Association statistics under the PPL framework

Genetic Epidemiology

Volumn 34, Issue 8, 2010, Pages 835-845

  Huang, Yungui ^a   Vieland, Veronica J ^a,b  

^a THE RESEARCH INSTITUTE AT NATIONWIDE CHILDREN S HOSPITAL   (United States)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

Bayes ratios; Epistasis; Linkage disequilibrium; Sequential updating

Indexed keywords

ARTICLE; CASE CONTROL STUDY; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; DOMINANT INHERITANCE; GENE FREQUENCY; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC EPISTASIS; GENETIC SCREENING; HUMAN; NULL HYPOTHESIS; POPULATION GENETIC STRUCTURE; POSTERIOR PROBABILITY OF LINKAGE FRAMEWORK; RECESSIVE INHERITANCE; SAMPLE SIZE; SEQUENTIAL ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL DISTRIBUTION; STATISTICAL MODEL;

CASE-CONTROL STUDIES; COMPUTER SIMULATION; EPISTASIS, GENETIC; FAMILY; GENES, DOMINANT; GENES, RECESSIVE; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PEDIGREE; PROBABILITY;

EID: 78649526217     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20537     Document Type: Article

References (42)

1. Armitage P. 1955. Tests for linear trends in proportions and frequencies. Biometrics 11:11.
2. Badner JA, Goldin LR. 1999. Meta-analysis of linkage studies. Genet Epidemiol 17:S485-S490.
3. Bartlett CW, Vieland VJ. 2006. Accumulating quantitative trait linkage evidence across multiple datasets using the posterior probability of linkage. Genet Epidemiol 31:91-102. PMID: 17123305.
4. Dersimonian R, Laird N. 1986. Meta-analysis in clinical trials. Control Clin Trials 7:177-188.
5. Edwards A. 1992. Likelihood. Baltimore: Johns Hopkins University Press.
6. Elston RC. 1989. Man bites dog? The validity of maximizing lod scores to determine mode of inheritance. Am J Med Genet 34:487-488.
7. Elston RC, Lange K. 1975. An approximation for the prior probability of autosomal linkage. Cytogenet Cell Genet 14:290-292.
8. Ewens WJ, Shute NC. 1986. A resolution of the ascertainment sampling problem. I. Theory. Theor Popul Biol 30:388-412.
9. Goldstein DR, Sain SR, Guerra R, Etzel CJ. 1999. Meta-analysis by combining parameter estimates: simulated linkage studies. Genet Epidemiol 17:S581-S586.
10. Gorroochurn P. 2008. Perils in the use of linkage disequilibrium for fine gene mapping: simple insights from population genetics. Cancer Epidemiol Biomarkers Prev 17:6.
11. Govil M, Vieland VJ. 2008. Practical considerations for dividing data into subsets prior to PPL analysis. Hum Hered 66:223-237.
12. Greenberg DA. 1989. Inferring mode of inheritance by comparison of lod scores. Am J Med Genet 34:480-486.
13. Greenberg DA. 1999. Summary of analyses of problem 2 simulated data for GAW 11. Genet Epidemiol 17:S449-S459.
14. Greenberg DA, MacCluer JW, Spence MA, Falk CT, Hodge SE. 1999. Simulated data for a complex genetic trait (problem 2 for GAW11): how the model was developed, and why. Genet Epidemiol 17:S449-S459.
15. Guerra R, Etzel CJ, Goldstein DR, Sain SR. 1999. Meta-analysis by combining p-values: simulated linkage studies. Genet Epidemiol 17:S605-S609.
16. Huang Y, Bartlett CW, Segre AM, O'Connell JR, Mangin L, Vieland VJ. 2007. Exploiting gene x gene interaction in linkage analysis. BMC Proceedings 1:S64(1)-S64(5). PMID: 18466565.
17. Huang Y, Segre AM, O'Connell J, Valentine-Cooper WH, Seok S-C, Vieland VJ. 2008. A 2nd Generation Software Package for Computation of the PPL Framework. Presented at the annual meeting of The American Society of Human Genetics, Philadelphia, Pennsylvania, November, 2008. Available from:
18. Lewontin RC. 1964. The Interaction of selection and linkageg. I. General considerations; heterotic models. Genetics 49:49-67.
