Forward-time simulation of realistic samples for genome-wide association studies

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Peng, Bo ^a   Amos, Christopher I ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX STRUCTURE; COMPUTATIONAL CONSTRAINTS; ENVIRONMENTAL FACTORS; GENOME-WIDE ASSOCIATION STUDIES; POPULATION GENETICS; QUANTITATIVE TRAITS; SIMULATION ENVIRONMENT; STRUCTURED POPULATION;

DISEASE CONTROL; TRANSIENTS;

GENES;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOLUTION; GENETIC ASSOCIATION; GENETIC MARKER; GENETIC PREDISPOSITION; HUMAN; HUMAN GENOME; METHODOLOGY; POPULATION GENETICS; VALIDATION STUDY;

ALGORITHMS; COMPUTER SIMULATION; EVOLUTION; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC;

EID: 77956480238     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-442     Document Type: Article

References (61)

1. Sham PC, Purcell S, Cherny SS, Abecasis GR. Powerful regression-based quantitative-trait linkage analysis of general pedigrees. Am J Hum Genet 2002, 71(2):238-253. 10.1086/341560, 379157, 12111667.
2. Amos CI, Krushkal J, Thiel TJ, Young A, Zhu DK, de Andrade EBM. Comparison of model-free linkage mapping strategies for the study of a complex trait. Genet Epidemiol 1996, 14:743-748.
3. Reich D, Patterson N. Will admixture mapping work to find disease genes?. Phil Trans R Soc B 2005, 360:1605-1607. 10.1098/rstb.2005.1691, 1609196, 16096110.
4. Mehta T, Tanik M, Allison DB. Towards sound epistemological foundations of statistical methods for high-dimensional biology. Nat Genet 2004, 36(9):943-947. 10.1038/ng1422, 15340433.
5. Amos CI, Wu X, Broderick P, Gorlov IP, Gu J, Eisen T, Dong Q, Zhang Q, Gu X, Vijayakrishnan J, et al. Genome-wide association scan of tag SNPs identifies a susceptibility locus for lung cancer at 15q25.1. Nat Genet 2008, 40(5):616-622. 10.1038/ng.109, 2713680, 18385676.
6. McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JP, Hirschhorn JN. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 2008, 9(5):356-369. 10.1038/nrg2344, 18398418.
7. Carvajal-Rodriguez A. Simulation of Genomes: A review. Current Genomics 2008, 9:155-159. 10.2174/138920208784340759, 2679650, 19440512.
8. Wiltshire S, Morris AP, Zeggini E. Examining the statistical properties of fine-scale mapping in large-scale association studies. Genet Epidemiol 2008, 32(3):204-214. 10.1002/gepi.20295, 18064636.
9. Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 2007, 39(7):906-913. 10.1038/ng2088, 17572673.
10. Spencer CC, Su Z, Donnelly P, Marchini J. Designing genome-wide association studies: sample size, power, imputation, and the choice of genotyping chip. PLoS Genet 2009, 5(5):e1000477. 10.1371/journal.pgen.1000477, 2688469, 19492015.
11. Chai HS, Sicotte H, Bailey KR, Turner ST, Asmann YW, Kocher JP. GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. BMC Bioinformatics 2009, 10:102. 10.1186/1471-2105-10-102, 2678095, 19344520.
12. Bochdanovits Z, Verhage M, Smit AB, de Geus EJ, Posthuma D, Boomsma DI, Penninx BW, Hoogendijk WJ, Heutink P. Joint reanalysis of 29 correlated SNPs supports the role of PCLO/Piccolo as a causal risk factor for major depressive disorder. Mol Psychiatry 2009, 14(7):650-652. 10.1038/mp.2009.37, 19546850.
13. Tan HY, Callicott JH, Weinberger DR. Intermediate phenotypes in schizophrenia genetics redux: is it a no brainer?. Mol Psychiatry 2008, 13(3):233-238. 10.1038/sj.mp.4002145, 18285755.
14. Wright FA, Huang H, Guan X, Gamiel K, Jeffries C, Barry WT, Pardo-Manuel F, Sullivan PF, Wilhelmsen KC, Zou F. Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics 2007,
15. Li C, Li M. GWAsimulator: a rapid whole-genome simulation program. Bioinformatics 2008, 24(1):140-142. 10.1093/bioinformatics/btm549, 18006546.
