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    Axenovich, Tatiana I. and Zorkoltseva, Irina V. 2012. GADS software for parametric linkage analysis of quantitative traits distributed as a point-mass mixture. Computational Biology and Chemistry, Vol. 36, p. 13.


Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes

  • DOI:
  • Published online: 03 March 2010

Increasingly researchers are conducting quantitative trait locus (QTL) mapping in metabolomics and proteomics studies. These data often are distributed as a point-mass mixture, consisting of a spike at zero in combination with continuous non-negative measurements. Composite interval mapping (CIM) is a common method used to map QTL that has been developed only for normally distributed or binary data. Here we propose a two-part CIM method for identifying QTLs when the phenotype is distributed as a point-mass mixture. We compare our new method with existing normal and binary CIM methods through an analysis of metabolomics data from Arabidopsis thaliana. We then conduct a simulation study to further understand the power and error rate of our two-part CIM method relative to normal and binary CIM methods. Our results show that the two-part CIM has greater power and a lower false positive rate than the other methods when a continuous phenotype is measured with many zero observations.

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*Corresponding author: One Shields Avenue, Department of Statistics, University of California, Davis, CA95616, USA. Tel: +1 (916) 248 1963. Fax: +1 (530) 752 7099. e-mail:
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K. W. Broman , H. Wu , S. Sen & G. A. Churchill (2003). R/qtl: QTL mapping in experimental crosses. Bioinformatics 19, 889890.

W. Deng , H. Chen & Z. Li (2006). A logistic regression mixture model for interval mapping of genetic trait loci affecting binary phenotypes. Genetics 172, 13491358.

G. Diao , D. Y. Lin & F. Zou (2004). Mapping quantitative trait loci with censored observations. Genetics 168, 16891698.

J. P. Fine , F. Zou & B. S. Yandell (2004). Nonparametric estimation of the effects of quantitative trait loci. Biostatistics 5, 501513.

C. A. Hackett & J. I. Weller (1995). Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics 51, 12521263.

C. S. Haley & S. A. Knott (1992). A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69, 315324.

C. Jin , J. P. Fine & B. S. Yandell (2007). A unified semiparametric framework for quantitative trait loci analyses, with application to spike phenotypes. Journal of the American Statistical Association 102, 5667.

W. Li & Z. Chen (2009). Multiple interval mapping for quantitative trait loci with a spike in the trait distribution. Genetics 182, 337342.

O. Loudet , E. S. Chaillou , C. Camilleri , D. Bouchez & F. Daniel-Vedele (2002). Bay-0×Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis. Theoretical and Applied Genetics 104, 11721184.

O. Martinez & R. N. Curnow (1992). Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theoretical and Applied Genetics 85, 480488.

L. H. Moulton & N. A. Halsey (1995). A mixture model with detection limits for regression analyses of antibody response to vaccine. Biometrics 51, 15701578.

L. H. Moulton , F. C. Curriero & P. F. Barroso (2002). Mixture models for quantitative HIV RNA data. Statistical Methods in Medical Research 11, 317325.

H. C. Rowe , B. G. Hansen , B. A. Halkier & D. J. Kliebenstein (2008). Biochemical networks and epistasis shape in the Arabidopsis thaliana metabolome. Plant Cell 20, 11991216.

P. C. Thomson (2003). A generalized estimating equations approach to quantitative trait locus detection of non-normal traits. Genetics Selection Evolution 35, 257280.

S. Xu & W. R. Atchley (1996). Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 143, 14171424.

F. Zou , J. P. Fine & B. S. Yandell (2002). On empirical likelihood for a semiparametric mixture model. Biometrika 89, 6175.

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Genetics Research
  • ISSN: 0016-6723
  • EISSN: 1469-5073
  • URL: /core/journals/genetics-research
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