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  • Print publication year: 2013
  • Online publication date: November 2013

Chapter 2 - Methods in complex trait analysis: mapping the genetic basis of sleep using model organisms

from Section 1 - Generalprinciples of genetics and genomics
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The Genetic Basis of Sleep and Sleep Disorders
  • Online ISBN: 9781139649469
  • Book DOI: https://doi.org/10.1017/CBO9781139649469
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References

1. Flint J. Mapping quantitative traits and strategies to find quantitative trait genes. Methods. 2011;53:163–74.
2. Tafti M, Chollet D, Valatx JL, et al. Quantitative trait loci approach to the genetics of sleep in recombinant inbred mice. J Sleep Res. 1999;8(Suppl 1):37–43.
3. Darvasi A. Experimental strategies for the genetic dissection of complex traits in animal models. Nat Genet. 1998;18:19–24.
4. Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics. 1994;138:963–71.
5. Visscher PM, Thompson R, Haley CS. Confidence intervals in QTL mapping by bootstrapping. Genetics. 1996;143:1013–20.
6. Lander ES, Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989;121:185–99.
7. R Development Core Team. A language and environment for statistical computing. Computing RFfS, editor. Vienna: R Foundation for Statistical Computing; 2004.
8. Broman KW, Wu H, Sen S, et al. R/qtl: QTL mapping in experimental crosses. Bioinformatics. 2003;19:889–90.
9. Mackay TF, Richards S, Stone EA, et al. The Drosophila melanogaster Genetic Reference Panel. Nature. 2012;482:173–78.
10. Wang J, Williams RW, Manly KF. WebQTL: web-based complex trait analysis. Neuroinformatics. 2003;1:299–308.
11. Peirce JL, Lu L, Gu J, et al. A new set of B×D recombinant inbred lines from advanced intercross populations in mice. BMC Genet. 2004;5:7.
12. Williams RW, Bennett B, Lu L, et al. Genetic structure of the L×S panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis. Mamm Genome. 2004;15:637–47.
13. Voigt B, Kuramoto T, Mashimo T, et al. Evaluation of LEXF/FXLE rat recombinant inbred strains for genetic dissection of complex traits. Physiol Genomics. 2008;32:335–42.
14. Pravenec M, Klir P, Kren V, et al. An analysis of spontaneous hypertension in spontaneously hypertensive rats by means of new recombinant inbred strains. J Hypertens. 1989;7:217–21.
15. Defays R, Bertoli CI. Quantitative trait loci for response to ethanol in an intercontinental set of recombinant inbred lines of Drosophila melanogaster. Alcohol. 2012;46:737–45.
16. Gaertner BE, Phillips PC. Caenorhabditis elegans as a platform for molecular quantitative genetics and the systems biology of natural variation. Genetics Res. 2010;92:331–48.
17. Churchill GA, Airey DC, Allayee H, et al. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet. 2004;36:1133–37.
18. Collaborative Cross Consortium. The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics. 2012;190:389–401.
19. Aylor DL, Valdar W, Foulds-Mathes W, et al. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res. 2011;21:1213–22.
20. Durrant C, Tayem H, Yalcin B, et al. Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection. Genome Res. 2011;21:1239–48.
21. Mott R, Talbot CJ, Turri MG, et al. A method for fine mapping quantitative trait loci in outbred animal stocks. Proc Natl Acad Sci USA. 2000;97:12649–54.
22. Keane TM, Goodstadt L, Danecek P, et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature. 2011;477:289–94.
23. Moen CJ, van der Valk MA, Snoek M, et al. The recombinant congenic strains – a novel genetic tool applied to the study of colon tumor development in the mouse. Mamm Genome. 1991;1:217–27.
24. Nadeau JH, Singer JB, Matin A, et al. Analysing complex genetic traits with chromosome substitution strains. Nat Genet. 2000;24:221–25.
25. Glauser DA, Chen WC, Agin R, et al. Heat avoidance is regulated by transient receptor potential (TRP) channels and a neuropeptide signaling pathway in Caenorhabditis elegans. Genetics. 2011;188:91–103.
26. Caligari PDS, Mather K. Genotype–environment interaction. 3. Interactions in Drosophila melanogaster. Proc R Soc London B Biol Sci. 1975;191:387–411.
27. Hollocher H, Ting CT, Wu ML, et al. Incipient speciation by sexual isolation in Drosophila melanogaster: extensive genetic divergence without reinforcement. Genetics. 1997;147:1191–201.
28. Mattson DL, Dwinell MR, Greene AS, et al. Chromosome substitution reveals the genetic basis of Dahl salt-sensitive hypertension and renal disease. Am J Physiol Renal Physiol. 2008;295:F837–42.
