Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/1418
Title: HaploRec: efficient and accurate large-scale reconstruction of haplotypes
Authors: Eronen, L
GEERTS, Floris 
Toivonen, H
Issue Date: 2006
Publisher: BIOMED CENTRAL LTD
Source: BMC BIOINFORMATICS, 7. p. 542-...
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. Results: 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. Conclusion: 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 samples it was competitive with the best available methods ( real data). HaploRec is several orders of magnitude faster than Phase and comparable to the other methods; the running times are roughly linear in the number of subjects and the number of markers. HaploRec is publicly available at http://www.cs.helsinki.fi/group/genetics/haplotyping.html.
Keywords: LINKAGE-DISEQUILIBRIUM; GENOTYPE DATA; INFERENCE; POPULATION; SAMPLES; GENOME; ASSOCIATION; LIKELIHOOD; RESOLUTION; ALGORITHM
Document URI: http://hdl.handle.net/1942/1418
Link to publication: http://www.cs.helsinki.fi/group/genetics/haplorec/
ISSN: 1471-2105
e-ISSN: 1471-2105
DOI: 10.1186/1471-2105-7-542
ISI #: 000243434400002
Category: A1
Type: Journal Contribution
Appears in Collections:Research publications

Files in This Item:
File Description SizeFormat 
paperBMC.pdfPostprint214.46 kBAdobe PDFView/Open
Show full item record

SCOPUSTM   
Citations

43
checked on Sep 2, 2020

WEB OF SCIENCETM
Citations

38
checked on May 21, 2022

Page view(s)

30
checked on May 25, 2022

Download(s)

68
checked on May 25, 2022

Google ScholarTM

Check

Altmetric


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.