Complex-trait genetics: Emergence of multivariate strategies

Nature Reviews Neuroscience

Volumn 3, Issue 6, 2002, Pages 478-485

  Phillips, Tamara J ^a   Belknap, John K ^a  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; CHROMOSOME MAP; CLUSTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION REGULATION; GENETIC VARIABILITY; GENETICS; GENOMICS; HUMAN; MULTIFACTORIAL INHERITANCE; MULTIVARIATE ANALYSIS; MUTATION; REVIEW; TRANSGENIC ANIMAL;

ANIMALS; ANIMALS, GENETICALLY MODIFIED; CHROMOSOME MAPPING; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOMICS; HUMANS; MULTIFACTORIAL INHERITANCE; MULTIVARIATE ANALYSIS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; VARIATION (GENETICS);

EID: 0036598330     PISSN: 1471003X     EISSN: 14710048     Source Type: Journal    
DOI: 10.1038/nrn847     Document Type: Article

References (69)

1. Phillips, T. J. et al. Harnessing the mouse to unravel the genetics of human disease. Genes Brain Behav. 1, 14-26 (2002).
2. Gerlai, R. Gene targeting: technical confounds and potential solutions in behavioral brain research. Brain Res. Behav. Brain Res. 125, 13-21 (2001).
3. Low, M. J., Kelly, M. A., Rubinstein, M. & Grandy, D. K. Single genes and complex phenotypes. Mol. Psychiatry 3, 373-377 (1998).
4. Bale, T. L. et al. Mice deficient for both corticotropin- releasing factor receptor 1 (CRFR1) and CRFR2 have impaired stress response and display sexually dichotomous anxiety-like behavior. J. Neurosci. 22, 193-199 (2002).
5. Naveilhan, P., Canals, J. M., Arenas, E. & Ernfors, P. Distinct roles of the Y1 and Y2 receptors on neuropeptide Y — induced sensitization to sedation. J. Neurochem. 78, 1201-1207 (2001).
6. Wang, S. W. et al. Brn3b/Brn3c double knockout mice reveal an unsuspected role for Brn3c in retinal ganglion cell axon outgrowth. Development 129, 467-477 (2002).
7. Hamilton, B. et al. The vibrator mutation causes neurodegeneration via reduced expression of PITPα: positional complementation cloning and extragenic suppression. Neuron 18, 711-722 (1997).
8. Phillips, T. J., Hen, R. & Crabbe, J. C. Complications associated with genetic background effects in research using knockout mice. Psychopharmacology. 147, 5-7 (1999).
9. Dietrich, W. et al. A genetic map of the mouse suitable for typing intraspecific crosses. Genetics 131, 423-447 (1992).
10. Lincoln, S. E., Daly, M. & Lander, E. S. Mapping genes controlling quantitative traits with MAPMAKER/QTL 1.1. Whitehead Institute Technical Report 2nd edn (Whitehead institute, MIT, Cambridge, Massachusetts, 1993).
11. Belknap, J. K. et al. QTL analysis and genomewide mutagenesis in mice: complementary genetic approaches to the dissection of complex traits. Behav. Genet. 31, 5-15 (2001).
12. Flint, J. & Mott, R. Finding the molecular basis of quantitative traits: successes and pitfalls. Nature Rev. Genet. 2, 437-445 (2001).
13. Aitman, T. J. et al. Identification of Cd36 (Fat) as an insulin-resistance gene causing defective fatty acid and glucose metabolism in hypertensive rats. Nature Genet. 21, 76-83 (1999).
14. Karp, C. L. et al. Identification of complement factor 5 as a susceptibility locus for experimental allergic asthma. Nature Immunol. 1, 221-226 (2000).
15. Rozzo, S. J. et al. Evidence for an interferon-inducible gene, Ifi202, in the susceptibility to systemic lupus. Immunity. 15, 435-443 (2001).
16. Nadeau, J. H. & Frankel, W. N. The roads from phenotypic variation to gene discovery: mutagenesis vs QTLs. Nature Genet. 25, 381-384 (2000).
17. Jiang, C. & Zeng, Z. B. Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics. 140, 1111-1127 (1995).
18. Jansen, R. C. Interval mapping of multiple quantitative trait loci. Genetics 135, 205-211 (1993).