29. Nadeau JH, Singer JB, Matin A, et al. Analysing complex genetic traits with chromosome substitution strains. Nat Genet. 2000;24:221–25.
30. Singer JB, Hill AE, Burrage L, et al. Genetic dissection of complex traits with chromosome substitution strains of mice. Science. 2004;304:445–48.
31. Takada T, Mita A, Maeno A, et al. Mouse inter-subspecific consomic strains for genetic dissection of quantitative complex traits. Genome Res. 2008;18:500–08.
32. Gregorova S, Divina P, Storchova R, et al. Mouse consomic strains: exploiting genetic divergence between Mus m. musculus and Mus m. domesticus subspecies. Genome Res. 2008;18:509–15.
33. Grupe A, Germer S, Usuka J, et al. In silico mapping of complex disease-related traits in mice. Science. 2001;292:1915–18.
34. Yang H, Wang JR, Didion JP, et al. Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet. 2011;43:648–55.
35. Yalcin B, Wong K, Agam A, et al. Sequence-based characterization of structural variation in the mouse genome. Nature. 2011;477:326–29.
36. Kang HM, Zaitlen NA, Wade CM, et al. Efficient control of population structure in model organism association mapping. Genetics. 2008;178:1709–23.
37. Bennett BJ, Farber CR, Orozco L, et al. A high-resolution association mapping panel for the dissection of complex traits in mice. Genome Research. 2010;20:281–90.
38. Yang H, Bell TA, Churchill GA, et al. On the subspecific origin of the laboratory mouse. Nat Genet. 2007;39:1100–07.
39. Doroszuk A, Snoek LB, Fradin E, et al. A genome-wide library of CB4856/N2 introgression lines of Caenorhabditis elegans. Nucleic Acids Res. 2009;37:e110
40. Davis RC, Schadt EE, Smith DJ, et al. A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background. Genomics. 2005;86:259–70.
41. Davis RC, Jin A, Rosales M, et al. Genome-wide set of congenic mouse strains derived from CAST/Ei on a C57BL/6 background. Genomics. 2007;90:306–13.
42. Burgio G, Szatanik M, Guenet JL, et al. Interspecific recombinant congenic strains between C57BL/6 and mice of the Mus spretus species: a powerful tool to dissect genetic control of complex traits. Genetics. 2007;177:2321–33.
43. Tomida S, Mamiya T, Sakamaki H, et al. Usp46 is a quantitative trait gene regulating mouse immobile behavior in the tail suspension and forced swimming tests. Nat Genet. 2009;41:688–95.
44. Legare ME, Bartlett FS, Frankel WN. A major effect QTL determined by multiple genes in epileptic EL mice. Genome Res. 2000;10:42–48.
45. Stylianou IM, Christians JK, Keightley PD, et al. Genetic complexity of an obesity QTL (Fob3) revealed by detailed genetic mapping. Mamm Genome. 2004;15:472–81.
46. Christians JK, Keightley PD. Fine mapping of a murine growth locus to a 1.4-cM region and resolution of linked QTL. Mamm Genome. 2004;15:482–91.
47. Darvasi A, Soller M. Advanced intercross lines, an experimental population for fine genetic mapping. Genetics. 1995;141:1199–207.
48. Han B, Kang HM, Seo MS, et al. Efficient association study design via power-optimized tag SNP selection. Ann Hum Genet. 2008;72:834–47.
49. Talbot CJ, Nicod A, Cherny SS, et al. High-resolution mapping of quantitative trait loci in outbred mice. Nat Genet. 1999;21:305–08.
50. Johannesson M, Lopez-Aumatell R, Stridh P, et al. A resource for the simultaneous high-resolution mapping of multiple quantitative trait loci in rats: the NIH heterogeneous stock. Genome Res. 2009;19:150–58.
51. Yalcin B, Nicod J, Bhomra A, et al. Commercially available outbred mice for genome-wide association studies. PLoS Genet. 2010;6.
52. Yalcin B, Flint J. Association studies in outbred mice in a new era of full-genome sequencing. Mamm Genome. 2012;23:719–26.
53. Bogue MA, Grubb SC, Maddatu TP, et al. Mouse Phenome Database (MPD). Nucleic Acids Res. 2007;35:D643–49.
54. Aylor DL, Valdar W, Foulds-Mathes W, et al. Genetic analysis of complex traits in the emerging Collaborative Cross. Genome Res. 2011;21:1213–22.
55. Philip VM, Sokoloff G, Ackert-Bicknell CL, et al. Genetic analysis in the Collaborative Cross breeding population. Genome Res. 2011;21:1223–38.
56. Durrant C, Tayem H, Yalcin B, et al. Collaborative Cross mice and their power to map host susceptibility to Aspergillus fumigatus infection. Genome Res. 2011;21:1239–48.
57. Valdar W, Flint J, Mott R. Simulating the collaborative cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics. 2006;172:1783–97.
58. Huang W, Richards S, Carbone MA, et al. Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci USA. 2012;109:15553–59.