19. Mantel N, Haenszel W. 1959. Statisical aspects of the analysis of data from the retrospective analysis of disease. J Natl Cancer Inst 22:719-748.
20. Purcell S. 2009. PLINK v1.07. Available from:
21. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, Bender D, Maller J, Sklar P, de Bakker P, Daly M, et al. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81:559-575.
22. Roeder K, Bacanu S-A, Wasserman L, Devlin B. 2006. Using linkage genome scans to improve power of association in genome scans. Am J Hum Genet 78:10.
23. Royall R. 1997. Statistical Evidence: A likelihood Paradigm. London: Chapman & Hall.
24. Seok S-C, Evans M, Vieland VJ. 2009. Fast and accurate calculation of a computationally intensive statistic for mapping disease genes. J Comput Biol 16:659-676.
25. Smith CAB. 1963. Testing for heterogeneity of recombination fraction values in human genetics. Ann Hum Genet 27:175-182.
26. Spielman RS, McGinnis RE, Ewens WJ. 1993. Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506-516.
27. Strug LJ, Hodge SE. 2006. An alternative foundation for the planning and evaluation of linkage analysis I. Decoupling "error probabilities" from "measures of evidence". Hum Hered 61:166-188.
28. Vieland VJ. 1998. Bayesian linkage analysis, or: how I learned to stop worrying and love the posterior probability of linkage. Am J Hum Genet 63:947-954. PMID: 9758634.
29. Vieland VJ. 2006. Thermometers: something for statistical geneticists to think about. Hum Hered 61:144-156. PMID: 16770079.
30. Vieland VJ, Hodge SE. 1995. Inherent intractability of the ascertainment problem for pedigree data: a general likelihood framework. Am J Hum Genet 56:33-43. PMID: 7825595.
31. Vieland VJ, Hodge SE. 1996. The problem of ascertainment for linkage analysis. Am J Hum Genet 58:1072-1084. PMID: 8651268.
32. Vieland VJ, Hodge SE. 1998. Review of statistical evidence: a likelihood paradigm. Am J Hum Genet 63:283-289.
33. Vieland VJ, Huang J. 2003. Two-locus heterogeneity cannot be distinguished from two-locus epistasis on the basis of affected-sib-pair data. Am J Hum Genet 73:223-232. PMID: 12830401.
34. Vieland VJ, Huang Y, Bartlett C, Davies TF, Tomer Y. 2008. A multilocus model of the genetic architecture of autoimmune thyroid disorder, with clinical implications. Am J Hum Genet 82:1349-1356. PMID: 18485327.
35. Vieland VJ, Ludington EA, Wang K, Huang J. 2000. The posterior probability of linkage (PPL) incorporating prior genomic information is efficient for detection of linkage and estimation of male/female recombination rates. Am J Hum Genet 67:1823.
36. Vieland VJ, Wang K, Huang J. 2001. Power to detect linkage based on multiple sets of data in the presence of locus heterogeneity: comparative evaluation of model-based linkage methods for affected sib pair data. Hum Hered 51:199-208. PMID: 11287741.
37. Wang K, Huang J, Vieland VJ. 1999. A Bayesian approach to replication of linkage studies. Genet Epidemol 17:S749-S754.
38. Wang K, Huang J, Vieland VJ. 2000. The consistency of the posterior probability of linkage. Ann Hum Genet 64:533-553.
39. Wigginton JE, Abecasis GR. 2005. PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data. Bioinformatics 21:2.
40. Wise LH, Lewis CM. 1999. A method for meta-analysis of genome searches: application to simulated data. Genet Epidemiol 17:S767-S771.
41. Wratten NS, Memoli H, Huang Y, Dulencin AM, Matteson PG, Cornacchia MA, Azaro MA, Messenger J, Hayter JE, Bassett AS, et al. 2009. Identification of a schizophrenia-associated functional noncoding variant in NOS1AP. Am J Psychiatry 166:434-441.
42. Yang X, Huang J, Logue MW, Vieland VJ. 2005. The posterior probability of linkage allowing for linkage disequilibrium and a new estimate of disequilibrium between a trait and a marker. Hum Hered 59:210-219. PMID: 16015031.