Genome reshuffling for Advanced Intercross Permutation (GRAIP) : Simulation and Permutation for advanced intercross population analysis

PLoS ONE

Volumn 3, Issue 4, 2008, Pages

  Peirce, Jeremy L ^a   Broman, Karl W ^b   Lu, Lu ^a   Chesler, Elissa J ^a   Zhou, Guomin ^a   Airey, David C ^a   Birmingham, Amanda E ^c   Williams, Robert W ^a  

^a UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c Dharmacon Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; FALSE POSITIVE RESULT; FEMALE; GENE LOCUS; GENOME ANALYSIS; GENOME RESHUFFLING FOR ADVANCED INTERCROSS PERMUTATION; GENOTYPE; HAPLOTYPE; HIPPOCAMPUS; MALE; MOUSE; NONHUMAN; PHENOTYPE; POPULATION STRUCTURE; PROMOTER REGION; QUANTITATIVE TRAIT LOCUS MAPPING; SIMULATION; ANIMAL; BIOLOGY; CHROMOSOME; CHROMOSOME MAP; COMPUTER PROGRAM; COMPUTER SIMULATION; CROSS BREEDING; GENETIC LINKAGE; GENETICS; GENOME; GROWTH, DEVELOPMENT AND AGING; INBREEDING; METHODOLOGY; MOUSE STRAIN; ORGAN SIZE; PIGMENTATION; QUANTITATIVE TRAIT LOCUS;

ANIMALIA; MUS;

ANIMALS; CHROMOSOME MAPPING; CHROMOSOMES, MAMMALIAN; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CROSSES, GENETIC; FEMALE; GENOME; HIPPOCAMPUS; INBREEDING; LOD SCORE; MALE; MICE; MICE, INBRED STRAINS; ORGAN SIZE; PHENOTYPE; PIGMENTATION; QUANTITATIVE TRAIT LOCI; SOFTWARE;

EID: 44349151774     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001977     Document Type: Article

References (37)

