ALTree: association detection and localization of susceptibility sites using haplotype phylogenetic trees

Finding the genes involved in complex diseases susceptibility and among those genes, localizing the variant sites explaining this susceptibility is a major goal of genetic epidemiology. In this context, haplotypic methods that use the joint information on several markers may be of particular interest. When the number of haplotypes is large, a grouping may be required. Phylogenetic trees allow such groupings of haplotypes based on their evolutionary history and may help in the detection and localization of disease susceptibility sites. In this paper, we present a new software to perform phylogeny-based association and localization analysis.

[1]  E. Boerwinkle,et al.  A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. , 1987, Genetics.

[2]  Vincent Danjean,et al.  On the use of haplotype phylogeny to detect disease susceptibility loci , 2005, BMC Genetics.

[3]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[4]  Andrew P Morris,et al.  Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. , 2004, American journal of human genetics.

[5]  A. Templeton,et al.  A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. Analysis of case/control sampling designs: Alzheimer's disease and the apoprotein E locus. , 1995, Genetics.

[6]  P. Donnelly,et al.  A new statistical method for haplotype reconstruction from population data. , 2001, American journal of human genetics.

[7]  Michael Knapp,et al.  A powerful strategy to account for multiple testing in the context of haplotype analysis. , 2004, American journal of human genetics.

[8]  S. Dudoit,et al.  Resampling-based multiple testing for microarray data analysis , 2003 .

[9]  D. Swofford.  PAUP*: Phylogenetic analysis using parsimony (*and other methods), Version 4.0b10 , 2002 .

[10]  Peter H. Westfall,et al.  Testing Association of Statistically Inferred Haplotypes with Discrete and Continuous Traits in Samples of Unrelated Individuals , 2002, Human Heredity.

[11]  Peter Donnelly,et al.  A comparison of bayesian methods for haplotype reconstruction from population genotype data. , 2003, American journal of human genetics.

[12]  M. P. Cummings.  PHYLIP (Phylogeny Inference Package) , 2004 .

[13]  K. Roeder,et al.  Evolutionary‐based association analysis using haplotype data , 2003 .

[14]  M. Xiong,et al.  Haplotypes vs single marker linkage disequilibrium tests: what do we gain? , 2001, European Journal of Human Genetics.

[15]  David Swofford,et al.  PAUP* 4.0 : Phylogenetic Analysis Using Parsimony , 2002 .

[16]  C. Sing,et al.  A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. , 1992, Genetics.