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Citation
Schrider, D.R., Begun, D.J., Hahn, M.W. (2013). Detecting highly differentiated copy-number variants from pooled population sequencing.  Pacific Symp. Biocomputing : 344--355.
FlyBase ID
FBrf0220853
Publication Type
Research paper
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.
PubMed ID
PubMed Central ID
PMC3587772 (PMC) (EuropePMC)
DOI
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Secondary IDs
    Language of Publication
    English
    Additional Languages of Abstract
    Parent Publication
    Publication Type
    Compendium
    Abbreviation
    Pacific Symp. Biocomputing
    Title
    Pacific Symposium on Biocomputing
    Publication Year
    1996-
    ISBN/ISSN
    1793-5091 2335-6936
    Data From Reference