16. Hudson RR. Generating samples under a Wright-Fisher neutral model. Bioinformatics 2002, 18:337-338. 10.1093/bioinformatics/18.2.337, 11847089.
17. Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L. CoaSim: A flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 2005, 6:252. 10.1186/1471-2105-6-252, PMC1274299, 16225674.
18. Liang L, Zollner S, Abecasis GR. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 2007, 23(12):1565-1567. 10.1093/bioinformatics/btm138, 17459963.
19. Carvajal-Rodriguez A. GENOMEPOP: a program to simulate genomes in populations. BMC Bioinformatics 2008, 9:223. 10.1186/1471-2105-9-223, 2386491, 18447924.
20. Lambert BW, Terwilliger JD, Weiss KM. ForSim: a tool for exploring the genetic architecture of complex traits with controlled truth. Bioinformatics 2008, 24(16):1821-1822. 10.1093/bioinformatics/btn317, 2732213, 18565989.
21. Peng B, Amos CI, Kimmel M. Forward-time simulations of human populations with complex diseases. PLoS Genetics 2007, 3:e47. 10.1371/journal.pgen.0030047, 1829403,1829403, 17381243.
22. Consortia TH. A haplotype map of the human genome. Nature 2005, 437(7063):1299-1320. 10.1038/nature04226, 16255080.
23. Zollner S, von Haeseler A. A coalescent approach to study linkage disequilibrium between single-nucleotide polymorphisms. Am J Hum Genet 2000, 66(2):615-628. 10.1086/302766, 1288114, 10677321.
24. Wang Y, Rannala B. In Silico Analysis of Disease-Association Mapping Strategies Using the Coalescent Process and Incorporating Ascertainment and Selection. Am J Hum Genet 2005, 76:1066-1073. 10.1086/430472, 1196444, 15818531.
25. McVean GA, Cardin NJ. Approximating the coalescent with recombination. Philos Trans R Soc Lond B Biol Sci 2005, 360(1459):1387-1393. 10.1098/rstb.2005.1673, 1569517, 16048782.
26. Marjoram P, Wall JD. Fast "coalescent" simulation. BMC Genet 2006, 7:16. 10.1186/1471-2156-7-16, PMC1458357, 16539698.
27. Chen GK, Marjoram P, Wall JD. Fast and flexible simulation of DNA sequence data. Genome Res 2009, 19(1):136-142. 10.1101/gr.083634.108, 2612967, 19029539.
28. Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De Iorio M, Balding DJ. Fregene: Simulation of realistic sequence-level data in populations and ascertained samples. Bmc Bioinformatics 2008, 9:11. 10.1186/1471-2105-9-364, 2246154, 18184432.
29. Peng B, Kimmel M. simuPOP: a forward-time population genetics simulation environment. Bioinformatics 2005, 21(18):3686-3687. 10.1093/bioinformatics/bti584, 16020469.
30. Wu CC, Shete S, Chen WV, Peng B, Lee AT, Ma J, Gregersen PK, Amos CI. Detection of disease-associated deletions in case-control studies using SNP genotypes with application to rheumatoid arthritis. Hum Genet 2009, 126(2):303-315. 10.1007/s00439-009-0672-3, 19415332.
31. Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P. A haplotype map of the human genome. Nature 2005, 437:1299-1320. 10.1038/nature04226, 1880871, 16255080.
32. Wise J. Consortium hopes to sequence genome of 1000 volunteers. BMJ 2008, 336(7638):237. 10.1136/bmj.39472.676481.DB, 18244979.
33. Wall JD, Przeworski M. When did the human population size start increasing?. Genetics 2000, 155(4):1865-1874. 1461207, 10924481.
34. Ewens WJ. Mathematical Population Genetics 2004, Springer.
35. Myers S, Bottolo L, Freeman C, McVean G, Donnelly P. A fine-scale map of recombination rates and hotspots across the human genome. Science 2005, 310(5746):247-248. 10.1126/science.1117196, 16224010.
36. Kimura M, Weiss GH. The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 1964, 49(4):561-576. 1210594, 17248204.
37. Hoggart CJ, Chadeau-Hyam M, Clark TG, Lampariello R, Whittaker JC, Iorio MD, Balding DJ. Sequence-level population simulations over large genomic regions. Genetics 2007, 177(3):1725-1731. 10.1534/genetics.106.069088, 2147962, 17947444.
