The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Reconstituting the Frequency Spectrum of Ascertained Single-Nucleotide Polymorphism Data
Abstract
Most of the available SNP data have eluded valid population genetic analysis because most population genetical methods do not correctly accommodate the special discovery process used to identify SNPs. Most of the available SNP data have allele frequency distributions that are biased by the ascertainment protocol. We here show how this problem can be corrected by obtaining maximum-likelihood estimates of the true allele frequency distribution. In simple cases, the ML estimate of the true allele frequency distribution can be obtained analytically, but in other cases computational methods based on numerical optimization or the EM algorithm must be used. We illustrate the new correction method by analyzing some previously published SNP data from the SNP Consortium. Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of the International HapMap Project.
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The International HapMap Project
†The International HapMap Consortium, Genotyping centres: Baylor College of Medicine and ParAllele BioScience, Gibbs, R. A., Belmont, J. W., Hardenbol, P., Willis, T. D., Yu, F., Chinese HapMap Consortium, Yang, H., Ch'ang, L.-Y., et al. (2003) · Nature · doi:10.1038/nature02168 · Cited by 6,057
Detecting recent positive selection in the human genome from haplotype structure
Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z. P., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., et al. (2002) · Nature · doi:10.1038/nature01140 · Cited by 2,106
Prospects for whole-genome linkage disequilibrium mapping of common disease genes
Kruglyak, L. (1999) · Nature Genetics · doi:10.1038/9642 · Cited by 1,416
Cited by
Gutenkunst, R. N., Hernandez, R. D., Williamson, S. H., & Bustamante, C. D. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000695 · Cited by 1,906
“In some cases of ascertained data [33], the resulting bias can be corrected by modifying the above equation [11, 34].”
Molecular Signatures of Natural Selection
Nielsen, R. (2005) · Annual Review of Genetics · doi:10.1146/annurev.genet.39.073003.112420 · Cited by 1,641
Self-citationTesting for ancient admixture between closely related populations
Durand, E. Y., Patterson, N., Reich, D., & Slatkin, M. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr048 · Cited by 1,375
Detecting Natural Selection in Genomic Data
Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133526 · Cited by 694
Assessing the evolutionary impact of amino acid mutations in the human genome.
Boyko, A. R., Williamson, S. H., Indap, A. R., Degenhardt, J. D., Hernandez, R. D., Lohmueller, K. E., Adams, M. D., Schmidt, S., Sninsky, J. J., Sunyaev, S. R., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000083 · Cited by 628
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Metadata
- Authors
- Nielsen, R., Hubisz, M. J., & Clark, A. G.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2004-12-01
- Volume
- 168
- Issue
- 4
- Pages
- 2373-2382
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W1982588258
- Cited by
- 162
- References
- 3
- FWCI
- 5.89
- Type
- journal article
- Language
- en
- Open access
- closed
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