19. Basten, C., Weir, B. S. & Zeng, Z.-B. QTL Cartographer [online] (cited 03 May 02) (2001).
20. Nadeau, J. H. Modifer genes in mice and humans. Nature Rev. Genet. 2, 165-174 (2001).
21. Rozmahel, R. et al. Modulation of disease severity in cystic fibrosis transmembrane conductance regulator deficient mice by a secondary genetic factor. Nature Genet. 12, 274-277 (1996).
22. Kao, C.-H., Zeng, Z.-B. & Teasdale, R. D. Multiple interval mapping for quantitative trait loci. Genetics. 152, 1203-1216 (1999).
23. Sen, S. & Churchill, G. A. A statistical framework for quantitative trait mapping. Genetics. 159, 371-387 (2001).
24. Cheverud, J. M. & Routman, E. J. Epistasis and its contribution to genetic variance components. Genetics 139, 1455-1461 (1995).
25. Omholt, S. W., Plahte, E., Oyehaug, L. & Xiang, K. Gene regulatory networks generating the phenomena of additivity, dominance and epistasis. Genetics. 155, 969-980 (2000).
26. Sugiyama, F. et al. Concordance of murine quantitative trait loci for salt-induced hypertension with rat and human loci. Genomics 71, 70-77 (2001).
27. Shimomura, K. et al. Genome-wide epistatic interaction analysis reveals complex determinants of circadian behavior in mice. Genome Res. 6, 959-980 (2001).
28. Hood, H., Belknap, J. K., Crabbe, J. C. & Buck, K. J. Genome-wide search for epistasis in a complex trait: pentobarbital withdrawal convulsions in mice. Behav. Genet. 31, 93-100 (2001).
29. Miles, M. F. Microarrays: lost in a storm of data? Nature Rev. Neurosci. 2, 441-443 (2001).
30. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA 95, 14863-14868 (1998).
31. Quackenbush, J. Computational analysis of microarray data. Nature Rev. Genet. 2, 418-427 (2001).
32. Hill, A. A., Hunter, C. P., Tsung, B. T., Tucker-Kellogg, G. & Brown, E. L. Genomic analysis of gene expression in C. elegans. Science 290, 809-812 (2000).
33. Pilpel, Y., Sudarsanam, P. & Church, G. M. Identifying regulatory networks by combinatorial analysis of promotor elements. Nature Genet. 29, 153-159 (2001).
34. Aldenderfer, M. S. & Blashfield, R. K. Cluster Analysis (Sage Publications, Hollywood, California, 1984).
35. Kruskal, J. B. & Wish, M. Multidimensional Scaling (Sage Univ. Press, Beverly Hills, California, 1978).
36. Manly, B. F. J. Multivariate Statistical Methods: a Primer (Chapman & Hall, Bristol, UK, 1986).
37. Crabbe, J. C., Phillips, T. J., Kosobud, A. & Belknap, J. K. Estimation of genetic correlation: interpretation of experiments using selectively bred and inbred animals. Alcohol Clin. Exp. Res. 14, 141-151 (1990).
38. Metten, P. & Crabbe, J. C. Common genetic determinants of severity of acute withdrawal from ethanol, pentobarbital and diazepam in inbred mice. Behav. Pharmacol. 5, 533-547 (1994).
39. Crabbe, J. C., Gallaher, E. J., Cross, S. J. & Belknap, J. K. Genetic determinants of sensitivity to diazepam in inbred mice. Behav. Neurosci. 112, 668-677 (1998).
40. Lariviere, W. R. et al. Heritability of nociception. III. Genetic relationships among commonly used assays of nociception and hypersensitivity. Pain (in the press).
41. Grupe, A. et al. In silico mapping of complex disease- related traits in mice. Science 292, 1915-1918 (2001).
42. Paigen, K. & Eppig, J. T. A mouse phenome project. Mamm. Genome. 11, 715-717 (2000).
43. Mott, R., Talbot, C. J., Turri, M. G., Collins, A. C. & Flint, J. A method for fine mapping quantitative trait loci in outbred animal stocks. Proc. Natl Acad. Sci. USA 97, 12649-12654 (2000).
44. Turri, M. G., Datta, S. R., DeFries, J., Henderson, N. D. & Flint, J. QTL analysis identifies multiple behavioral dimensions in ethological tests of anxiety in laboratory mice. Curr. Biol. 11, 725-734 (2001).
45. Fernandez-Teruel, A. et al. A quantitative trait locus influencing anxiety in the laboratory rat. Genome Res. 12, 618-626 (2002).
