The DOI matches its Crossref record; 14 of the 14 references it cites were found in a registry or an index.
Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population.
Open accessAbstract
Molecular techniques allow the survey of a large number of linked polymorphic loci in random samples from diploid populations. However, the gametic phase of haplotypes is usually unknown when diploid individuals are heterozygous at more than one locus. To overcome this difficulty, we implement an expectation-maximization (EM) algorithm leading to maximum-likelihood estimates of molecular haplotype frequencies under the assumption of Hardy-Weinberg proportions. The performance of the algorithm is evaluated for simulated data representing both DNA sequences and highly polymorphic loci with different levels of recombination. As expected, the EM algorithm is found to perform best for large samples, regardless of recombination rates among loci. To ensure finding the global maximum likelihood estimate, the EM algorithm should be started from several initial conditions. The present approach appears to be useful for the analysis of nuclear DNA sequences or highly variable loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci. Although the algorithm, in principle, can accommodate an arbitrary number of loci, there are practical limitations because the computing time grows exponentially with the number of polymorphic loci.
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“Often, genotypes can be resolved into several possible haplotypes, and inferred frequencies of rare haplotypes can be quite wrong10.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [10]
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Arlequin (version 3.0): An integrated software package for population genetics data analysis
Excoffier, L., Laval, G., & Schneider, S. (2005) · Evolutionary Bioinformatics · doi:10.1177/117693430500100003 · Cited by 14,265
Self-citationTopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
A New Statistical Method for Haplotype Reconstruction from Population Data
Stephens, M., Smith, N. J. C., & Donnelly, P. (2001) · The American Journal of Human Genetics · doi:10.1086/319501 · Cited by 7,512
Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,454
Mendelian randomization: Using genes as instruments for making causal inferences in epidemiology
Lawlor, D. A., Harbord, R. M., Sterne, J. A. C., Timpson, N., & Davey Smith, G. (2008) · Statistics in Medicine · doi:10.1002/sim.3034 · Cited by 4,618
Metadata
- Authors
- Excoffier, L., & Slatkin, M.
- Affiliations
- University of Geneva (CH)
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 1995-09
- Volume
- 12
- Issue
- 5
- Pages
- 921-7
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W1891283710
- Cited by
- 1,950
- References
- 14
- Citations by year
- 2026: 5 · 2025: 8 · 2024: 14 · 2023: 19 · 2022: 18 · 2021: 20 · 2020: 32 · 2019: 29 · 2018: 30 · 2017: 20 · 2016: 46 · 2015: 41 · 2014: 52 · 2013: 69 · 2012: 76
- FWCI
- 3.10
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (39847)
- National Institutes of Health
- National Institute of General Medical Sciences (GM-40282, R01GM040282)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- haplotype frequencies, maximum likelihood estimation, expectation-maximization algorithm, Hardy-Weinberg equilibrium, recombination, heterozygosity, diploid populations, multilocus analysis, computational complexity
- MeSH terms
- Algorithms, Animals, Diploidy, Gene Frequency, Haplotypes, Humans, Genetic Linkage, Mathematics, Models, Genetic, Monte Carlo Method, Probability, Regression Analysis, Models, Statistical
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