Login to MyKarger

New to MyKarger? Click here to sign up.

Login with Facebook

Forgot Password? Reset your password

Authors, Editors, Reviewers

For Manuscript Submission, Check or Review Login please go to Submission Websites List.

Submission Websites List

Institutional Login

For the academic login, please select your country in the dropdown list. You will be redirected to verify your credentials.

Journal Mobile Options
Table of Contents
Vol. 74, No. 2, 2012
Issue release date: March 2013
Section title: Original Paper
Hum Hered 2012;74:83-96
(DOI:10.1159/000345181)

Joint Analysis for Integrating Two Related Studies of Different Data Types and Different Study Designs Using Hierarchical Modeling Approaches

Li R.a, e · Conti D.V.a, c · Diaz-Sanchez D.d · Gilliland F.b · Thomas D.C.a
Divisions of aBiostatistics and bEnvironmental Health, Department of Preventive Medicine, and cZilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, Calif., dUS Environmental Protection Agency, Chapel Hill, N.C., and eNovartis Molecular Diagnostics, Cambridge, Mass., USA
email Corresponding Author

Duncan C. Thomas, PhD

Division of Biostatistics, Department of Preventive Medicine

University of Southern California

Los Angeles, CA 90089 (USA)

E-Mail dthomas@usc.edu


References

  1. Capanu M, Begg CB: Hierarchical modeling for estimating relative risks of rare genetic variants: properties of the pseudo-likelihood method. Biometrics 2010;67:371-380.
  2. Capanu M, Concannon P, Haile RW, Bernstein L, Malone KE, Lynch CF, Liang X, Teraoka SN, Diep AT, Thomas DC, Bernstein JL, Begg CB: Assessment of rare BRCA1 and BRCA2 variants of unknown significance using hierarchical modeling. Genet Epidemiol 2011;35:389-397.
  3. Capanu M, Orlow I, Berwick M, Hummer AJ, Thomas DC, Begg CB: The use of hierarchical models for estimating relative risks of individual genetic variants: An application to a study of melanoma. Stat Med 2008;27:1973-1992.
  4. Chen GK, Thomas DC: Using biological knowledge to discover higher order interactions in genetic association studies. Genet Epidemiol 2010;34:863-878.
  5. Hoffmann TJ, Marini NJ, Witte JS: Comprehensive approach to analyzing rare genetic variants. PLoS One 2010;5:e13584.
  6. Hung RJ, Baragatti M, Thomas D, McKay J, Szeszenia-Dabrowska N, Zaridze D, Lissowska J, Rudnai P, Fabianova E, Mates D, Foretova L, Janout V, Bencko V, Chabrier A, Moullan N, Canzian F, Hall J, Boffetta P, Brennan P: Inherited predisposition of lung cancer: a hierarchical modeling approach to DNA repair and cell cycle control pathways. Cancer Epidemiol Biomarkers Prev 2007;16:2736-2744.
  7. Hung RJ, Brennan P, Malaveille C, Porru S, Donato F, Boffetta P, Witte JS: Using hierarchical modeling in genetic association studies with multiple markers: Application to a case-control study of bladder cancer. Cancer Epidemiol Biomarkers Prev 2004;13:1013-1021.
  8. Lewinger JP, Conti DV, Baurley JW, Triche TJ, Thomas DC: Hierarchical Bayes prioritization of marker associations from a genome-wide association scan for further investigation. Genet Epidemiol 2007;31:871-882.
  9. Quintana MA, Berstein JL, Thomas DC, Conti DV: Incorporating model uncertainty in detecting rare variants: the Bayesian risk index. Genet Epidemiol 2011;35:638-649.
  10. Thomas DC, Conti DV, Baurley J, Nijhout F, Reed M, Ulrich CM: Use of pathway information in molecular epidemiology. Hum Genomics 2009;4:21-42.
  11. Wilson MA, Baurley JW, Thomas DC, Conti DV: Complex system approaches to genetic analysis Bayesian approaches. Adv Genet 2010;72:47-71.
  12. Peters JM, Avol E, Gauderman WJ, Linn WS, Navidi W, London SJ, Margolis H, Rappaport E, Vora H, Gong H Jr, Thomas DC: A study of twelve Southern California communities with differing levels and types of air pollution. II. Effects on pulmonary function. Am J Respir Crit Care Med 1999;159:768-775.
  13. Peters JM, Avol E, Navidi W, London SJ, Gauderman WJ, Lurmann F, Linn WS, Margolis H, Rappaport E, Gong H, Thomas DC: A study of twelve Southern California communities with differing levels and types of air pollution. I. Prevalence of respiratory morbidity. Am J Respir Crit Care Med 1999;159:760-767.
