A confidence set inference method for identifying SNPs that regulate quantitative phenotypes

Human Heredity

Volumn 73, Issue 3, 2012, Pages 174-183

  Papachristou, Charalampos ^a   Lin, Shili ^b  

^a UNIVERSITY OF THE SCIENCES   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Confidence set inference; Disease gene localization; Family based association test; Genome wide association studies; High density lipoprotein; Linear mixed models; Quantitative traits

Indexed keywords

HIGH DENSITY LIPOPROTEIN;

ANALYTIC METHOD; ARTICLE; CONCEPTUAL FRAMEWORK; CONFIDENCE SET INFERENCE; CONTROLLED STUDY; DATA ANALYSIS; FOLLOW UP; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; LIPOPROTEIN BLOOD LEVEL; MEDICAL RECORD; PHENOTYPE; QUANTITATIVE TRAIT; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; COMPUTER SIMULATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LIPOPROTEINS, HDL; MODELS, GENETIC; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84863509296     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000339178     Document Type: Article

References (43)

1. Yang HH, Hu N, Taylor PR, Lee MP: Whole genome-wide association study using affymetrix SNP chip: a two-stage sequential selection method to identify genes that increase the risk of developing complex diseases. Methods Mol Med 2008; 141: 23-35.
2. Manolio TA: Genomewide association studies and assessment of the risk of disease. N Engl J Med 2010; 363: 166-176.
3. Dickson SP, Wang K, Krantz I, Hakonarson H, Goldstein DB: Rare variants create synthetic genome-wide associations. PLoS Biol 2010; 8::e1000294.
4. Yoo YJ, Bull SB, Paterson AD, Waggott D, Sun L: Were genome-wide linkage studies a waste of time? Exploiting candidate regions within genome-wide association studies. Genet Epidemiol 2010; 34: 107-118.
5. Stewart WC, Peljto AL, Greenberg DA: Multiple subsampling of dense SNP data localizes disease genes with increased precision. Hum Hered 2010; 69: 152-159.
6. Bull SB, John S, Briollais L: Fine mapping by linkage and association in nuclear family and case-control designs. Genet Epidemiol 2005; 29(suppl 1)::48-58.
7. Papachristou C, Lin S: A comparison of methods for intermediate fine mapping. Genet Epidemiol 2006; 30: 677-689. (Pubitemid 44851515)
8. Rohlfs RV, Taylor C, Mirea L, Bull SB, Corey M, Anderson AD: One-stage design is empirically more powerful than two-stage design for family-based genome-wide association studies. BMC Proc 2007; 1(suppl 1)::S137.
9. Sinha R, Igo RP, Saini SK, Elston RC, Luo Y: Bayesian intervals for linkage locations. Genet Epidemiol 2009; 33: 604-616.
10. Liang KY, Chiu YF, Beaty TH: A robust identity-by-descent procedure using affected sib pairs: multipoint mapping for complex diseases. Hum Hered 2001; 51: 64-78.
11. Hossjer O: Assessing accuracy in linkage analysis by means of confidence regions. Genet Epidemiol 2003; 25: 59-72. (Pubitemid 36791327)
12. Schaid DJ, Sinnwell JP, Thibodeau SN: Robust multipoint identical-by-descent mapping for affected relative pairs. Am J Hum Genet 2005; 76: 128-138. (Pubitemid 40023771)
13. Biernacka JM, Sun L, Bull SB: Tests for the presence of two linked disease susceptibility genes. Genet Epidemiol 2005; 29: 389-401. (Pubitemid 41720956)
14. Ott J: Analysis of Human Genetic Linkage, ed 3. Baltimore, Johns Hopkins University Press, 1999.
15. Lander ES, Botstein D: Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989; 121: 185-199.
16. Walling GA, Visscher PM, Haley CS: A comparison of bootstrap methods to construct confidence intervals in QTL mapping. Genet Res 1998; 71: 171-180. (Pubitemid 28370504)
17. Ooijen JW: Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 1992; 84: 803-811.
18. Mangin B, Goffinet B, Rebai A: Constructing confidence intervals for QTL location. Genetics 1994; 138: 1301-1308. (Pubitemid 24375272)
19. Bennewitz J, Reinsch N, Kalm E: Improved confidence intervals in quantitative trait loci mapping by permutation bootstrapping. Genetics 2002; 160: 1673-1686. (Pubitemid 34454388)
20. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J: Complement factor H polymorphism in age-related macular degeneration. Science 2005; 308: 385-389. (Pubitemid 40530070)
21. De Gobbi M, Viprakasit V, Hughes JR, Fisher C, Buckle VJ, Ayyub H, Gibbons RJ, Vernimmen D, Yoshinaga Y, de Jong P, Cheng JF, Rubin EM, Wood WG, Bowden D, Higgs DR: A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science 2006; 312: 1215-1217. (Pubitemid 43801147)
