ArticleGenetics2009
Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- EGGS: Empirical Genotype Generalizer for Samples.Bioinformatics advances · 2026Article
- Article
- A Large Panel of Drosophila simulans Reveals an Abundance of Common Variants.Genome biology and evolution · 2018Article
- Population genomics of the eastern cottonwood (Ecology and evolution · 2017Article
- Environmental versus geographical effects on genomic variation in wild soybean (Glycine soja) across its native range in northeast Asia.Ecology and evolution · 2016Article
- Inferring positive selection in humans from genomic data.Investigative genetics · 2015Article
- A bioinformatics workflow for detecting signatures of selection in genomic data.Frontiers in genetics · 2014Article
- Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.BMC bioinformatics · 2013Article
- Genetic diversity analysis of elite European maize (Zea mays L.) inbred lines using AFLP, SSR, and SNP markers reveals ascertainment bias for a subset of SNPs.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Evolution and functional impact of rare coding variation from deep sequencing of human exomes.Science (New York, N.Y.) · 2012Article
- Rare variant density across the genome and across populations.BMC proceedings · 2011Article
- Deciphering the genetic basis of animal domestication.Proceedings. Biological sciences · 2011Review
- Even small SNP clusters are non-randomly distributed: is this evidence of mutational non-independence?Proceedings. Biological sciences · 2010Article
- Diversity and evolution of 11 innate immune genes in Bos taurus taurus and Bos taurus indicus cattle.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Sequencing and analysis of an Irish human genome.Genome biology · 2010Article
- Widespread genomic signatures of natural selection in hominid evolution.PLoS genetics · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Most single-nucleotide polymorphism (SNP) data suffer from an ascertainment bias caused by the process of SNP discovery followed by SNP genotyping. The final genotyped data are biased toward an excess of common alleles compared to directly sequenced data, making standard genetic methods of analysis inapplicable to this type of data. We here derive corrected estimators of the fundamental population genetic parameter = 4N(e)mu (N(e), effective population size; mu, mutation rate) on the basis of the average number of pairwise differences and on the basis of the number of segregating sites. We also derive the variances and covariances of these estimators and provide a corrected version of Tajima's D statistic. We reanalyze a human genomewide SNP data set and find substantial differences in the results with or without ascertainment bias correction.
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