Genome-wide association studies and the problem of relatedness among advanced intercross lines and other highly recombinant populations

Genetics

Volumn 185, Issue 3, 2010, Pages 1033-1044

  Cheng, Riyan ^a   Lim, Jackie E ^b   Samocha, Kaitlin E ^a   Sokoloff, Greta ^a   Abney, Mark ^a   Skol, Andrew D ^a   Palmer, Abraham A ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METHAMPHETAMINE;

ADVANCED INTERCROSS LINE; ANIMAL EXPERIMENT; ARTICLE; CHROMOSOME 18; CONTROLLED STUDY; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RECOMBINATION; GENETIC TRAIT; GENOTYPE; HERITABILITY; INBRED STRAIN; LOCOMOTION; MALE; MOUSE; MULTIFACTORIAL INHERITANCE; NONHUMAN; PHENOTYPE; POPULATION DYNAMICS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; ANIMAL BEHAVIOR; BIOLOGY; CHROMOSOME; CHROMOSOME MAP; CROSS BREEDING; GENETIC LINKAGE; GENETICS; GENOME; HUMAN; QUANTITATIVE TRAIT LOCUS;

MUS;

ANIMALS; BEHAVIOR, ANIMAL; CHROMOSOME MAPPING; CHROMOSOMES, MAMMALIAN; COMPUTATIONAL BIOLOGY; CROSSES, GENETIC; GENOME; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE (GENETICS); MICE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RECOMBINATION, GENETIC;

EID: 77957157030     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.116863     Document Type: Article

References (56)

