Hierarchical modeling of clinical and expression quantitative trait loci

Heredity

Volumn 101, Issue 3, 2008, Pages 271-284

  Sillanpaa M J ^a   Noykova, N ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Bayes; cQTLs; eQTLs; MCMC; Model selection

Indexed keywords

GENE EXPRESSION; MARKOV CHAIN; MODELING; MONTE CARLO ANALYSIS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS;

ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; FUNGAL GENE; GENE EXPRESSION; GENETIC MARKER; GENETICS; GENOTYPE; HUMAN; MONTE CARLO METHOD; PHENOTYPE; PROBABILITY; QUANTITATIVE TRAIT LOCUS; SACCHAROMYCES CEREVISIAE; STATISTICAL ANALYSIS;

BAYES THEOREM; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION; GENES, FUNGAL; GENETIC MARKERS; GENOTYPE; HUMANS; MARKOV CHAINS; MODELS, GENETIC; MONTE CARLO METHOD; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SACCHAROMYCES CEREVISIAE;

EID: 50049130432     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/hdy.2008.58     Document Type: Article

References (72)

1. Aune TM, Parker JS, Mass K, Liu Z, Olson NJ, Moore JH (2004). Co-localization of differentially expressed genes and shared susceptibility loci in human autoimmunity. Genet Epidemiol 27: 162-172.
2. Bhattacharjee M, Sillanpää MJ (2008). Bayesian joint disease-marker-expression analysis applied to clinical characteristics of chronic fatigue syndrome. (To appear in a book concluding the selected papers from CAMDA 2006.).
3. Brem R, Yvert G, Clinton R, Kruglyak L (2002). Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
4. Bueno Filho JSS, Gilmour SG, Rosa GJS (2006). Design of microarray experiments for genetical genomics studies. Genetics 174: 945-957.
5. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T et al. (2005). Uncovering regulatory pathways affecting hematopoietic stem cell function using 'genetical genomics'. Nat Genet 37: 225-232.
6. Chen M, Kendziorski C (2007). A statistical framework for expression quantitative trait loci mapping. Genetics 177: 761-771.
7. Chessler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J et al. (2005). Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37: 233-242.
8. Conti DV, Witte JS (2003). Hierarchical modeling of linkage disequilibrium: genetic structure and spatial relations. Am J Hum Genet 72: 351-363.
9. Corander J, Sillanpää MJ (2002). A unified approach to joint modeling of multiple quantitative and qualitative traits in gene mapping. J Theor Biol 218: 435-446.
10. de Koning D-J, Haley CS (2005). Genetical genomics in humans and model organisms. Trends Genet 21: 377-381.
11. Draghici S, Khatri P, Eklund AC, Swallasi Z (2006). Reliability and reproducibility issues in DNA microarray measurements. Trends Genet 22: 101-109.
12. Foss EJ, Radulovic D, Shaffer SA, Ruderfer DM, Bedalov A, Goodlett DR et al. (2007). Genetic basis of proteome variation in yeast. Nat Genet 39: 1369-1375.
13. Fu J, Jansen RC (2006). Optimal design and analysis of genetic studies on gene expression. Genetics 172: 1993-1999.
14. Gelfond JAL, Ibrahim JG, Zou F (2007). Proximity model for expression quantitative trait loci (eQTL) detection. Biometrics 63: 1108-1116.
15. Gelman A (2006). Prior distributions for variance parameters in hierarchical models. Bayesian Analysis 1: 515-533.
16. Geweke J (1996). Variable selection and model comparison in regression. In: Bernando JM, Berger JO, Dawid AP, Smith AFM (eds). Bayesian Statistics 5. Oxford Press: Oxford, pp 609-620.
17. Gibson G, Weir B (2005). The quantitative genetics of transcription. Trends Genet 11: 616-622.
18. Goddard ME (2001). The validity of genetic models underlying quantitative traits. Livest Prod Sci 72: 117-127.
19. Grünewald M (2004). Genetic association studies with complex ascertainment. Licentiate thesis. Research Report 2004: 5. Mathematical Statistics, Stockholm University, Sweden.
