ArticlePloS one2012
Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
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- A mechanistic basis for genetic assimilation in natural fly populations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A Comprehensive Assessment of Ultraviolet-Radiation-Induced Mutations inJournal of fungi (Basel, Switzerland) · 2024Article
- Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes.Evolutionary applications · 2024Article
- Population Genomics of Pooled Samples: Unveiling Symbiont Infrapopulation Diversity and Host-Symbiont Coevolution.Life (Basel, Switzerland) · 2023Article
- Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species.Evolutionary biology · 2023Article
- High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing.Plant methods · 2022Article
- Drosophila Evolution over Space and Time (DEST): A New Population Genomics Resource.Molecular biology and evolution · 2021Article
- Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.PLoS genetics · 2021Article
- Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation ineLife · 2021Article
- Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data.Molecular ecology resources · 2021Article
- Comparative study of population genomic approaches for mapping colony-level traits.PLoS computational biology · 2020Article
- High accuracy of pooled DNA genotyping by 2b-RAD sequencing in the Pacific white shrimp, Litopenaeus vannamei.PloS one · 2020Article
- Population Genomics on the Fly: Recent Advances in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2020Review
- Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments.G3 (Bethesda, Md.) · 2019Article
- Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.Ecology and evolution · 2019Article
- Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Ecology and evolution · 2019Article
- Association mapping desiccation resistance within chromosomal inversions in the African malaria vector Anopheles gambiae.Molecular ecology · 2019Article
- A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies.Scientific reports · 2018Article
- Inter and Intraspecific Genomic Divergence in Drosophila montana Shows Evidence for Cold Adaptation.Genome biology and evolution · 2018Article
Corrections and comments
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4 authors.
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Abstract
The sequencing of pooled non-barcoded individuals is an inexpensive and efficient means of assessing genome-wide population allele frequencies, yet its accuracy has not been thoroughly tested. We assessed the accuracy of this approach on whole, complex eukaryotic genomes by resequencing pools of largely isogenic, individually sequenced Drosophila melanogaster strains. We called SNPs in the pooled data and estimated false positive and false negative rates using the SNPs called in individual strain as a reference. We also estimated allele frequency of the SNPs using "pooled" data and compared them with "true" frequencies taken from the estimates in the individual strains. We demonstrate that pooled sequencing provides a faithful estimate of population allele frequency with the error well approximated by binomial sampling, and is a reliable means of novel SNP discovery with low false positive rates. However, a sufficient number of strains should be used in the pooling because variation in the amount of DNA derived from individual strains is a substantial source of noise when the number of pooled strains is low. Our results and analysis confirm that pooled sequencing is a very powerful and cost-effective technique for assessing of patterns of sequence variation in populations on genome-wide scales, and is applicable to any dataset where sequencing individuals or individual cells is impossible, difficult, time consuming, or expensive.
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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.