1. Korstanje R, Paigen B (2002) From QTL to gene: the harvest begins. Nat Genet 31: 235-236.
2. Abiola O, Angel JM, Avner P, Bachmanov AA, Belknap JK, et al. (2003) The nature and identification of quantitative trait loci: a community's view. Nat Rev Genet 4: 911-916.
3. Darvasi A, Soller M (1995) Advanced intercross lines, an experimental population for fine genetic mapping. Genetics 141: 1199-1207.
4. Sheng J, Jagodic M, Dahlman I, Becanovic K, Nohra R, et al. (2005) Eacl 9, a new locus on rat chromosome 15 regulating experimental autoimmune encephalomyelitis. Genetics.
5. Jagodic M, Becanovic K, Sheng JR, Wu X, Backdahl L, 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.
6. Iraqi F, Clapcott SJ, Kumari P, Haley CS, Kemp SJ, et al. (2000) Fine mapping of trypanosomiasis resistance loci in murine advanced intercross lines. Mamm Genome 11: 645-648.
7. Wang X, Le Roy I, Nicodeme E, Li R, Wagner R, et al. (2003) Using advanced intercross lines for high-resolution mapping of HDL cholesterol quantitative trait loci. Genome Res 13: 1654-1664.
8. Wang M, Lemon WJ, Liu G, Wang Y, Iraqi FA, et al. (2003) Fine mapping and identification of candidate pulmonary adenoma susceptibility 1 genes using advanced intercross lines. Cancer Res 63: 3317-3324.
9. 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.
10. Silver LM (1995) Mouse Genetics. New York: Oxford University Press.
11. Weller JI, Kashi Y, Soller M (1990) Power of daughter and granddaughter designs for determining linkage between marker loci and quantitative trait loci in dairy cattle. J Dairy Sci 73: 2525-2537.
12. Peirce JL, Chesler EJ, Williams RW, Lu L (2003) Genetic architecture of the mouse hippocampus: identification of gene loci with selective regional effects. Genes Brain Behav 2: 238-252.
13. Lu L, Airey DC, Williams RW (2001) Complex trait analysis of the hippocampus: mapping and biometric analysis of two novel gene loci with specific effects on hippocampal structure in mice. J Neurosci 21: 3503-3514.
14. Palmer AA, Airey DC (2003) Inappropriate choice of the experimental unit leads to a dramatic overestimation of the significance of quantitative trait loci for prepulse inhibition and startle response in recombinant congenic mice. Neuropsychopharmacology 28: 818; author reply 819.
15. Peirce JL, Broman K, Lu L, Williams RW. A simple method for combining QTL maps from multiple data sources. PLoS ONE 2(10): e1036.
16. Zou F, Gelfond J, Airey DC, Lu L, Manly KF, et al. Quantitative trait locus analysis using recombinant inbred intercrosses (RIX): theoretical and empirical considerations..
17. Tsaih S-W, Lu L, Airey DC, Williams RW, Churchill GA (2005) Quantitative trait mapping in a diallel cross of recombinant inbred lines. Mamm Genome 16: 344-355.
18. Peirce JL, Lu L, Gu J, Silver LM, Williams RW (2004) A new set of BXD recombinant inbred lines from advanced intercross populations in mice. BMC Genet 5: 7.
19. Broman KW (2005) The genomes of recombinant inbred lines. Genetics 169: 1133-1146.
20. Churchill GA, Airey DC, Allayee H, Angel JM, Attie AD, et al. (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat Genet 36: 1133-1137.
21. Williams RW, Bennett B, Lu L, Gu J, DeFries JC, et al. (2004) Genetic structure of the LXS panel of recombinant inbred mouse strains: a powerful resource for complex trait analysis. Mamm Genome 15: 637-647.
22. Chesler EJ, Lu L, Shou S, Qu Y, Gu 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.
23. Chesler EJ, Wang J, Lu L, Qu Y, Manly KF, et al. (2003) Genetic correlates of gene expression in recombinant inbred strains: a relational model system to explore neurobehavioral phenotypes. Neuroinformatics 1: 343-357.
24. Zou F, Gelfond JA, Airey DC, Lu L, Manly KF, et al. (2005) Quantitative trait locus analysis using recombinant inbred intercrosses (RIX): theoretical and empirical considerations. Genetics.
25. Iakoubova OA, Olsson CL, Dains KM, Ross DA, Andalibi A, et al. (2001) Genome-tagged mice (GTM): two sets of genome-wide congenic strains. Genomics 74: 89-104.
26. Abney M, Ober C, McPeek MS (2002) Quantitative-trait homoygosity and association mapping and empirical genomewide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites. Am J Hum Genet 70: 920-934.
27. Zhou G, Williams RW (1999) Eye 1 and Eye2: gene loci that modulate eye size, lens weight, and retinal area in the mouse. Invest Ophthalmol Vis Sci 40: 817-825.
28. Taylor BA (1989) Recombinant inbred strains. In: Lyon ML, Searle AG, eds. Genetic Variants and Strains of the Laboratory Mouse. Oxford: Oxford UP. pp 773-796.
29. Taylor BA, Wnek C, Kotlus BS, Roemer N, MacTaggart T, et al. (1999) Genotyping new BXD recombinant inbred mouse strains and comparison of BXD and consensus maps. Mamm Genome 10: 335-348.
30. Williams RW, Gu J, Qi S, Lu L (200 1) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biol 2: RESEARCH0046.
31. Sobel E, Sengul H, Weeks DE (2001) Multipoint estimation of identity-by-descent probabilities at arbitrary positions among marker loci on general pedigrees. Hum Hered 52: 121-131.
32. Sobel E, Lange K (1996) Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker-sharing statistics. Am J Hum Genet 58: 1323-1337.
33. Broman KW, Rowe LB, Churchill GA, Paigen K (2002) Crossover interference in the mouse. Genetics 160: 1123-1131.
34. Sen S, Churchill GA (2001) A statistical framework for quantitative trait mapping. Genetics 159: 371-387.
35. Broman KW, Wu H, Sen S, Churchill GA (2003) R/qd: QTL mapping in experimental crosses. Bioinformatics 19: 889-890.
36. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971.
37. Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Computational and Graphical Statistics 5: 299-314.