20. Hazelton M, Gurrin LC (2003). A note on genetic variance components in mixed models. Genet Epidemiol 24: 297-301.
21. Hoti F, Sillanpää MJ (2006). Bayesian mapping of genotype x expression interactions in quantitative and qualitative traits. Heredity 97: 4-18.
22. Hung RJ, Brennan P, Malaveille C, Porru S, Donato F, Boffetta P et al. (2004). Using hierarchical modeling in genetic association studies with multiple markers: application to a case-control study of bladder cancer. Cancer Epidemiol Biomarkers Prev 13: 1013-1021.
23. Jannink J-L (2005). Selective phenotyping to accurately map quantitative trait loci. Crop Sci 45: 901-908.
24. Jansen RC (2003). Studying complex biological systems using multifactorial perturbation. Nat Rev Genet 4: 145-151.
25. Jansen RC, Nap J-P (2001). Genetical genomics: the added value from segregation. Trends Genet 17: 388-391.
26. Jansen RC, Nap J-P (2004). Regulating gene expression: surprises still in store. Trends Genet 20: 223-225.
27. Jia Z, Xu S (2007). Mapping quantitative trait loci for expression abundance. Genetics 176: 611-623.
28. Jiang C, Zeng Z-B (1997). Mapping quantitative trait loci in dominant and missing markers in various crosses from two inbred lines. Genetica 101: 47-58.
29. Jin C, Lan H, Attie AD, Churchill GA, Bulutuglo D, Yandell BS (2004). Selective phenotyping for increased efficiency in genetic mapping studies. Genetics 168: 2285-2293.
30. Kendziorski CM, Chen M, Yuan M, Lan H, Attie AD (2006). Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics 62: 19-27.
31. Kilpikari R, Sillanpää MJ (2003). Bayesian analysis of multilocus association in quantitative and qualitative traits. Genet Epidemiol 25: 122-135.
32. Kuo L, Mallick B (1998). Variable selection for regression models. Sankhya Ser B 60: 65-81.
33. Lan H, Stoehr JP, Nadler ST, Schueler KL, Yandell BS, Attie AD (2004). Dimension reduction for mapping mRNA abundance as quantitative traits. Genetics 164: 1607-1614.
34. Li R, Tsaih S-W, Shockley K, Stylianou IM, Wergedal J, Paigen B et al. (2006). Structural model analysis of multiple quantitative traits. PLoS Genet 7: e114.
35. Luan Y, Li H (2008). Group additive regression models for genomic data analysis. Biostatistics 9: 100-113.
36. Malo N, Libiger O, Schork NJ (2008). Accommodating linkage disequilibrium in genetic-association analyses via ridge regression. Am J Hum Genet 82: 375-385.
37. Mehrabian M, Allayee H, Stockton J, Lum PY, Drake TA, Castellani LW et al. (2005). Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits. Nat Genet 37: 1224-1233.
38. Meuwissen THE, Goddard ME (2004). Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data. Genet Sel Evol 36: 261-279.
39. Meuwissen THE, Hayes BJ, Goddard ME (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
40. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS et al. (2004). Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
41. Mueller M, Goel A, Thimma M, Dickens NJ, Aitman TJ, Mangion J (2006). eQTL Explorer: integrated mining of combined linkage and expression experiments. Bioinformatics 22: 509-511.
42. Parmigiani G, Garrett ES, Irizarry R, Zeger SL (2003). The Analysis of Gene Expression Data: Methods and Software. Springer Verlag: New York.
43. Perez-Enciso M, Quevedo JR, Bahamonde A (2007). Genetical genomics: use all data. BMC Genomics 8: 69.
44. Perez-Enciso M, Toro MA, Tenenhaus M, Gianola D (2003). Combining gene expression and molecular marker information for mapping complex trait genes: a simulation study. Genetics 164: 1597-1606.
45. Qu Y, Xu S (2006). Quantitative trait associated microarray gene expression data analysis. Mol Biol Evol 23: 1558-1573.
