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Gong Y, Zou F. Varying coefficient models for mapping quantitative trait loci using recombinant inbred intercrosses. Genetics 2012; 190:475-86. [PMID: 22345613 PMCID: PMC3276639 DOI: 10.1534/genetics.111.132522] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Accepted: 11/17/2011] [Indexed: 12/13/2022] Open
Abstract
There has been a great deal of interest in the development of methodologies to map quantitative trait loci (QTL) using experimental crosses in the last 2 decades. Experimental crosses in animal and plant sciences provide important data sources for mapping QTL through linkage analysis. The Collaborative Cross (CC) is a renewable mouse resource that is generated from eight genetically diverse founder strains to mimic the genetic diversity in humans. The recombinant inbred intercrosses (RIX) generated from CC recombinant inbred (RI) lines share similar genetic structures of F(2) individuals but with up to eight alleles segregating at any one locus. In contrast to F(2) mice, genotypes of RIX can be inferred from the genotypes of their RI parents and can be produced repeatedly. Also, RIX mice typically do not share the same degree of relatedness. This unbalanced genetic relatedness requires careful statistical modeling to avoid false-positive findings. Many quantitative traits are inherently complex with genetic effects varying with other covariates, such as age. For such complex traits, if phenotype data can be collected over a wide range of ages across study subjects, their dynamic genetic patterns can be investigated. Parametric functions, such as sigmoidal or logistic functions, have been used for such purpose. In this article, we propose a flexible nonparametric time-varying coefficient QTL mapping method for RIX data. Our method allows the QTL effects to evolve with time and naturally extends classical parametric QTL mapping methods. We model the varying genetic effects nonparametrically with the B-spline bases. Our model investigates gene-by-time interactions for RIX data in a very flexible nonparametric fashion. Simulation results indicate that the varying coefficient QTL mapping has higher power and mapping precision compared to parametric models when the assumption of constant genetic effects fails. We also apply a modified permutation procedure to control overall significance level.
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Affiliation(s)
- Yi Gong
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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Zou F, Xu Z, Vision T. Assessing the significance of quantitative trait loci in replicable mapping populations. Genetics 2006; 174:1063-8. [PMID: 16888335 PMCID: PMC1602090 DOI: 10.1534/genetics.106.059469] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Replicable populations, such as panels of recombinant inbred or doubled haploid lines, are convenient resources for the mapping of QTL. To increase mapping power, replications are often collected within each RI line and a common way to analyze such data is to include in the QTL model only a single measurement from each line that represents the average among the replicates (a line means model). An obvious, but seldom explored, alternative, is to include every replicate in the model (a full data model). Here, we use simulations to compare these two approaches. Further, we propose an extension of the standard permutation procedure that is required to correctly control the type I error in mapping populations with nested structure.
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Affiliation(s)
- Fei Zou
- Department of Biostatistics, University of North Carolina, North Carolina 27599, USA.
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Zou F, Gelfond JAL, Airey DC, Lu L, Manly KF, Williams RW, Threadgill DW. Quantitative trait locus analysis using recombinant inbred intercrosses: theoretical and empirical considerations. Genetics 2005; 170:1299-311. [PMID: 15879512 PMCID: PMC1451174 DOI: 10.1534/genetics.104.035709] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We describe a new approach, called recombinant inbred intercross (RIX) mapping, that extends the power of recombinant inbred (RI) lines to provide sensitive detection of quantitative trait loci (QTL) responsible for complex genetic and nongenetic interactions. RIXs are generated by producing F1 hybrids between all or a subset of parental RI lines. By dramatically extending the number of unique, reproducible genomes, RIXs share some of the best properties of both the parental RI and F2 mapping panels. These attributes make the RIX method ideally suited for experiments requiring analysis of multiple parameters, under different environmental conditions and/or temporal sampling. However, since any pair of RIX genomes shares either one or no parental RIs, this cross introduces an unusual population structure requiring special computational approaches for analysis. Herein, we propose an efficient statistical procedure for QTL mapping with RIXs and describe a novel empirical permutation procedure to assess genome-wide significance. This procedure will also be applicable to diallel crosses. Extensive simulations using strain distribution patterns from CXB, AXB/BXA, and BXD mouse RI lines show the theoretical power of the RIX approach and the analysis of CXB RIXs demonstrates the limitations of this procedure when using small RI panels.