22. Chen WM, Abecasis GR: Family-based association tests for genomewide association scans. Am J Hum Genet 2007; 81: 913-926. (Pubitemid 47580246)
23. Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002; 30: 97-101.
24. Kraja AT, Culverhouse R, Daw EW, Wu J, Van Brunt A, Province MA, Borecki IB: The Genetic Analysis Workshop 16 Problem 3: simulation of heritable longitudinal cardiovascular phenotypes based on actual genome-wide single-nucleotide polymorphisms in the Framingham Heart Study. BMC Proc 2009; 3(suppl 7)::S4.
25. Jaquard A: The genetic structure of populations. New York: Springer-Verlag, 1974.
26. Abney M, McPeek MS, Ober C: Estimation of variance components of quantitative traits in inbred populations. Am J Hum Genet 2000; 66: 629-650. (Pubitemid 30468840)
27. Haseman JK, Elston RC: The investigation of linkage between a quantitative trait and a marker locus. Behav Genet 1972; 2: 3-19.
28. Kathiresan S, Manning AK, Demissie S, D'Agostino RB, Surti A, Guiducci C, Gianniny L, Burtt NP, Melander O, Orho-Melander M, Arnett DK, Peloso GM, Ordovas JM, Cupples LA: A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. BMC Med Genet 2007; 8(suppl 1)::S17.
29. Papachristou C: Confidence set of putative quantitative trait loci in whole genome scans with application to the Genetic Analysis Workshop 17 simulated data. BMC Proc 2011; 5(suppl 9)::S58.
30. Leal SM, Yan K, Muller-Myhsok B: SimPed: a simulation program to generate haplotype and genotype data for pedigree structures. Hum Hered 2005; 60: 119-122. (Pubitemid 41540639)
31. Heid IM, Boes E, Muller M, Kollerits B, Lamina C, Coassin S, Gieger C, Doring A, Klopp N, Frikke-Schmidt R, Tybjaerg-Hansen A, Brandstatter A, Luchner A, Meitinger T, Wichmann HE, Kronenberg F: Genomewide association analysis of high-density lipoprotein cholesterol in the populationbased KORA study sheds new light on intergenic regions. Circ Cardiovasc Genet 2008; 1: 10-20.
32. Ma L, Yang J, Runesha HB, Tanaka T, Ferrucci L, Bandinelli S, Da Y: Genome-wide association analysis of total cholesterol and high-density lipoprotein cholesterol levels using the Framingham heart study data. BMC Med Genet 2010; 11: 55.
33. Piccolo SR, Abo RP, Allen-Brady K, Camp NJ, Knight S, Anderson JL, Horne BD: Evaluation of genetic risk scores for lipid levels using genome-wide markers in the Framingham Heart Study. BMC Proc 2009; 3(suppl 7)::S46.
34. Waterworth DM, Ricketts SL, Song K, et al: Genetic variants influencing circulating lipid levels and risk of coronary artery disease. Arterioscler Thromb Vasc Biol 2010; 30: 2264-2276.
35. Raychaudhuri S, Thomson BP, Remmers EF, et al: Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk. Nat Genet 2009; 41: 1313-1318.
36. Toms TE, Panoulas VF, Smith JP, Douglas KM, Metsios GS, Stavropoulos-Kalinoglou A, Kitas GD: Rheumatoid arthritis susceptibility genes associate with lipid levels in patients with rheumatoid arthritis. Ann Rheum Dis 2011; 70: 1025-1032.
37. van Halm VP, Nielen MM, Nurmohamed MT, van Schaardenburg D, Reesink HW, Voskuyl AE, Twisk JW, van de Stadt RJ, de Koning MH, Habibuw MR, van der Horst-Bruinsma IE, Dijkmans BA: Lipids and inflammation: serial measurements of the lipid profile of blood donors who later developed rheumatoid arthritis. Ann Rheum Dis 2007; 66: 184-188. (Pubitemid 46226052)
38. Arya R, Lehman D, Hunt KJ, Schneider J, Almasy L, Blangero J, Stern MP, Duggirala R: Evidence for bivariate linkage of obesity and HDL-C levels in the Framingham Heart Study. BMC Genet 2003; 4(suppl 1)::S52.
39. Charlesworth JC, Peralta JM, Drigalenko E, Goring HH, Almasy L, Dyer TD, Blangero J: Toward the identification of causal genes in complex diseases: a gene-centric joint test of significance combining genomic and transcriptomic data. BMC Proc 2009; 3(suppl 7)::S92.
40. Borecki IB, Province MA: Genetic and genomic discovery using family studies. Circulation 2008; 118: 1057-1063.
41. Rosenthal EA, Wijsman EM: Joint linkage and segregation analysis under multiallelic trait inheritance: simplifying interpretations for complex traits. Genet Epidemiol 2010; 34: 344-353.
42. Vieland VJ, Hodge SE, Greenberg DA: Adequacy of single-locus approximations for linkage analyses of oligogenic traits. Genet Epidemiol 1992; 9: 45-59.
43. Vieland VJ, Greenberg DA, Hodge SE: Adequacy of single-locus approximations for linkage analyses of oligogenic traits: extension to multigenerational pedigree structures. Hum Hered 1993: 43: 329-336. (Pubitemid 23353845)