46. Korol, A. B., Ronin, Y I., Itskovich, A. M., Peng, J. & Nevo, E. Enhanced efficiency of quantitative trait loci mapping analysis based on multivariate complexes of quantitative traits. Genetics 157, 1789-1803 (2001).
47. Shoemaker, J. S., Painter, I. S. & Weir, B. S. Bayesian statistics in genetics. Trends Genet. 15, 354-358 (1999).
48. Huelsenbeck, J. P., Ronquist, F., Nielsen, R. & Bollack, J. P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2316 (2001).
49. Bayes, T. An essay towards solving a problem in the doctrine of chances. Phil. Trans. R. Soc. 53, 370-418 (1763).
50. Edwards, A. W. F. Likelihood (Johns Hopkins Univ. Press, Baltimore, Maryland, 1972).
51. Wolf, F. M. Meta-analysis: Quantitative Methods for Research Synthesis (Sage Publications, Beverly Hills, California, 1986).
52. Cooper, H. & Hedges, L. V. The Handbook of Research Synthesis (Russell Sage Foundation, New York, 1994).
53. Goffinet, B. & Gerber, S. Quantitative trait loci: a meta- analysis. Genetics 155, 463-473 (2000)
54. Allison, D. B. & Heo, M. Meta-Analysis of linkage data under worst-case conditions: a demonstration using the human OB region. Genetics 148, 859-865 (1998).
55. Rosenthal, R. in The Handbook of Research Synthesis (eds Cooper, H. & Hedges, L. V.) 232-244 (Russell Sage Foundation, New York, 1994).
56. Becker, B. J. in The Handbook of Research Synthesis (eds Cooper, H. & Hedges, L. V.) 216-230 (Russell Sage Foundation, New York, 1994).
57. Stangl, D. K. & Berry, D. A. Meta-analysis in Medicine and Health Policy (Marcel Dekker, New York, 2000).
58. Belknap, J. K. & Atkins, A. L. The replicability of QTLs for murine alcohol preference drinking behavior across eight independent studies. Mamm. Genome 12, 893-899 (2001).
59. Metten, P. et al. Reduced ethanol withdrawal severity predicts higher ethanol consumption. Mamm. Genome 9, 983-990 (1998).
60. 1B receptors. Nature Genet. 14, 98-101 (1996).
61. Phillips, T. J., Crabbe, J. C., Metten, P & Belknap, J. K. Localization of genes affecting alcohol drinking in mice. Alcohol Clin. Exp. Res. 18, 931-941 (1994).
62. Belknap, J. K., Richards, S. P, O'Toole, L. A., Helms, M. L. & Phillips, T. J. Short-term selective breeding as a tool for QTL mapping: alcohol preference drinking in mice. Behav. Genet. 27, 55-66 (1997).
63. Neumann, P. E. & Seyfried, T. N. Mapping of two genes that influence susceptibility to audiogenic seizures in crosses of C57BL/6J and DBA/2J mice. Behav. Genet. 20, 307-323 (1990).
64. Buck, K. J., Metten, P, Belknap, J. K. & Crabbe, J. C. Quantitative trait loci involved in genetic predisposition to acute alcohol withdrawal in mice. J. Neurosci. 17, 3946-3955 (1997).
65. Crabbe, J. C. Provisional mapping of quantitative trait loci for chronic ethanol withdrawal severity in BXD recombinant inbred mice. J. Pharmacol. Exp. Ther. 286, 263-271 (1998).
66. Hain, H. S., Crabbe, J. C., Bergeson, S. E. & Belknap, J. K. Cocaine-induced seizure thresholds: quantitative trait loci detection and mapping in two populations derived from the C57BL/6 and DBA/2 mouse strains. J. Pharmacol. Exp. Ther. 293, 180-187 (2000).
67. McCall, R. D. & Frierson, D. Jr. Evidence that two loci predominantly determine the difference in susceptibility to the high pressure neurologic syndrome type I seizure in mice. Genetics 99, 285-307 (1981).
68. Belknap, J. K. et al. Quantitative trait loci (QTL) applications to substances of abuse: physical dependence studies with nitrous oxide and ethanol in BXD mice. Behav. Genet. 23, 213-222 (1993).
69. Buck, K., Metten, P, Belknap, J. & Crabbe, J. Quantitative trait loci affecting risk for pentobarbital withdrawal map near alcohol withdrawal loci on mouse chromosomes 1, 4, and 11. Mamm. Genome 10, 431-437 (1999).