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Affiliation(s)
- Fei Zou
- Department of Biostatistics, Lineberger Comprehensive Cancer Center and Center for Environmental Health and Susceptibility, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jonathan A. L. Gelfond
- Department of Biostatistics, Lineberger Comprehensive Cancer Center and Center for Environmental Health and Susceptibility, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David C. Airey
- Center for Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163
- Department of Anatomy and Neuroscience, University of Tennessee, Memphis, Tennessee 38163
| | - Lu Lu
- Center for Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163
- Department of Anatomy and Neuroscience, University of Tennessee, Memphis, Tennessee 38163
| | - Kenneth F. Manly
- Center for Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163
- Department of Pathology, University of Tennessee, Memphis, Tennessee 38163
| | - Robert W. Williams
- Center for Genomics and Bioinformatics, University of Tennessee, Memphis, Tennessee 38163
- Department of Anatomy and Neuroscience, University of Tennessee, Memphis, Tennessee 38163
| | - David W. Threadgill
- Department of Genetics and the Carolina Center for Genome Sciences, Lineberger Comprehensive Cancer Center and Center for Environmental Health and Susceptibility, University of North Carolina, Chapel Hill, North Carolina 27599
- Corresponding author: Department of Genetics, CB 7264, University of North Carolina, Chapel Hill, NC 27599. E-mail:
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De Haan G, Van Zant G. Genetic analysis of hemopoietic cell cycling in mice suggests its involvement in organismal life span. FASEB J 1999; 13:707-13. [PMID: 10094931 DOI: 10.1096/fasebj.13.6.707] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Normal somatic cells undergo replicative senescence in vitro but the significance of this process in organismic aging remains controversial. We have shown previously that hemopoietic stem cells of common inbred strains of mice vary widely in cycling activity and that this parameter is inversely correlated with strain-dependent mean life span. To assess whether cell cycling and life span are causally related, we searched for quantitative trait loci (QTLs) that contributed to variation of these traits in BXH and BXD recombinant inbred mice. Two QTLs, mapping to exactly the same intervals on chromosomes 7 and 11, were identified that were associated with variation of both cell cycling and life span. The locus on chromosome 11 mapped to the cytokine cluster, a segment that shows synteny with human chromosome 5q, in which deletions are strongly associated with myelodysplastic syndrome. These data indicate that steady-state cell turn-over, here measured in hemopoietic progenitor cells, may have a significant effect on the mean life span of mammals.
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Affiliation(s)
- G De Haan
- Blood and Marrow Transplant Program, Division of Hematology/Oncology, University of Kentucky Medical Center, Lexington, Kentucky 40536-0093, USA
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Rodriguez LA, Plomin R, Blizard DA, Jones BC, McClearn GE. Alcohol acceptance, preference, and sensitivity in mice. I. Quantitative genetic analysis using BXD recombinant inbred strains. Alcohol Clin Exp Res 1994; 18:1416-22. [PMID: 7695038 DOI: 10.1111/j.1530-0277.1994.tb01444.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Although the recombinant inbred strain method was designed for molecular genetic analysis of linkage, it also provides powerful quantitative genetic analyses of heritability and genetic correlations. Measures of alcohol acceptance, alcohol preference, and hypnotic dose sensitivity (HDS) were assessed in 21 strains of mice from the BXD RI series. Sex differences were found to be significant at a phenotypic level. However, heritability estimates for acceptance, preference, and HDS are similar in males and females. Heritability estimates for the three measures are approximately 0.20 for acceptance and preference, and 0.10 for HDS. Analyses of genetic correlations reveal that acceptance and preference share some degree of genetic influence, although they mostly operate under different genetically mediated mechanisms. HDS did not show a significant genetic relationship to either acceptance or preference. Strong correlations were obtained when acceptance, preference, and HDS strain means were correlated across male and female recombinant inbreds, suggesting substantial genetic similarity across sexes.