  14. Islam T, Gauderman WJ, Berhane K, McConnell R, Avol E, Peters JM, Gilliland FD: Relationship between air pollution, lung function and asthma in adolescents. Thorax 2007;62:957-963.
  15. Gilliland FD, Berhane K, Islam T, McConnell R, Gauderman WJ, Gilliland SS, Avol E, Peters JM: Obesity and the risk of newly diagnosed asthma in school-age children. Am J Epidemiol 2003;158:406-415.
  16. McConnell R, Berhane K, Molitor J, Gilli-land F, Kunzli N, Thorne PS, Thomas D, Gauderman WJ, Avol E, Lurmann F, Rappaport E, Jerrett M, Peters JM: Dog ownership enhances symptomatic responses to air pollution in children with asthma. Environ Health Perspect 2006;114:1910-1915.
  17. Gauderman WJ, Avol E, Lurmann F, Kuenzli N, Gilliland F, Peters J, McConnell R: Childhood asthma and exposure to traffic and nitrogen dioxide. Epidemiology 2005;16:737-743.
  18. Li YF, Langholz B, Salam MT, Gilliland FD: Maternal and grandmaternal smoking patterns are associated with early childhood asthma. Chest 2005;127:1232-1241.
  19. Salam MT, Li YF, Langholz B, Gilliland FD: Early-life environmental risk factors for asthma: findings from the children's health study. Environ Health Perspect 2004;112:760-765.
  20. Jerrett M, Shankardass K, Berhane K, Gauderman WJ, Kunzli N, Avol E, Gilliland F, Lurmann F, Molitor JN, Molitor JT, Thomas DC, Peters J, McConnell R: Traffic-related air pollution and asthma onset in children: a prospective cohort study with individual exposure measurement. Environ Health Perspect 2008;116:1433-1438.
  21. McConnell R, Berhane K, Gilliland F, London SJ, Islam T, Gauderman WJ, Avol E, Margolis HG, Peters JM: Asthma in exercising children exposed to ozone: a cohort study. Lancet 2002;359:386-391.
  22. McConnell R, Berhane K, Gilliland F, Molitor J, Thomas D, Lurmann F, Avol E, Gauderman WJ, Peters JM: Prospective study of air pollution and bronchitic symptoms in children with asthma. Am J Respir Crit Care Med 2003;168:790-797.
  23. McConnell R, Berhane K, Yao L, Jerrett M, Lurmann F, Gilliland F, Kunzli N, Gauderman J, Avol E, Thomas D, Peters J: Traffic, susceptibility, and childhood asthma. Environ Health Perspect 2006;114:766-772.
  24. Barfknecht TR, Hites RA, Cavaliers EL, Thilly WG: Human cell mutagenicity of polycyclic aromatic hydrocarbon components of diesel emissions. Dev Toxicol Environ Sci 1982;10:277-294.
  25. Bastain TM, Gilliland FD, Li YF, Saxon A, Diaz-Sanchez D: Intraindividual reproducibility of nasal allergic responses to diesel exhaust particles indicates a susceptible phenotype. Clin Immunol 2003;109:130-136.
  26. Chen GK, Witte JS: Enriching the analysis of genomewide association studies with hierarchical modeling. Am J Hum Genet 2007;81:397-404.
  27. Gelman A, Bois F, Jiang J: Physiological pharmacokinetic analysis using population modeling and informative prior distributions. J Am Statist Assoc 1996;91:1400-1412.
    External Resources
  28. Gilliland FD, Gauderman WJ, Vora H, Rappaport E, Dubeau L: Effects of glutathione-s-transferase m1, t1, and p1 on childhood lung function growth. Am J Respir Crit Care Med 2002;166:710-716.
  29. Lee YL, McConnell R, Berhane K, Gilliland FD: Ambient ozone modifies the effect of tumor necrosis factor g-308a on bronchitic symptoms among children with asthma. Allergy 2009;64:1342-1348.
  30. Li YF, Gauderman WJ, Avol E, Dubeau L, Gilliland FD: Associations of tumor necrosis factor g-308a with childhood asthma and wheezing. Am J Respir Crit Care Med 2006;173:970-976.
  31. Li YF, Gauderman WJ, Conti DV, Lin PC, Avol E, Gilliland FD: Glutathione s-transferase p1, maternal smoking, and asthma in children: a haplotype-based analysis. Environ Health Perspect 2008;116:409-415.
  32. Li YF, Tsao YH, Gauderman WJ, Conti DV, Avol E, Dubeau L, Gilliland FD: Intercellular adhesion molecule-1 and childhood asthma. Hum Genet 2005;117:476-484.
  33. Millstein J, Conti DV, Gilliland FD, Gauderman WJ: A testing framework for identifying susceptibility genes in the presence of epistasis. Am J Hum Genet 2006;78:15-27.
  34. Salam MT, Gauderman WJ, McConnell R, Lin PC, Gilliland FD: Transforming growth factor-1 c-509t polymorphism, oxidant stress, and early-onset childhood asthma. Am J Respir Crit Care Med 2007;176:1192-1199.
