A comparison of methods for intermediate fine mapping

Genetic Epidemiology

Volumn 30, Issue 8, 2006, Pages 677-689

  Papachristou, Charalampos ^a   Lin, Shili ^b  

^a UNIVERSITY OF CHICAGO   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Bootstrap intervals; Confidence set inference; Disease gene localization; Generalized estimating equations; Lod support intervals

Indexed keywords

ACCURACY; ARTICLE; CONFIDENCE INTERVAL; CONFIDENCE SET INTERFERENCE PROCEDURE; DATA ANALYSIS; GENE LOCUS; GENE MAPPING; GENERALIZED ESTIMATING EQUATION METHOD; GENETIC ANALYSIS; GENETIC TRAIT; GENOME; GENOME ANALYSIS; HUMAN; INTERMETHOD COMPARISON; LINKAGE ANALYSIS; LOD SUPPORT APPROACH; MATHEMATICAL MODEL; METHODOLOGY; PROBABILITY; SAMPLE SIZE; SIMULATION;

ARTHRITIS, RHEUMATOID; CHROMOSOME MAPPING; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENETIC DISEASES, INBORN; GENETIC TECHNIQUES; GENOME; HUMANS; LOD SCORE; MODELS, GENETIC; MODELS, STATISTICAL; MODELS, THEORETICAL; PROBABILITY; SOFTWARE;

EID: 33845219792     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20179     Document Type: Article

References (38)

