ArticlePacific Symposium on Biocomputing. Pacific Symposium on Biocomputing2013
Detecting highly differentiated copy-number variants from pooled population sequencing.
Article in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Metabolic resistance of the tiger mosquito to pyrethroid insecticides in La Réunion Island likely results from local adaptation.Genome biology and evolution · 2026Article
- A major 6 Mb superlocus is involved in pyrethroid resistance in the common bed bugEvolutionary applications · 2023Article
- Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach.G3 (Bethesda, Md.) · 2022Article
- The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Genomic Variant Analyses in Pyrethroid Resistant and Susceptible Malaria Vector,G3 (Bethesda, Md.) · 2020Article
- Patterns of transposable element variation and clinality in Drosophila.Molecular ecology · 2019Article
- Parallel Evolution of Copy-Number Variation across Continents in Drosophila melanogaster.Molecular biology and evolution · 2016Article
- Identifying Loci Contributing to Natural Variation in Xenobiotic Resistance in Drosophila.PLoS genetics · 2015Article
- Revisiting classic clines in Drosophila melanogaster in the age of genomics.Trends in genetics : TIG · 2015Review
- Sequencing pools of individuals - mining genome-wide polymorphism data without big funding.Nature reviews. Genetics · 2014Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Copy-number variants (CNVs) represent a functionally and evolutionarily important class of variation. Here we take advantage of the use of pooled sequencing to detect CNVs with large differences in allele frequency between population samples. We present a method for detecting CNVs in pooled population samples using a combination of paired-end sequences and read-depth. Highly differentiated CNVs show large differences in the number of paired-end reads supporting individual alleles and large differences in readdepth between population samples. We complement this approach with one that uses a hidden Markov model to find larger regions differing in read-depth between samples. Using novel pooled sequence data from two populations of Drosophila melanogaster along a latitudinal cline, we demonstrate the utility of our method for identifying CNVs involved in local adaptation.
Indexed as
Identifiers
23424139PMC3587772What OpenQuestion holds
Registered trials
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.