Computer simulation is an undervalued tool for genetic analysis: A historical view and presentation of SHIMSHON-A web-based genetic simulation package

Human Heredity

Volumn 72, Issue 4, 2011, Pages 247-257

  Greenberg, David A ^a  

^a Department of Medicine   (United States)

Author keywords

Affected sib pairs; Association analysis; GWAS; Linkage analysis; LOD scores; Mode of inheritance; Type 1 error

Indexed keywords

ARTICLE; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE IDENTIFICATION; GENE LOCUS; GENE SEGREGATION; GENETIC ANALYSIS; GENETIC LINKAGE; HAPLOTYPE; HUMAN; METHODOLOGY; NONHUMAN;

COMPUTER SIMULATION; GENETIC LINKAGE; HUMANS; INHERITANCE PATTERNS; INTERNET; LOD SCORE; MODELS, GENETIC;

EID: 84055184753     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000330633     Document Type: Article

References (36)

1. Greenberg DA, Barry CD, Marshall GR: Investigation and parametrization of a molecular dielectric function. J Am Chem Soc 1978; 100:4020-4026.
2. Greenberg DA: Simulation studies of segregation analysis: application to two-locus models. Am J Hum Genet 1984; 36: 16 7-176.
3. MacLean CJ, Morton NE, Lew R: Analysis of family resemblance. IV. Operational characteristics of segregation analysis. Am J Hum Genet 1975; 27:365-384.
4. Greenberg DA: The effect of proband designation on segregation analysis. Am J Hum Genet 1986; 39:329-339. (Pubitemid 17170835)
5. Vieland VJ, Hodge SE: Inherent intractability of the ascertainment problem for pedigree data: a general likelihood framework. Am J Hum Genet 1995; 56: 33-4 3.
6. Hodge SE, Vieland VJ: The essence of single ascertainment. Genetics 1996; 144: 1215-1223. (Pubitemid 26378684)
7. Morton NE: Genetic tests under incomplete ascertainment. Am J Hum Genet 1959; 11:1-16.
8. Greenberg DA: Inferring mode of inheritance by comparison of lod scores. Am J Hu m Genet 1989; 34: 480-486. (Pubitemid 20033568)
9. Vieland VJ, Hodge SE: The problem of ascertainment for linkage analysis. Am J Hum Genet 1996; 58: 1072-10 8 4. (Pubitemid 26115179)
10. Elston RC: Man bites dog. The validity of maximizing lod scores to determine mode of inheritance. Am J Hum Genet 1989; 34: 487-488. (Pubitemid 20033569)
11. Hodge SE, Elston RC: Lods, wrods, and mods: the interpretation of lod scores calculated under different models. Genet Epidemiol 1994; 11:329-342. (Pubitemid 24313594)
12. Greenberg DA, Abreu P, Hodge SE: The power to detect linkage in complex disease by means of simple lod-score analyses. Am J Hum Genet 1998; 63: 870-879. (Pubitemid 30422688)
13. Greenberg DA, Abreu PC: Determining trait locus position from multipoint analysis: accuracy and power of three different statistics. Genet Epidemiol 2001; 21:299-314. (Pubitemid 33104503)
14. Greenberg DA: Linkage analysis assuming a single-locus mode of inheritance for traits determined by two loci: inferring mode of inheritance and estimating penetrance. Genet Epidemiol 1990; 7:467-479.
15. Knapp M, Seuchter SA, Baur MP: Linkage analysis in nuclear families. 2. Relationship between affected sib-pair tests and lod score ana lysis. Hum Hered 1994; 44: 44-51. (Pubitemid 24025660)
16. Hodge SE: Exact ELODS and exact power for affected sib pairs analyzed for linkage under simple right and wrong models. Am J Med Genet 1998; 81: 66-72. (Pubitemid 28114854)
17. Whittemore AS: Genome scanning for linkage: an overview. Am J Hum Genet 1996; 59: 704-716. (Pubitemid 26269049)
