Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster
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{"title"=>"Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster", "type"=>"journal", "authors"=>[{"first_name"=>"Yuan", "last_name"=>"Zhu", "scopus_author_id"=>"55367567200"}, {"first_name"=>"Alan O.", "last_name"=>"Bergland", "scopus_author_id"=>"8371159100"}, {"first_name"=>"Josefa", "last_name"=>"González", "scopus_author_id"=>"35236647400"}, {"first_name"=>"Dmitri A.", "last_name"=>"Petrov", "scopus_author_id"=>"7103238750"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203", "scopus"=>"2-s2.0-84864832228", "pui"=>"365407209", "doi"=>"10.1371/journal.pone.0041901", "issn"=>"19326203", "pmid"=>"22848651", "sgr"=>"84864832228"}, "id"=>"b6c084c2-31a2-3aa6-8760-f7ade285a892", "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.", "link"=>"http://www.mendeley.com/research/empirical-validation-pooled-whole-genome-population-resequencing-drosophila-melanogaster", "reader_count"=>134, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>8, "Researcher"=>39, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>4, "Student > Master"=>23, "Other"=>4, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>8, "Researcher"=>39, "Student > Ph. D. Student"=>41, "Student > Postgraduate"=>4, "Student > Master"=>23, "Other"=>4, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>2, "Environmental Science"=>7, "Biochemistry, Genetics and Molecular Biology"=>10, "Mathematics"=>1, "Agricultural and Biological Sciences"=>104, "Medicine and Dentistry"=>3, "Social Sciences"=>2, "Computer Science"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>104}, "Computer Science"=>{"Computer Science"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>7}}, "reader_count_by_country"=>{"United States"=>2, "United Kingdom"=>1, "Switzerland"=>1, "Portugal"=>1, "Spain"=>1, "Canada"=>1, "Austria"=>3, "Netherlands"=>1, "Belgium"=>2, "Ireland"=>1, "Brazil"=>1, "Australia"=>1, "Germany"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/601815"], "description"=>"<p>DNA contributions of each strain as observed from representation of unique SNPs in pool. Each vertical line represents pooled frequency estimates of singleton SNPs unique to a single strain. Edges of lines represent values at 2 standard deviations from mean (thick horizontal line). Strain RAL-301 was dropped from analysis due to low unique SNP count. Y-axis: DNA contribution in the form of pool frequency estimate from library A. X-axis: Strains sorted in order of mean DNA contribution.</p>", "links"=>[], "tags"=>["strains"], "article_id"=>272318, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Yuan Zhu", "Alan O. Bergland", "Josefa González", "Dmitri A. Petrov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041901.g002", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_DNA_contribution_of_strains_in_Library_A_/272318", "title"=>"DNA contribution of strains in Library A.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-26 00:38:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/602044"], "description"=>"<p>Pooled Libraries.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>272539, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Yuan Zhu", "Alan O. Bergland", "Josefa González", "Dmitri A. Petrov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041901.t001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pooled_Libraries_/272539", "title"=>"Pooled Libraries.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-26 00:42:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/601737"], "description"=>"<p>Libraries A, B1, B2 and B4 were constructed pooling flies from different number of DGRP strains. Libraries B3, B5 and B6 are the result of merging reads from libraries B1, B2 and B4.</p>", "links"=>[], "tags"=>["pooled", "libraries"], "article_id"=>272230, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Yuan Zhu", "Alan O. Bergland", "Josefa González", "Dmitri A. Petrov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041901.g001", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_representation_of_the_pooled_libraries_used_in_this_study_/272230", "title"=>"Schematic representation of the pooled libraries used in this study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-26 00:37:10"}
  • {"files"=>["https://ndownloader.figshare.com/files/315400"], "description"=>"<div><p>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 <em>Drosophila melanogaster</em> 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.</p> </div>", "links"=>[], "tags"=>["empirical", "validation", "pooled", "genome", "re-sequencing"], "article_id"=>122255, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Yuan Zhu", "Alan O. Bergland", "Josefa González", "Dmitri A. Petrov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041901", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Empirical_Validation_of_Pooled_Whole_Genome_Population_Re_Sequencing_in_Drosophila_melanogaster_/122255", "title"=>"Empirical Validation of Pooled Whole Genome Population Re-Sequencing in <em>Drosophila melanogaster</em>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-26 00:37:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/601945"], "description"=>"<p>False positive and false negative rates of novel SNP discovery from pooled library B6. Y-axis: Error rate. Z-axis: Folded allele frequency from DGRP genotypes.</p>", "links"=>[], "tags"=>["genetics and genomics", "Evolutionary biology"], "article_id"=>272441, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Yuan Zhu", "Alan O. Bergland", "Josefa González", "Dmitri A. Petrov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041901.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SNP_Discovery_Error_Rates_/272441", "title"=>"SNP Discovery Error Rates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-26 00:40:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/602070"], "description"=>"<p>Library allele frequency estimate comparison to 162 DGRP strains.</p>", "links"=>[], "tags"=>["allele", "162", "dgrp"], "article_id"=>272566, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Yuan Zhu", "Alan O. Bergland", "Josefa González", "Dmitri A. Petrov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041901.t002", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Library_allele_frequency_estimate_comparison_to_162_DGRP_strains_/272566", "title"=>"Library allele frequency estimate comparison to 162 DGRP strains.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-26 00:42:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/601884"], "description"=>"<p>Correlation coefficients between observed or simulated pooled allele frequency estimates and actual estimates as a function of the number of strains pooled. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041901#s2\" target=\"_blank\">Materials and Methods</a> for a description of the libraries. Y-axis: Expected (triangles) and observed (circles) correlation coefficients of the 7 libraries compared to a perfectly binomial library, color-coded by library. X-axis: Libraries ordered by number of strains pooled.</p>", "links"=>[], "tags"=>["observed", "pooled"], "article_id"=>272383, "categories"=>["Genetics", "Evolutionary Biology"], "users"=>["Yuan Zhu", "Alan O. Bergland", "Josefa González", "Dmitri A. Petrov"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041901.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expected_and_observed_pooled_frequency_estimates_/272383", "title"=>"Expected and observed pooled frequency estimates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-26 00:39:43"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Molecular biology", "average_usage"=>[324, 551, 679, 782, 879, 971, 1064, 1154, 1245, 1328, 1406, 1476, 1541, 1617, 1683, 1754, 1818, 1893, 1962, 2025, 2092, 2164, 2227, 2294, 2355]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[304, 506, 616, 712, 799, 879, 968, 1052, 1134, 1212, 1284, 1357, 1427, 1494, 1557, 1621, 1689, 1756, 1823, 1883, 1944, 1997, 2056, 2118, 2171]}, {"subject_area"=>"/Physical sciences/Mathematics", "average_usage"=>[325, 522, 627, 718, 804, 884, 969, 1052, 1131, 1207, 1277, 1346, 1415, 1478, 1542, 1605, 1663, 1723, 1776, 1839, 1895, 1955, 2008, 2066, 2123]}]}
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