Haplotyping via minimum recombinant paradigm
نویسندگان
چکیده
BACKGROUND Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium. METHODS Haplotyping was based on the minimum recombinant paradigm, whereby a phase is obtained only if it uniquely minimises the number of recombinants within a full sib family. Performance of this method was tested across three different data sets, consisting of genotypes and pedigree. RESULTS The percentage of phased alleles ranged from ~80% to ~95%, and the percentage of correct phases reached ~99% in all cases. A measure of uncertainty was obtained via simulations. A partial haplotyping algorithm consisting of four deterministic rules was almost as effective as a full one consisting of six deterministic rules, and took up to 5 times less time to compute. CONCLUSION Haplotyping via the minimum recombinant paradigm is consistently reliable and computationally efficient. A single simulation is enough to produce a population-wide uncertainty estimate associated with a set of all reconstructed haplotypes.
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عنوان ژورنال:
- BMC Proceedings
دوره 3 شماره
صفحات -
تاریخ انتشار 2009