18. Huang J, Vieland VJ: Comparison of 'model-free' and 'model-based' linkage statistics in the presence of locus heterogeneity: single data set and multiple data set applications. Hum Hered 20 01; 51: 217-225. (Pubitemid 32260827)
19. Dizier MH, Babron MC, Clerget-Darpoux F: Conclusions of lod-score analysis for family data generated under two-locus models. Am J Hum Genet 1996; 58: 1338-134 6. (Pubitemid 26153845)
20. Kidd KK: Can we find genes for schizophrenia? Am J Med Genet 1997; 74:104-111.
21. Durner M, Vieland VJ, Greenberg DA: Further evidence for the increased power of lod scores compared with nonparametric methods. Am J Hum Genet 1999; 64:281-289. (Pubitemid 30428981)
22. Vieland VJ, Hodge SE, Greenberg DA: Adequacy of single-locus approximations for linkage analyses of oligogenic traits. Genet Epidemiol 1992; 9: 45-59.
23. 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)
24. Hodge SE, Rodriguez-Murillo L, Strug LJ, Greenberg DA: Multipoint lods provide reliable linkage evidence despite unknown limiting distribution: type I error probabilities de-crea se wit h s a mple si ze for mu lt ipoi nt lo d s and mods. Genet Epidemiol 2008; 32:800-815.
25. Xing C, Elston RC: Distribution and magnitude of type I error of model-based multipoint lod scores: implications for multipoint mod scores. Genet Epidemiol 2006; 30:447-458. (Pubitemid 43993291)
26. Greenberg DA, Durner M, Keddache M, Shinnar S, Resor SR, Moshe SL, Rosenbaum D, Cohen J, Harden C, Kang H, Wallace S, Luciano D, Ballaban-Gil K, Tomasini L, Zhou G, Klotz I, Dicker E: Reproducibility and complications in gene searches: linkage on chromosome 6, heterogeneity, association and maternal inheritance in juvenile myoclonic epilepsy. Am J Hum Genet 2000; 66:508-516. (Pubitemid 30468829)
27. Smalley SL: Sex-specific recombination frequencies: a consequence of imprinting? Am J Hum Genet 1993; 52:210-212. (Pubitemid 23059067)
28. Greenberg DA, Monti MC, Feenstra B, Zhang J, Hodge SE: The essence of linkage-based imprinting detection: comparing power, type 1 error, and the effects of con-founders in two different analysis approaches. Ann Hum Genet 2010; 74: 248-262.
29. Greenberg DA, MacCluer JW, Spence MA, Falk CT, Hodge SE: Simulated data for a complex genetic trait (problem 2 for GAW11): how the model was developed, and why. Genet Epidemiol 1999; 17: S 4 49-S459.
30. Greenberg DA, Zhang J, Shmulewitz D, Strug LJ, Zimmerman R, Singh V, Marathe S: Construction of the model for the genetic analysis workshop 14 simulated data: genotype-phenotype relationships, gene interaction, linkage, association, disequilibrium, and ascertainment effects for a complex phenotype. BMC Genet 2005; 6(suppl 1):S3.
31. Greenberg DA: Summary of analyses of problem 2 simulated data for GAW11. Genet Epidemiol 1999; 17(suppl 1):S429-S447.
32. Vieland VJ: Heterogeneity: GAW group 15. Genet Epidemiol 2005; 29(suppl 1):S110-S115. (Pubitemid 43062734)
33. Kruglyak L, Daly MJ, Reeve-Daly MP, Lander ES: Parametric and nonparametric linkage analysis: a unified multipoint approach. Am J Hum Genet 1996; 58: 1347-1363. (Pubitemid 26153846)
34. Gudbjartsson DF, Thorvaldsson T, Kong A, Gunnarsson G, Ingolfsdottir A: Allegro version 2. Nat Genet 20 05; 37: 1015-1016.
35. Abecasis GR, Cherny SS, Cookson WO, Car-don LR: Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002; 30:97-101.
36. Heiman GA, Hodge SE, Gorroochurn P, Zhang J, Greenberg DA: Effect of population stratification on case-control association studies. I. Elevation in false positive rates and comparison to confounding risk ratios (a simulation study). Hum Hered 2004; 58: 30-39. (Pubitemid 39664274)