1. ABNEY, M., 2009 A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. Bioinformatics 25: 1561-1563.
2. ABNEY, M., M. S. MCPEEK and C. OBER, 2000 Estimation of variance components of quantitative traits in inbred populations. Am. J. Hum. Genet. 66: 629-650.
3. AULCHENKO, Y. S., D. J. DE KONING and C. HALEY, 2007 Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177: 577-585.
4. BÄCKDAHL, L., J. P. GUO, M. JAGODIC, K. BECANOVIC, B. DING et al., 2009 Definition of arthritis candidate risk genes by combining rat linkage-mapping results with human case control association data. Ann. Rheum. Dis. 68: 1925-1932.
5. BALINT-KURTI, P. J., J. C. ZWONITZER, R. J. WISSER, M. L. CARSON, M. A. OROPEZA-ROSAS et al., 2007 Precise mapping of quantitative trait loci for resistance to southern leaf blight, caused by cochliobolus heterostrophus race O, and flowering time using advanced intercross maize lines. Genetics 176: 645-657.
6. BECANOVIC, K., M. JAGODIC, J. R. SHENG, I. DAHLMAN, F. ABOUL-ENEIN et al., 2006 Advanced intercross line mapping of Eae5 reveals ncf-1 and CLDN4 as candidate genes for experimental autoimmune encephalomyelitis. J. Immunol. 176: 6055-6064.
7. BEHNKE, J. M., F. A. IRAQI, J. M. MUGAMBI, S. CLIFFORD, S. NAGDA et al., 2006 High resolution mapping of chromosomal regions controlling resistance to gastrointestinal nematode infections in an advanced intercross line of mice. Mamm. Genome 17: 584-597.
8. BENNETT, K. E., D. FLICK, K. H. FLEMING, R. JOCHIM, B. J. BEATY et al., 2005 Quantitative trait loci that control dengue-2 virus dissemination in the mosquito Aedes aegypti. Genetics 170: 185-194.
9. BRYANT, C. D., M. E. GRAHAM, M. G. DISTLER, M. B. MUNOZ, D. LI et al., 2009 A role for casein kinase 1 epsilon in the locomotor stimulant response to methamphetamine. Psychopharmacology 203: 703-711.
10. CHURCHILL, G. A., and R. W. DOERGE, 1994 Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
11. DARVASI, A., 1998 Experimental strategies for the genetic dissection of complex traits in animal models. Nat. Genet. 18: 19-24.
12. DARVASI, A., and M. SOLLER, 1995 Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199-1207.
13. FLINT, J., W. VALDAR, S. SHIFMAN and R. MOTT, 2005 Strategies for mapping and cloning quantitative trait genes in rodents. Nat. Rev. Genet. 6: 271-286.
14. GHAZALPOUR, A., S. DOSS, H. KANG, C. FARBER, P. Z. WEN et al., 2008 High-resolution mapping of gene expression using association in an outbred mouse stock. PLoS Genet. 4: e1000149.
15. GOMEZ-MACHORRO, C., K. E. BENNETT, M. DEL LOURDES MUNOZ and W. C. BLACK, IV, 2004 Quantitative trait loci affecting dengue midgut infection barriers in an advanced intercross line of aedes aegypti. Insect Mol. Biol. 13: 637-648.
16. HALEY, C. S., and S. A. KNOTT, 1992 A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69: 315-324.
17. HARRIS, D. L., 1964 Genotypic covariances between inbred relatives. Genetics 50: 1319-1348.
18. IRAQI, F., 2000 Fine mapping of quantitative trait loci using advanced intercross lines of mice and positional cloning of the corresponding genes. Exp. Lung Res. 26: 641-649.
19. IRAQI, F., S. J. CLAPCOTT, P. KUMARI, C. S. HALEY, S. J. KEMP et al., 2000 Fine mapping of trypanosomiasis resistance loci in murine advanced intercross lines. Mamm. Genome 11: 645-648.
20. JACQUARD, A., 1974 The Genetic Structure of Populations (Biomathematics, Vol. 5). Springer-Verlag, Berlin/Heidelberg, Germany/New York.
21. JAGODIC, M., K. BECANOVIC, J. R. SHENG, X. WU, L. BACKDAHL et al., 2004 An advanced intercross line resolves Eae18 into two narrow quantitative trait loci syntenic to multiple sclerosis candidate loci. J. Immunol. 173: 1366-1373.
22. JENNEN, D. G., A. L. VEREIJKEN, H. BOVENHUIS, R. M. CROOIJMANS, J. J. VAN DER POEL et al., 2005 Confirmation of quantitative trait loci affecting fatness in chickens. Genet. Sel. Evol. 37: 215-228.
23. KARIGL, G., 1981 A recursive algorithm for the calculation of identity coefficients. Ann. Hum. Genet. 45: 299-305.
24. KRAUS, D. M., G. S. ELLIOTT, H. CHUTE, T. HORAN, K. H. PFENNINGER et al., 2006 CSMD1 is a novel multiple domain complement-regulatory protein highly expressed in the central nervous system and epithelial tissues. J. Immunol. 176: 4419-4430.
25. LAURIE, C. C., D. A. NICKERSON, A. D. ANDERSON, B. S. WEIR, R. J. LIVINGSTON et al., 2007 Linkage disequilibrium in wild mice. PLoS Genet. 3: e144.
26. LEHMANN, E. L., 1997 Testing Statistical Hypotheses (Springer Texts in Statistics). Springer, Berlin/Heidelberg, Germany/New York.
27. LEVRAN, O., D. LONDONO, K. O'HARA, D. A. NIELSEN, E. PELES et al., 2008 Genetic susceptibility to heroin addiction: a candidate gene association study. Genes Brain Behav. 7: 720-729.
28. MACCLUER, J. W., J. L. VANDERBERG, B. READ and O. A. RYDER, 1986 Pedigree analysis by computer simulation. Zoo Biol. 5: 147-160.
29. MACDONALD, S. J., and A. D. LONG, 2007 Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261-1281.
