HaploRec: efficient and accurate large-scale reconstruction of haplotypes

BMC Bioinformatics
Lauri EronenHannu Toivonen

Abstract

Haplotypes extracted from human DNA can be used for gene mapping and other analysis of genetic patterns within and across populations. A fundamental problem is, however, that current practical laboratory methods do not give haplotype information. Estimation of phased haplotypes of unrelated individuals given their unphased genotypes is known as the haplotype reconstruction or phasing problem. We define three novel statistical models and give an efficient algorithm for haplotype reconstruction, jointly called HaploRec. HaploRec is based on exploiting local regularities conserved in haplotypes: it reconstructs haplotypes so that they have maximal local coherence. This approach--not assuming statistical dependence for remotely located markers--has two useful properties: it is well-suited for sparse marker maps, such as those used in gene mapping, and it can actually take advantage of long maps. Our experimental results with simulated and real data show that HaploRec is a powerful method for the large scale haplotyping needed in association studies. With sample sizes large enough for gene mapping it appeared to be the best compared to all other tested methods (Phase, fastPhase, PL-EM, Snphap, Gerbil; simulated data), with small sam...Continue Reading

References

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Citations

Sep 20, 2007·Archives of Toxicology·Klaus GolkaSilvia Selinski
Feb 9, 2011·Nature Reviews. Genetics·Ryan TewheyNicholas J Schork
Oct 11, 2008·Bioinformatics·Yuzhong ZhaoGuoliang Chen
Nov 18, 2011·Genome Research·Ninad DewalItsik Pe'er
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May 12, 2007·BMC Bioinformatics·Niels LandwehrHeikki Mannila
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiang WanWeichuan Yu
May 14, 2011·Molecular Ecology Resources·Zu-Shi Huang, De-Xing Zhang

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Methods Mentioned

BETA
genotyping

Software Mentioned

fastPhase
coalescence simulator
HaploRec
PL
VMM
Snphap
FMM
EM
Gerbil
MathType

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