The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Haplotype reconstruction from genotype data using Imperfect Phylogeny
Open accessAbstract
Critical to the understanding of the genetic basis for complex diseases is the modeling of human variation. Most of this variation can be characterized by single nucleotide polymorphisms (SNPs) which are mutations at a single nucleotide position. To characterize the genetic variation between different people, we must determine an individual's haplotype or which nucleotide base occurs at each position of these common SNPs for each chromosome. In this paper, we present results for a highly accurate method for haplotype resolution from genotype data. Our method leverages a new insight into the underlying structure of haplotypes that shows that SNPs are organized in highly correlated ‘blocks’. In a few recent studies, considerable parts of the human genome were partitioned into blocks, such that the majority of the sequenced genotypes have one of about four common haplotypes in each block. Our method partitions the SNPs into blocks, and for each block, we predict the common haplotypes and each individual's haplotype. We evaluate our method over biological data. Our method predicts the common haplotypes perfectly and has a very low error rate (<2% over the data) when taking into account the predictions for the uncommon haplotypes. Our method is extremely efficient compared with previous methods such as PHASE and HAPLOTYPER. Its efficiency allows us to find the block partition of the haplotypes, to cope with missing data and to work with large datasets. Availability: The algorithm is available via a Web server at http://www.calit2.net/compbio/hap/
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Cites
The Structure of Haplotype Blocks in the Human Genome
Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. (2002) · Science · doi:10.1126/science.1069424 · Cited by 5,863
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.
(1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040269 · Cited by 1,950
Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21
Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., et al. (2001) · Science · doi:10.1126/science.1065573 · Cited by 1,145
Inference of haplotypes from PCR-amplified samples of diploid populations.
(1990) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040591 · Cited by 765
EFFICIENT RECONSTRUCTION OF HAPLOTYPE STRUCTURE VIA PERFECT PHYLOGENY
ESKIN, E., HALPERIN, E., & KARP, R. M. (2003) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720003000174 · Cited by 131
Self-citation
Cited by
Reference-based phasing using the Haplotype Reference Consortium panel
Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3679 · Cited by 1,723
Detection of sharing by descent, long-range phasing and haplotype imputation
Kong, A., Masson, G., Frigge, M. L., Gylfason, A., Zusmanovich, P., Thorleifsson, G., Olason, P. I., Ingason, A., Steinberg, S., Rafnar, T., et al. (2008) · Nature Genetics · doi:10.1038/ng.216 · Cited by 447
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
Marchini, J., Cutler, D., Patterson, N., Stephens, M., Eskin, E., Halperin, E., Lin, S., Qin, Z. S., Munro, H. M., Abecasis, G. R., et al. (2006) · The American Journal of Human Genetics · doi:10.1086/500808 · Cited by 341
Self-citationCannon, T. D., Hennah, W., van Erp, T. G. M., Thompson, P. M., Lonnqvist, J., Huttunen, M., Gasperoni, T., Tuulio-Henriksson, A., Pirkola, T., Toga, A. W., et al. (2005) · Archives of General Psychiatry · doi:10.1001/archpsyc.62.11.1205 · Cited by 337
Zhang, L., Rao, F., Zhang, K., Khandrika, S., Das, M., Vaingankar, S. M., Bao, X., Rana, B. K., Smith, D. W., Wessel, J., et al. (2007) · Journal of Clinical Investigation · doi:10.1172/jci31093 · Cited by 90
Metadata
- Authors
- Halperin, E., & Eskin, E.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-02-26
- Volume
- 20
- Issue
- 12
- Pages
- 1842-1849
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2103647262
- Cited by
- 213
- References
- 5
- FWCI
- 16.33
- Type
- journal article
- Language
- en
- Open access
- bronze
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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