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Affiliation(s)
- L A Rodriguez
- Center for Developmental and Health Genetics, Pennsylvania State University, University Park 16802
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Abstract
Recombinant inbred (RI) strains can make an important contribution toward the merger of molecular genetics and quantitative genetics in the quest for quantitative trait loci (QTL). We present preliminary analyses of alcohol-related processes from our ongoing research using the BXD RI series. Issues concerning reliability, genetic correlations, and RI QTL analysis are discussed. Several strategies for replication and extension of QTL candidate regions are considered: F1 crosses between RI strains, F2 crosses, heterogeneous stock, interspecific backcrosses, QTL selection, and the use of murine QTL in chromosomal regions syntenic to human chromosomes as candidate chromosomal regions for human QTL.
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Affiliation(s)
- R Plomin
- Center for Developmental and Health Genetics, College of Health and Human Development, Pennsylvania State University, University Park 16802
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Blizard DA. Recombinant-inbred strains: general methodological considerations relevant to the study of complex characters. Behav Genet 1992; 22:621-33. [PMID: 1290450 DOI: 10.1007/bf01066634] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
If appropriately determined, recombinant-inbred (RI) strain means provide an excellent method for determining genetic correlations among complex characters. However, little systematic attention has been paid to important environmental influences on strain means such as random effects due to litter membership or systematic maternal influences, which are inevitably confounded with genetic effects. It is suggested that users of RI strains would do well to control for litter effects by sampling appropriately from many litters and assessing the potential role of maternal influences by appropriate fostering procedures. Concern for these and other environmental sources of variation has caused reliability of strain means to emerge as an important issue in studies with RIs which focus on complex characters. Examples of estimating the reliability of RI strain means are provided to draw attention to the value of this kind of information in both gene-mapping studies and genetic correlational analyses. In addition, particularly in the case of behavioral tests which are susceptible to considerable day-to-day variation, repeated testing of the same animals can serve to diminish the influence of extreme deviations which are due to random variations in the manner in which the test is conducted on any given day. The advantages of RIs for gene mapping are well established. However, via the power of genetic correlational analysis, the RI methodology is emerging as a major alternative method, e.g., as distinct from lesion studies, pharmacological interventions, etc., in the bio-behavioral sciences to explore relationships between different domains of inquiry. Via its cumulative and integrative power, it is likely to make a major contribution to investigations of relationships between complex characters at various levels of and this application which should be considered separately from its application to gene mapping.
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Affiliation(s)
- D A Blizard
- Center for Developmental and Health Genetics, Pennsylvania State University, University Park 16802
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Belknap JK, Crabbe JC. Chromosome mapping of gene loci affecting morphine and amphetamine responses in BXD recombinant inbred mice. Ann N Y Acad Sci 1992; 654:311-23. [PMID: 1632590 DOI: 10.1111/j.1749-6632.1992.tb25977.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- J K Belknap
- Research Service, VA Medical Center, Portland, Oregon 97201-3098
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Belknap JK, Crabbe JC, Plomin R, McClearn GE, Sampson KE, O'Toole LA, Gora-Maslak G. Single-locus control of saccharin intake in BXD/Ty recombinant inbred (RI) mice: some methodological implications for RI strain analysis. Behav Genet 1992; 22:81-100. [PMID: 1590732 DOI: 10.1007/bf01066794] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The sac locus, with a major effect on saccharin preference, was discovered by Fuller (1974) in C57BL/6J (B6), DBA/2J (D2), and derived crosses, and is now supported in the BXD/Ty recombinant inbred (RI) series by a marked bimodal distribution in saccharin preference among 20 strains. The B6 allele led to increased saccharin preference compared to the D2 allele. Since the search for bimodal distributions reflecting major gene loci is an essential part of RI strain analysis, a new statistical method is proposed to test for bimodality, and comparisons are made to previously proposed methods. Another new RI method, quantitative trait loci (QTL) analysis, allows provisional detection and mapping of minor as well as major gene loci. Using this method as a screen, significant associations with saccharin preference were suggested with marker loci on portions of six chromosomes. One of these, the D12nyu1 locus on chromosome 12, was independently supported in a panel of standard (non-RI) inbred strains also tested for saccharin preference. It is unclear whether this reflects the sac locus.
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Affiliation(s)
- J K Belknap
- Research Service (151W), VA Medical Center, Portland Oregon
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