48-58.
29. Durrant C, Zondervan KT, Cardon LR, Hunt S, Deloukas P, Morris AP: Linkage disequilibrium mapping via cladistic analysis of single-nucleotique polymorphism haplotypes. Am J Hum Genet 2004, 75:35-43.
30. Hugot JP, Chamaillard M, Zouali H, Lesage S, Cézard JP, Belaiche J, Almer S, Tysk C, O'Morain CA, Gassull M, Binder V, Finkel Y, Cortot A, Modigliani R, Laurent-Puig P, Gower-Rousseau C, Macry J, Colombel JF, Sahbatou M, Thomas G: Association of NOD2 leucin-rich repeat variants with susceptibility to Crohn's disease. Nature 2001, 411:599-603.
31. Lazzeroni LC: Linkage disequilibrium and gene mapping: an empirical least-square approach. Am J Hum Genet 1998, 62:159-170.
32. McPeek MS, Strahs A: Assessment of linkage disequilibrium by the decay of haplotype sharing with application to fine-scale genetic mapping. Am J Hum Genet 1999, 65:858-875.
33. Rannala B, Reeve JP: High-resolution multipoint linkage-disequilibrium mapping in the context of a human genome sequence. Am J Hum Genet 2001, 69:159-178.
34. Zhao H, Pfeiffer R, Gail MH: Haplotype analysis in population genetics and association studies. Pharmacogenomics 2003, 4(2):171-178.
35. Niu T: Algorithms for inferring haplotypes. Genet Epidemiol 2004, 27.
36. Grassly NC, Rambaut A: Treevolve, version 1.32 2000.
37. Bourgain C, Génin E, Quesneville H, Clerget-Darpoux F: Search formultifactorial disease susceptibility genes in founder populations. Ann Hum Genet 2000, 64:255-265.
38. APOE T, Alzheimer Disease meta analysis consortium: Effects of age, gender and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. J Am Med Assoc 1997, 278:1349-1356.
39. Felsenstein J: Inferring phylogenies, Sinauer Associates, Inc. 2004 chap. Chapter one: Parsimony methods,:1-18. [ISBN:0878931775].
40. Swofford DL: PAUP Phylogenetic Analysis Using Parcimony. Version 4.0b10. Sunderland, Massachusetts: Sinauer Associates 2002.
41. Daly MJ, Kruglyak L, Pratt S, Houstis N, Reeve MP, Kirby A, Lander ES: Genehunter, version 2.1 2001.
42. Vermeire S, Wild G, Kocher K, Cousineau J, Dufresne L, Bitton A, Langelier D, Pare P, Lapointe G, Cohen A, Daly MJ, Rioux J: CARD15 genetic variation in a Quebec population: prevalence, genotype-phenotype relationship, and haplotype structure. Am J Hum Genet 2002, 71:74-83.
43. Becker T, Knapp M: A powerful strategy to account for multiple testing in the context of haplotype analysis. Am J Hum Genet 2004, 75(4):561-570.
44. Abecasis GR, Cookson WO: GOLD-graphical overview of linkage disequilibrium. Bioinformatics 2000, 16(2):182-183.