38. Slatkin M. Simulating genealogies of selected alleles in a population of variable size. Genetics Research 2001, 78:49-57. 10.1017/S0016672301005183, 11556137.
39. Slatkin M. Linkage disequibrium in gorwing and stable populations. Genetics 1994, 137:331-336. 1205949, 8056320.
40. McVean GAT. A Genealogical Interpretation of Linkage Disequilibrium. Genetics 2002, 162(2):987-991. 1462283, 12399406.
41. Peng B, Kimmel M. Simulations provide support for the common disease common variant hypothesis. Genetics 2007, 175:1-14. 10.1534/genetics.106.058164, 1774987, 17244759.
42. Li D, Conti DV. Detecting Gene-Environment Interactions Using a Combined Case-Only and Case-Control Approach. Am J Epidemiol 2009, 169(4):497-504. 10.1093/aje/kwn339, 2732970, 19074774.
43. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol 2006, 4:e87. 10.1371/journal.pbio.0040087, 1400604, 16524343.
44. Ayodo G, Price AL, Keinan A, Ajwang A, Otieno MF, Orago ASS, Patterson N, Reich D. Combining Evidence of Natural Selection with Association Analysis Increases Power to Detect Malaria-Resistance Variants. 2007, 81(2):234-242. 1950820, 17668374.
45. McVean G. The Structure of Linkage Disequilibrium Around a Selective Sweep. Genetics 2007, 175(3):1395-1406. 10.1534/genetics.106.062828, 1840056, 17194788.
46. Spencer CC, Coop G. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 2004, 20:3673-3675. 10.1093/bioinformatics/bth417, 15271777.
47. Li M, Boehnke M, Abecasis GR. Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal. Am J Hum Genet 2005, 76(6):934-949. 10.1086/430277, 1196453, 15877278.
48. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21(2):263-265. 10.1093/bioinformatics/bth457, 15297300.
49. Knowler W, Williams R, Pettitt D, Steinberg A. GM3-5,13,14 and type-2 diabetes-mellitus - an association in american-indians with genetic admixture. Am J Hum Genet 1988, 43(4):520-526. 1715499, 3177389.
50. Pritchard JK, Donnelly P. Case-control studies of association in structured or admixed populations. Theor Popul Biol 2001, 60(3):227-237. 10.1006/tpbi.2001.1543, 11855957.
51. Devlin B, Roeder K. Genomic control for association studies. Biometrics 1999, 55(4):997-1004. 10.1111/j.0006-341X.1999.00997.x, 11315092.
52. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006, 38(8):904-909. 10.1038/ng1847, 16862161.
53. Zhu X, Luke A, Cooper RS, Quertermous T, Hanis C, Mosley T, Gu CC, Tang H, Rao DC, Risch N, et al. Admixture mapping for hypertension loci with genome-scan markers. Nat Genet 2005, 37(2):177-181. 10.1038/ng1510, 15665825.
54. Smith MW, O'Brien SJ. Mapping by admixture linkage disequilibrium: advances, limitations and guidelines. Nat Rev Genet 2005, 6(8):623-632. 10.1038/nrg1657, 16012528.
55. Pfaff C, Parra E, Bonilla C, Hiester K, McKeigue P, Kamboh M, Hutchinson R, Ferrel R, Boerwinkle E, Shriver M. Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disquilibrium. Am J Hum Genet 2001, 68:198-207. 10.1086/316935, 1234913, 11112661.
56. Weir B, Cockerham C. Estimating F-Statistics for the Analysis of Population Structure. Evolution 1984, 38(6):1358-1370.
57. Long JC. The genetic structure of admixed populations. Genetics 1991, 127:417-428. 1204369, 2004712.
58. Peng B, Amos CI. Forward-time simulations of non-random mating populations using simuPOP. Bioinformatics 2008, 24(11):1408-1409. 10.1093/bioinformatics/btn179, 2691961, 18417488.
59. Tang H, Peng J, Wang P, Risch NJ. Estimation of individual admixture: analytical and study design considerations. Genetic epidemiology 2005, 28(4):289-301. 10.1002/gepi.20064, 15712363.
60. Pritchard JK, Stephens M, Donnelly P. Association mapping in structured populations. Am J Hum Genet 2000, 67:170-181. 10.1086/302959, 1287075, 10827107.
61. Lander E, Schork N. Genetic dissection of complex traits. Science 1994, 265:2037-2048. 10.1126/science.8091226, 8091226.