  35. Salam MT, Islam T, Gauderman WJ, Gilli-land FD: Roles of arginase variants, atopy, and ozone in childhood asthma. J Allergy Clin Immunol 2009;123:596-602, 602.e1-e8.
  36. Salam MT, Lin PC, Avol EL, Gauderman WJ, Gilliland FD: Microsomal epoxide hydrolase, glutathione s-transferase p1, traffic and childhood asthma. Thorax 2007;62:1050-1057.
  37. Wang C, Salam MT, Islam T, Wenten M, Gauderman WJ, Gilliland FD: Effects of in utero and childhood tobacco smoke exposure and beta2-adrenergic receptor genotype on childhood asthma and wheezing. Pediatrics 2008;122:e107-e114.
  38. Wenten M, Gauderman WJ, Berhane K, Lin PC, Peters J, Gilliland FD: Functional variants in the catalase and myeloperoxidase genes, ambient air pollution, and respiratory-related school absences: an example of epistasis in gene-environment interactions. Am J Epidemiol 2009;170:1494-1501.
  39. Wenten M, Li YF, Lin PC, Gauderman WJ, Berhane K, Avol E, Gilliland FD: In utero smoke exposure, glutathione s-transferase p1 haplotypes, and respiratory illness-related absence among schoolchildren. Pediatrics 2009;123:1344-1351.
  40. Gilliland FD, McConnell R, Peters J, Gong H Jr: A theoretical basis for investigating ambient air pollution and children's respiratory health. Environ Health Perspect 1999;107(suppl 3):403-407.
  41. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH: Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 2001;69:138-147.
  42. Breiman L: Random forests. Machine Learning 2001;45:5-32.
  43. Chen SH, Sun J, Dimitrov L, Turner AR, Adams TS, Meyers DA, Chang BL, Zheng SL, Gronberg H, Xu J, Hsu FC: A support vector machine approach for detecting gene-gene interaction. Genet Epidemiol 2008;32:152-167.
  44. Guyon I, Weston J, Barnhill S, Vapnik V: Gene selection for cancer classification using support vector machine. Machine Learning 2002;46:389-422.
  45. Vapnik V, Lerner A: Pattern recognition using generalized portrait method. Automat Remote Control 1963;24:774-780.
  46. Chasman DI: On the utility of gene set methods in genomewide association studies of quantitative traits. Genet Epidemiol 2008;32:658-668.
  47. Holden M, Deng S, Wojnowski L, Kulle B: GSEA-SNP: Applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics 2008;24:2784-2785.
  48. Wang K, Li M, Bucan M: Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 2007;81:1278-1283.
  49. Kann MG: Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform 2007;8:333-346.
  50. Lage K, Karlberg EO, Storling ZM, Olason PI, Pedersen AG, Rigina O, Hinsby AM, Tumer Z, Pociot F, Tommerup N, Moreau Y, Brunak S: A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol 2007;25:309-316.
  51. Lee DS, Park J, Kay KA, Christakis NA, Oltvai ZN, Barabasi AL: The implications of human metabolic network topology for disease comorbidity. Proc Natl Acad Sci USA 2008;105:9880-9885.
  52. Oti M, Brunner HG: The modular nature of genetic diseases. Clin Genet 2007;71:1-11.
  53. Ideker T, Sharan R: Protein networks in disease. Genome Res 2008;18:644-652.
  54. Scott J, Ideker T, Karp RM, Sharan R: Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol 2006;13:133-144.
  55. Sharan R, Ideker T: Modeling cellular machinery through biological network comparison. Nat Biotechnol 2006;24:427-433.
  56. Fleiss JL: The statistical basis of meta-analysis. Stat Methods Med Res 1993;2:121-145.
  57. Yesupriya A, Yu W, Clyne M, Gwinn M, Khoury MJ: The continued need to synthesize the results of genetic associations across multiple studies. Genet Med 2008;10:633-635.
  58. Agakov F, McKeigue P, Krohn J, Storkey A: Sparse instrumental variables (SPIV) for genome-wide studies. Advances in Neural Information Processing Systems 2010;23.
  59. McKeigue PM, Campbell H, Wild S, Vitart V, Hayward C, Rudan I, Wright AF, Wilson JF: Bayesian methods for instrumental variable analysis with genetic instruments (‘Mendelian randomization'): example with urate transporter SLC2A9 as an instrumental variable for effect of urate levels on metabolic syndrome. Int J Epidemiol 2010;39:907-918.
  60. Agakov F, McKeigue P, Krohn J, Flint J: Inference of causal relationships between biomarkers and outcomes in high dimensions. Journal of Systemics, Cybernetics and Informatics 2010;9:1-8.