30. MANOLIO, T. A., F. S. COLLINS, N. J. COX, D. B. GOLDSTEIN, L. A. HINDORFF et al., 2009 Finding the missing heritability of complex diseases. Nature 461: 747-753.
31. MCARDLE, P. F., H. DYTCH, J. R. O'CONNELL, A. R. SHULDINER, B. D. MITCHELL et al., 2007 Homozygosity by descent mapping of blood pressure in the old order Amish: evidence for sex specific genetic architecture. BMC Genet. 8: 66.
32. MCPEEK, M. S., 2000 From mouse to human: fine mapping of quantitative trait loci in a model organism. Proc. Natl. Acad. Sci. USA 97: 12389-12390.
33. NEWMAN, D. L., M. ABNEY, M. S. MCPEEK, C. OBER and N. J. COX, 2001 The importance of genealogy in determining genetic associations with complex traits. Am. J. Hum. Genet. 69: 1146-1148.
34. NORGARD, E. A., J. P. JARVIS, C. C. ROSEMAN, T. J. MAXWELL, J. P. KENNEY-HUNT et al., 2009 Replication of long-bone length QTL in the F9-F10 LG,SM advanced intercross. Mamm. Genome 20: 224-235.
35. O'GORMAN, T., 2005 The performance of randomization tests that use permutations of independent variables. Commun. Stat. Simul. Comput. 34: 895.
36. PALMER, A. A., M. VERBITSKY, R. SURESH, H. M. KAMENS, C. L. REED et al., 2005 Gene expression differences in mice divergently selected for methamphetamine sensitivity. Mamm. Genome 16: 291-305.
37. PEIRCE, J. L., K. W. BROMAN, L. LU, E. J. CHESLER, G. ZHOU et al., 2008 Genome reshuffling for advanced intercross permutation (GRAIP): simulation and permutation for advanced intercross population analysis PLoS One 3: e1977.
38. PETERS, L. L., R. F. ROBLEDO, C. J. BULT, G. A. CHURCHILL, B. J. PAIGEN et al., 2007 The mouse as a model for human biology: a resource guide for complex trait analysis. Nat. Rev. Genet. 8: 58-69.
39. PHILLIPS, T. J., H. M. KAMENS and J. M. WHEELER, 2008 Behavioral genetic contributions to the study of addiction-related amphetamine effects. Neurosci. Biobehav. Rev. 32: 707-759.
40. PRESS, W., B. FLANNERY, S. TEUKOLSKY and W. VETTERLING, 1992 Numerical Recipes in C: The Art of Scientific Computing. Cambridge University Press, Cambridge, UK/London/New York.
41. ROCKMAN, M. V., and L. KRUGLYAK, 2008 Breeding designs for recombinant inbred advanced intercross lines. Genetics 179: 1069-1078.
42. SHIFMAN, S., J. T. BELL, R. R. COPLEY, M. S. TAYLOR, R. W. WILLIAMS et al., 2006 A high-resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biol. 4: e395.
43. SWANBERG, M., O. LIDMAN, L. PADYUKOV, P. ERIKSSON, E. AKESSON et al., 2005 MHC2TA is associated with differential MHC molecule expression and susceptibility to rheumatoid arthritis, multiple sclerosis and myocardial infarction. Nat. Genet. 37: 486-494.
44. SWANBERG, M., K. HARNESK, M. STROM, M. DIEZ, O. LIDMAN et al., 2009 Fine mapping of gene regions regulating neurodegeneration. PLoS One 4: e5906.
45. SZATKIEWICZ, J. P., G. L. BEANE, Y. DING, L. HUTCHINS, F. PARDO-MANUEL DE VILLENA et al., 2008 An imputed genotype resource for the laboratory mouse. Mamm. Genome 19: 199-208.
46. TERCIC, D., A. HOLCMAN, P. DOVC, D. R. MORRICE, D. W. BURT et al., 2009 Identification of chromosomal regions associated with growth and carcass traits in an F full sib intercross line originating from a cross of chicken lines divergently selected on body weight. Anim. Genet. 40: 743-748.
47. VALDAR, W., L. C. SOLBERG, D. GAUGUIER, S. BURNETT, P. KLENERMAN et al., 2006 Genome-wide genetic association of complex traits in heterogeneous stock mice. Nat. Genet. 38: 879-887.
48. VALDAR, W., C. C. HOLMES, R. MOTT and J. FLINT, 2009 Mapping in structured populations by resample model averaging. Genetics 182: 1263-1277.
49. VEENSTRA-VANDERWEELE, J., A. QAADIR, A. A. PALMER, E. H. COOK, JR. and H. DE WIT, 2006 Association between the casein kinase 1 epsilon gene region and subjective response to D-amphetamine. Neuropsychopharmacology 31: 1056-1063.
50. VOIGHT, B. F., and J. K. PRITCHARD, 2005 Confounding from cryptic relatedness in case-control association studies. PLoS Genet. 1: e32.
51. WANG, M., W. J. LEMON, G. LIU, Y. WANG, F. A. IRAQI et al., 2003a Fine mapping and identification of candidate pulmonary adenoma susceptibility 1 genes using advanced intercross lines. Cancer Res. 63: 3317-3324.
52. WANG, X., I. LE ROY, E. NICODEME, R. LI, R. WAGNER et al., 2003b Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci. Genome Res. 13: 1654-1664.
53. YALCIN, B., S. A. WILLIS-OWEN, J. FULLERTON, A. MEESAQ, R. M. DEACON et al., 2004 Genetic dissection of a behavioral quantitative trait locus shows that Rgs2 modulates anxiety in mice. Nat. Genet. 36: 1197-1202.
54. YU, X., K. BAUER, P. WERNHOFF, D. KOCZAN, S. MOLLER et al., 2006 Fine mapping of collagen-induced arthritis quantitative trait loci in an advanced intercross line. J. Immunol. 177: 7042-7049.
55. YU, X., H. TENG, A. MARQUES, F. ASHGARI and S. M. IBRAHIM, 2009 High resolution mapping of Cia3: a common arthritis quantitative trait loci in different species. J. Immunol. 182: 3016-3023.
56. ZHANG, S., Y. LOU, T. M. AMSTEIN, M. ANYANGO, N. MOHIBULLAH et al., 2005 Fine mapping of a major locus on chromosome 10 for exploratory and fear-like behavior in mice. Mamm. Genome 16: 306-318.