On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit

American Journal of Human Genetics

Volumn 72, Issue 4, 2003, Pages 891-902

  Tzeng, Jung Ying ^a   Devlin, B ^b   Wasserman, Larry ^a   Roeder, Kathryn ^a  

^a CARNEGIE MELLON UNIVERSITY   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; EVOLUTION; GENE MUTATION; GENETIC ANALYSIS; GENOME; GENOTYPE; HAPLOTYPE; PRIORITY JOURNAL; SIMULATION; STATISTICAL ANALYSIS;

EID: 0345269986     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/373881     Document Type: Article

References (30)

1. Bourgain C, Génin E, Holopainen P, Mustalahti K, Mäki M, Partanen J (2001) Use of closely related affected individuals for the genetic study of complex diseases in founder populations. Am J Hum Genet 68:154-159
2. Bourgain C, Génin E, Quesneville H, Clerget-Darpoux F (2000) Search for multifactorial disease susceptibility genes in founder populations. Ann Hum Genet 64:255-265
3. Cheung VG, Nelson SF (1998) Genomic mismatch scanning identifies human genomic DNA shared identical by descent. Genomics 47:1-7
4. Clayton DG (1999) A generalization of the transmission/disequilibrium test for uncertain-haplotype transmission. Am J Hum Genet 65:1170-1177
5. Culverhouse R, Lin J, Liu KY, Suarez BK (2001) Exploiting linkage disequilibrium in population isolates. Genet Epidemiol 21 Suppl 1:S429-S434
6. de la Chapelle A, Wright FA (1998) Linkage disequilibrium mapping in isolated populations: the example of Finland revisited. Proc Natl Acad Sci USA 95:12416-12423
7. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997-1004
8. Devlin B, Roeder K, Bacanu SA (2001a) Unbiased methods for population-based association studies. Genet Epidemiol 21:273-284
9. Devlin B, Roeder K, Wasserman L (2000) Genomic control for association studies: a semiparametric test to detect excess-haplotype sharing. Biostatistics 1:369-387
10. _ (2001b) Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 60:155-166
11. Durham LK, Feingold E (1997) Genome scanning for segments shared identical by descent among distant relatives in isolated populations. Am J Hum Genet 61:830-842
12. Fallin D, Schork NJ (2000) Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 67:947-959
13. Fan R, Lange K (1998) Models for haplotype evolution in a nonstationary population. Theor Popul Biol 53:184-198
14. Feder JN, Gnirke A, Thomas W, Tsuchihashi Z, Ruddy DA, Basava A, Dormishian F, et al (1996) A novel MHC class I-like gene is mutated in patients with hereditary haemochromatosis. Nat Genet 13:399-408
15. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225-2229
16. Grant GR, Manduchi E, Cheung VG, Ewens WJ (1999) Significance testing for direct identity-by-descent mapping. Ann Hum Genet 63:441-454
17. Houwen RHJ, Baharloo S, Blankenship K, Raeymaekers P, Juyn J, Sandkuijl LA, Freimer NB (1994) Genome screening by searching for shared segments: Mapping a gene for benign recurrent intrahepatic cholestasis. Nat Genet 8:380-386
18. Jorde LB (2000) Linkage disequilibrium and the search for complex disease genes. Genome Res 10:1435-1444
19. Lain JC, Roeder K, Devlin B (2000) Haplotype fine mapping by evolutionary trees. Am J Hum Genet 66:659-673
20. Lee AJ (1990) U-statistics: theory and practice. Marcel Dekker, New York
21. MacLean CJ, Martin RB, Sham PC, Wang H, Straub RE, Kendler KS (2000) The trimmed-haplotype test for linkage disequilibrium. Am J Hum Genet 66:1062-1075
22. McPeek MS, Strahs A (1999) Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. Am J Hum Genet 65:858-875
23. Ophoff RA, Escamilla MA, Service SK, Spesny M, Meshi DB, Poon W, Molina J, Fournier E, Gallegos A, Mathews C, Neylan T, Batki SL, Roche E, Ramirez M, Silva S, De Mille MC, Dong P, Leon PE, Reus VI, Sandkuijl LA, Freimer NB (2002) Genomewide linkage disequilibrium mapping of severe bipolar disorder in a population isolate. Am J Hum Genet 71:565-574
24. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170-181
25. Puffenberger EG, Kauffman ER, Bolk S, Matise TC, Washington SS, Angrist M, Weissenbach J, Garver KL, Mascari M, Ladda R (1994) Identity by descent and association mapping of a recessive gene for Hirschsprung disease on human chromosome 13q22. Hum Mol Genet 3:1217-1225
26. Qian D, Thomas DC (2001) Genome scan of complex traits by haplotype sharing correlation. Genet Epidemiol 21 Suppl 1:S582-S587
27. Service SK, Temple Lange DW, Freimer NB, Sandkuijl LA (1999) Linkage-disequilibrium mapping of disease genes by reconstruction of ancestral haplotypes in founder populations. Am J Hum Genet 64:1728-1738
28. Thomas DC, Morrison JL, Clayton DG (2001) Bayes estimates of haplotype effects. Genet Epidemiol 21 Suppl 1:S712-S717
29. Tzeng JY, Byerley W, Devlin B, Roeder K, Wasserman L. Outlier detection and false discovery rates for whole-genome DNA matching. J Am Stat Assoc (in press)
30. Van der Meulen MA, Te Meerman GJ (1997) Haplotype sharing analysis in affected individuals from nuclear families with at least one affected offspring. Genet Epidemiol 14:915-920