HAPLOCLUSTERS

What is HAPLOCLUSTERS?

HAPLOCLUSTERS is a program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. This LD is often referred to as background LD.

HAPLOCLUSTERS employs a simple non parametric sharing statistic. It is particularly suited for genome wide scanning where the emphasis lies in the initial detection of excess sharing, not in the precise mapping of the locus. More precise mapping is carried out by selecting promising regions from the initial genome wide scan and covering these with further microsatellite markers. Ancestral haplotypes inferred by HAPLOCLUSTERS may also be used by other programs, in particular likelihood based methods.

p-values are determined by permutation testing. Output includes sorted case and control haplotypes and sharing drop off. An additional simplified output file allows easy plotting in R.

Please cite this software with this reference:

Bahlo M, Stankovich J, Speed TP, Rubio JP, Burfoot RK, Foote SJ. Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data. 2006 Mar;119(1-2):38-50.

Email bug reports & questions to Melanie Bahlo (bahlo@wehi.edu.au).