Zero-recombinant haplotyping: applications to fine mapping using SNPs.

As the number of single nucleotide polymorphisms (SNPs) available for genetic analysis increases, researchers will be saturating smaller and smaller regions of the genome with these biallelic markers in an effort to fine map complex diseases. An important tool in this fine-mapping effort is haplotyping. Algorithms are presented that find all possible haplotype configurations of the pedigree data under the assumption that there are no recombinants between the markers. These configurations can be used to estimate the haplotype frequencies, and identify the most common haplotypes in the data. These algorithms have been implemented into a software program (ZAPLO), and were tested on a published data set.