ArticleGenome biology and evolution2014
Population-genetic inference from pooled-sequencing data.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
63 citing papers in PubMed.
- Rare jackpot individuals drive rapid adaptation in Threespine Stickleback.Nature communications · 2026Article
- Limited directional selection but coevolutionary signals among imprinted genes inbioRxiv : the preprint server for biology · 2026Article
- Evolution of Hybrid Inviability Associated With Chromosome Fusions.Molecular ecology · 2025Article
- The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.Molecular biology and evolution · 2025Article
- Pooled, Long-read Sequencing for Structural Variant Characterization in Schistosome Populations.Genome biology and evolution · 2025Article
- A new method for ecologists to estimate heterozygote excess and deficit for multi-locus gene families.Ecology and evolution · 2024Article
- Meiotic drive against chromosome fusions in butterfly hybrids.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2024Article
- Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data.BMC bioinformatics · 2023Article
- FREQ-Seq2: a method for precise high-throughput combinatorial quantification of allele frequencies.G3 (Bethesda, Md.) · 2023Article
- Genomic selection pressure discovery using site-frequency spectrum and reduced local variability statistics in Pakistani Dera-Din-Panah goat.Tropical animal health and production · 2023Article
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- Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species.Evolutionary biology · 2023Article
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- Identification of a candidate sex determination gene in Culaea inconstans suggests convergent recruitment of an Amh duplicate in two lineages of stickleback.Journal of evolutionary biology · 2022Article
- A pan-genome data structure induced by pooled sequencing facilitates variant mining in heterogeneous germplasm.Molecular breeding : new strategies in plant improvement · 2022Article
- No evidence for temporally balanced selection on larval Pacific oystersProceedings. Biological sciences · 2022Article
- Selection of Genome-Wide SNPs for Pooled Allelotyping Assays Useful for Population Monitoring.Genome biology and evolution · 2022Article
- Slow Recovery from Inbreeding Depression Generated by the Complex Genetic Architecture of Segregating Deleterious Mutations.Molecular biology and evolution · 2022Article
- Detecting Genetic Variation of ColonizingFrontiers in bioinformatics · 2022Article
- Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource.Molecular biology and evolution · 2021Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Although pooled-population sequencing has become a widely used approach for estimating allele frequencies, most work has proceeded in the absence of a proper statistical framework. We introduce a self-sufficient, closed-form, maximum-likelihood estimator for allele frequencies that accounts for errors associated with sequencing, and a likelihood-ratio test statistic that provides a simple means for evaluating the null hypothesis of monomorphism. Unbiased estimates of allele frequencies [Formula: see text] (where N is the number of individuals sampled) appear to be unachievable, and near-certain identification of a polymorphism requires a minor-allele frequency [Formula: see text]. A framework is provided for testing for significant differences in allele frequencies between populations, taking into account sampling at the levels of individuals within populations and sequences within pooled samples. Analyses that fail to account for the two tiers of sampling suffer from very large false-positive rates and can become increasingly misleading with increasing depths of sequence coverage. The power to detect significant allele-frequency differences between two populations is very limited unless both the number of sampled individuals and depth of sequencing coverage exceed 100.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.