46. Quackenbush J (2001). Computational analysis of microarray data. Nat Rev Genet 2: 418-427.
47. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I et al. (2000). Genome-wide location and function of DNA binding proteins. Science 290: 2306-2309.
48. Robins JM, Smoller JW, Lunetta KL (2001). On the validity of the TDT test in the presence of comorbidity and ascertainment bias. Genet Epidemiol 21: 326-336.
49. Ronald J, Akey JM, Whittle J, Smith EN, Yvert G, Kruglyak L (2005). Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays. Genome Res 15: 284-291.
50. Rubin DB (1976). Inference and missing data. Biometrika 63: 581-592.
51. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, Guhathakurta D et al. (2005). An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 37: 710-717.
52. Schadt EE, Monks SA, Drake TA, Lusis AJ, Che N, Colinayo V et al. (2003). The genetics of gene expression surveyed in maize, mouse and man. Nature 422: 297-302.
53. Sillanpää MJ, Arjas E (1998). Bayesian mapping of multiple quantitative trait loci from incomplete inbred line cross data. Genetics 148: 1373-1388.
54. Sillanpää MJ, Bhattacharjee M (2005). Bayesian association-based fine mapping in small chromosomal segments. Genetics 169: 427-439.
55. Sillanpää MJ, Bhattacharjee M (2006). Association mapping of complex trait loci with context-dependent effects and unknown context variable. Genetics 174: 1597-1611.
56. Sladek R, Hudson TJ (2006). Elucidating cis- and trans-regulatory variation using genetical genomics. Trends Genet 22: 245-250.
57. Smith M, Kohn R (2002). Parsimonious covariance matrix estimation for longitudinal data. J Am Stat Assoc 97: 1141-1153.
58. Smoller J, Lunetta K, Robins J (2000). Implications of comorbidity and ascertainment bias for identifying disease genes. Am J Med Genet 96: 817-822.
59. Spiegelhalter D, Thomas A, Best N, Lunn D (2005). WinBUGS User Manual, Version 2.10. MRC Biostatistics Unit, Institute of Public Health: Cambridge, UK.
60. Thomas A, O'Hara RB, Ligges U, Sturtz S (2006). Making BUGS open. R News 6: 17-21.
61. Thomas DC (2005). The need for a systematic approach to complex pathways in molecular epidemiology. Cancer Epidemiol Biomarkers Prev 14: 557-559.
62. Uimari P, Hoeschele I (1997). Mapping linked quantitative trait loci using Bayesian analysis and Markov chain Monte Carlo algorithms. Genetics 146: 735-743.
63. Uimari P, Thaller G, Hoeschele I (1996). The use of multiple markers in a Bayesian method for mapping quantitative trait loci. Genetics 143: 1831-1842.
64. Van Dongen S (2006). Prior specification in Bayesian statistics: three cautionary tales. J Theor Biol 242: 90-100.
65. Verzilli CJ, Stallard N, Whittaker JC (2005). Bayesian modeling of multivariate quantitative traits using seemingly unrelated regressions. Genet Epidemiol 28: 313-325.
66. Vormfelde SV, Brockmöller J (2007). On the value of haplotype-based genotype-phenotype analysis and on data transformation in pharmacogenetics and -genomics. Nat Rev Genet (01 Dec 2007).
67. Wang K, Li M, Bucan M (2007). Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 81: 1278-1283.
68. Wang S, Basten CJ, Zeng Z-B (2006). Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University: Raleigh, NC.
69. West M, Ginsburg GS, Huang AT, Nevin JR (2006). Embracing the complexity of genomic data for personalized medicine. Genome Res 16: 559-566.
70. Xu Z, Zou F, Vision TJ (2005). Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics 170: 401-408.
71. Yanai I, Korbel JO, Boue S, McWeeney SK, Bork P, Lercher MJ (2006). Similar gene expression profiles do not imply similar tissue function. Trends Genet 22: 132-138.
72. Yi N, George V, Allison DB (2003). Stochastic search variable selection for identifying multiple quantitative trait loci. Genetics 164: 1129-1138.