1. Abecasis GR, Cherney SS, Cookson WO, Cardon LR. 2002. Merlin: rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97-101.
2. Bailey-Wilson JE, Almasy L, Edenberg H, Greenberg DA, Hansen MS, Kennedy CC, Thomas D, W Pugh E, Maccluer JW. 2005. Genetic analysis workshop 14: introduction to workshop summaries. Genet Epidemiol 29 (Suppl 1):S1-S6.
3. Bennewitz J, Reinsch N, Kalma E. 2002. Improved confidence intervals in quantitative trait loci mapping by permutation bootstrapping. Genetics 160:1673-1686.
4. Biernacka J, Sun L, Bull SB. 2005. Tests for the presence of two linked disease susceptibility genes. Genet Epidemiol 29:389-401.
5. Bull SB, John S, Briollais L. 2005. Fine mapping by linkage and association in nuclear family and case-control designs. Genet Epidemiol 29 (Suppl 1):S48-S58.
6. Cordell HJ. 2004. Bias towards the null hypothesis in model-free linkage analysis is highly dependent on the test statistic used. Am J Hum Genet 74:1294-1302.
7. Dupuis J, Siegmund D. 1999. Statistical methods for mapping quantitative trait loci from a dense set of markers. Genetics 151:373-386.
8. Fisher SA, Lanchbury JS, Lewis CM. 2003. Meta-analysis of four rheumatoid arthritis genome-wide linkage studies - confirmation of a susceptibility locus on chromosome 16. Arthritis Rheum 48:1200-1206.
9. Gregersen PK. 1999. Genetics of rheumatoid arthritis: confronting complexity. Arthritis Res 1:37-44.
10. Gudbjartsson DF, Jonasson K, Frigge M, Kong A. 2000. Allegro, a new computer program for multipoint linkage analysis. Nat Genet 25:12-13.
11. Holmans P. 1993. Asymptotic properties of affected sib-pair linkage analysis. Am J Hum Genet 52:362-374.
12. Hössjer O. 2003. Assessing accuracy in linkage analysis by means of confidence regions. Genet Epidemiol 25:59-72.
13. Hovatta I, Lichtermann D, Junoven H, Suvisaari J, Terwillinger JD, Arajarvi R, Kokko-Sahin M-L, Ekelund J, Lonnqvist J, Peltonen L. 1998. Linkage analysis of putative schizophrenia gene candidate region on chromosomes 3p, 5q, 6p, 8p, 20p and 22q in a population-based sampled Finnish family set. Mol Psychiatry 3:452-457.
14. John S, Hajeer A, Marlow A, Myerscough A, Silman AJ, Ollier WE, Worthington J. 1997. Investigation of candidate disease susceptibility genes in rheumatoid arthritis: principles and strategies. J Rheumatol 24:199-201.
15. John S, Shephard N, Lin G, Zeggini E, Cao M, Chen W, Vasavda N, Mills T, Barton A, Hinks A, Eyre S, Jones KW, Ollier W, Silman A,Gibson N, Worthington J, Kennedy GC. 2004. Whole-genome scan, in a complex disease, using 11,245 single-nucleotide polymorphisms: comparison with microsatellites. Am J Hum Genet 75:54-64.
16. Knapp M, Seuchter SA, Baur MP. 1994. Two-locus disease models with two marker loci: the power of affected-sib-pair tests. Am J Hum Genet 55:1030-1041.
17. Kong A, Cox N. 1997. Allele-sharing models: lod scores and accurate linkage tests. Am J Hum Genet 61:1179-1188.
18. Kruglyak L, Lander ES. 1995. Complete multipoint sib-pair analysis of qualitative and quantitative traits. Am J Hum Genet 57:439-454.
19. 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.
20. Lebrec J, Putter H, van Houwelingen JC. 2006. Potential bias in generalized estimating equations linkage methods under incomplete information. Genet Epidemiol 30:94-100.
21. Liang K-Y, Chiu YF, Beaty TH. 2001. A robust identity-by-descent procedure using affected sib pairs: multipoint mapping for complex disease. Hum Hered 51:64-78.
22. Lin S. 2002. Construction of a confidence set of markers for the location of a disease gene using affected-sib-pair data. Hum Hered 53:103-112.
23. Mackay K, Eyre S, Mysercough A, Milicic A, Barton A, Laval S, Barrett J, Lee D, White S, John S, Brown MA, Bell J, Silman A, Ollier W, Wordsworth P, Worthington J. 2002. Whole-genome linkage analysis of rheumatoid arthritis susceptibility loci in 252 affected sibling pairs in the United Kingdom. Arthritis Rheum 46:632639.
24. Mangin B, Goffinet B, Rebai A. 1994. Constructing confidence intervals for QTL location. Genetics 138:1301-1308.
25. Middleton FA, Pato MT, Gentile KL, Morley CP, Zhao X, Eisener AF, Brown A, Petryshen TL, Kirby AN, Medeiros H, Carvalho C, Macedo A, Dourado A, Coelho I, Valente J, Soares MJ, Ferreira CP, Lei M, Azevedo MH, Kennedy JL, Daly MJ, Sklar P, Pato CN. 2004. Genomewide linkage analysis of bipolar disorder by use of a high-density single-nucleotide-polymorphism (SNP) genotyping assay: a comparison with microsatellite marker assays and finding of significant linkage to chromosome 6q22. Am J Hum Genet 74:886-897.
26. Nemesure BB, Greenberg DA, Mendell NR. 1995. Simulation study comparing interval estimates for the recombination fraction. Genet Epidemiol 12:351-359.
27. O'Connell JR, Weeks DE. 1998. PedCheck: a program for identification of genotype incompatibilities in linkage analysis. Am J Hum Genet 63:259-266.
28. Ott J. 1999. Analysis of Human Genetic Linkage, 3rd edition. Baltimore: Johns Hopkins University Press.
29. Papachristou C, Lin S. 2006a. Microsatellites versus single-nucleotide polymorphisms in confidence interval estimation of disease loci. Genet Epidemiol 30:3-17.
30. Papachristou C, Lin S. 2006b. A two-step procedure for the construction of confidence regions for trait loci with application to a rheumatoid arthritis dataset. Genet Epidemiol 30:18-29.
31. Risch N. 1990. Linkage strategies for genetically complex traits. III. The effect of marker polymorphism on analysis of affected relative pairs. Am J Hum Genet 46:242-253.
32. Schaid DJ, Guenther JC, Christensen GB, Hebbring S, Rosenow C, Hilker CA, McDonnell SK, Cunningham JM, Slager SL, Blute ML, Thibodeau SN. 2004. Comparison of microsalellites versus single-nucleotide polymorphisms in a genome linkage screen for prostate cancer-susceptibility Loci. Am J Hum Genet 75:948-965.
33. Schaid DJ , Sinnwell JP, Thibodeau SN. 2005. Robust multipoint identical-by-descent mapping for affected relative pairs. Am J Hum Genet 76:128-138.
34. Sun L, Cox NJ, McPeek MS. 2002. A statistical method for identification of polymorphisms that explain a linkage result. Am J Hum Genet 70:399-411.
35. Van Ooijen JW. 1992. Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803-811.
36. Visscher PM, Thompson R, Haley CS. 1996. Confidence intervals in QTL mapping by bootstrapping. Genet 143:1013-1020.
37. Wordsworth BP, Bell JI. 1991. Polygenic susceptibility in rheumatoid arthritis. Ann Rheum Dis 50:343-346.
38. Worthington J, Ollier WE, Leach MK, Smith I, Hay EM, Thomson W, Pepper L, Carthy D, Farhan A, Martin S. 1994. The arthritis and rheumatism council's national repository of family material: pedigrees from the first 100 rheumatoid arthritis families containing affected sibling pairs. Br J Rheumatol 33:970-976.