CNVrd, a Read-Depth Algorithm for Assigning Copy-Number at the FCGR Locus: Population-Specific Tagging of Copy Number Variation at FCGR3B
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{"title"=>"CNVrd, a Read-Depth Algorithm for Assigning Copy-Number at the FCGR Locus: Population-Specific Tagging of Copy Number Variation at FCGR3B", "type"=>"journal", "authors"=>[{"first_name"=>"Hoang tan", "last_name"=>"Nguyen", "scopus_author_id"=>"55969211500"}, {"first_name"=>"Tony R.", "last_name"=>"Merriman", "scopus_author_id"=>"7003535346"}, {"first_name"=>"Michael A.", "last_name"=>"Black", "scopus_author_id"=>"57149920000"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84877005022", "pui"=>"368837437", "doi"=>"10.1371/journal.pone.0063219", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"84877005022", "pmid"=>"23646200"}, "id"=>"0ec8ee0b-dfeb-3f63-a741-100b00d7926b", "abstract"=>"The extent of contribution from common gene copy number (CN) variants in human disease is currently unresolved. Part of the reason for this is the technical difficulty in directly measuring CN variation (CNV) using molecular methods, and the lack of single nucleotide polymorphisms (SNPs) that can tag complex CNV that has arisen multiple times on different SNP haplotypes. One CNV locus implicated in human disease is FCGR. Here we aimed to use next-generation sequencing (NGS) data from the 1000 Genomes Project to assign CN at FCGR3A and FCGR3B and to comprehensively assess the ability of SNPs to tag specific CN variants. A read-depth algorithm was developed (CNVrd) and validated on a subset of HapMap samples using CN assignments that had previously been determined using molecular and microarray methods. At 7 out of 9 other complex loci there was >90% concordance with microarray data. However, given that some prior knowledge of CN is required, the generalizability of CNVrd is limited and should be applied to other complex CNV loci with caution. Subsequently, CN was assigned et FCGR3B using CNVrd in a total of 952 samples from the 1000 Genomes Project, using three classes and SNPs that correlated with duplication were identified. The best tag SNP was observed in the Mexican-American sample set for duplication at FCGR3B. This SNP (rs117435514, r² = 0.79) also tagged similar duplication in Chinese and Japanese (r² = 0.35-0.60), but not in Caucasian or African. No tag SNP for duplication at FCGR3A or deletion at FCGR3B was identified in any population. We conclude that it is possible to tag CNV at the FCGR locus, but CN and SNPs have to be characterized and correlated on a population-specific basis.", "link"=>"http://www.mendeley.com/research/cnvrd-readdepth-algorithm-assigning-copynumber-fcgr-locus-populationspecific-tagging-copy-number-var", "reader_count"=>16, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>5, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>14}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "reader_count_by_country"=>{"China"=>1, "United Kingdom"=>1, "Australia"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1049248"], "description"=>"<p>0/1 is deletion, 2 is CN = 2 and 3/4 is duplication.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene duplication", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "haplotypes", "Genetics of disease", "genomics", "Genome complexity", "Structural genomics", "Population biology", "epidemiology", "Disease informatics", "cnvnator", "cnvrd", "952", "1000", "genomes"], "article_id"=>694462, "categories"=>["Biological Sciences"], "users"=>["Hoang tan Nguyen", "Tony R. Merriman", "Michael A. Black"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0063219.g003", "stats"=>{"downloads"=>0, "page_views"=>40, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concordance_between_CNVnator_and_CNVrd_using_the_952_1000_Genomes_Project_samples_/694462", "title"=>"Concordance between CNVnator and CNVrd using the 952 1000 Genomes Project samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:14:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/1049245"], "description"=>"<p>The left graphs depict observed ratios while the right graphs depict z-scores (transformed ratios).</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene duplication", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "haplotypes", "Genetics of disease", "genomics", "Genome complexity", "Structural genomics", "Population biology", "epidemiology", "Disease informatics", "ratios", "observed"], "article_id"=>694459, "categories"=>["Biological Sciences"], "users"=>["Hoang tan Nguyen", "Tony R. Merriman", "Michael A. Black"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0063219.g001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_frequency_of_real_ratios_of_observed_and_expected_read_counts_/694459", "title"=>"The frequency of real ratios of observed and expected read counts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:14:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/1049256", "https://ndownloader.figshare.com/files/1049259", "https://ndownloader.figshare.com/files/1049262", "https://ndownloader.figshare.com/files/1049264", "https://ndownloader.figshare.com/files/1049282", "https://ndownloader.figshare.com/files/1049292", "https://ndownloader.figshare.com/files/1049326", "https://ndownloader.figshare.com/files/1049327", "https://ndownloader.figshare.com/files/1049329", "https://ndownloader.figshare.com/files/1049331", "https://ndownloader.figshare.com/files/1049333", "https://ndownloader.figshare.com/files/1049338", "https://ndownloader.figshare.com/files/1049341", "https://ndownloader.figshare.com/files/1049343"], "description"=>"<div><p>The extent of contribution from common gene copy number (CN) variants in human disease is currently unresolved. Part of the reason for this is the technical difficulty in directly measuring CN variation (CNV) using molecular methods, and the lack of single nucleotide polymorphisms (SNPs) that can tag complex CNV that has arisen multiple times on different SNP haplotypes. One CNV locus implicated in human disease is <i>FCGR</i>. Here we aimed to use next-generation sequencing (NGS) data from the 1000 Genomes Project to assign CN at <i>FCGR3A</i> and <i>FCGR3B</i> and to comprehensively assess the ability of SNPs to tag specific CN variants. A read-depth algorithm was developed (CNVrd) and validated on a subset of HapMap samples using CN assignments that had previously been determined using molecular and microarray methods. At 7 out of 9 other complex loci there was >90% concordance with microarray data. However, given that some prior knowledge of CN is required, the generalizability of CNVrd is limited and should be applied to other complex CNV loci with caution. Subsequently, CN was assigned et <i>FCGR3B</i> using CNVrd in a total of 952 samples from the 1000 Genomes Project, using three classes and SNPs that correlated with duplication were identified. The best tag SNP was observed in the Mexican-American sample set for duplication at <i>FCGR3B</i>. This SNP (rs117435514, r<sup>2</sup> = 0.79) also tagged similar duplication in Chinese and Japanese (r<sup>2</sup> = 0.35–0.60), but not in Caucasian or African. No tag SNP for duplication at <i>FCGR3A</i> or deletion at <i>FCGR3B</i> was identified in any population. We conclude that it is possible to tag CNV at the FCGR locus, but CN and SNPs have to be characterized and correlated on a population-specific basis.</p></div>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene duplication", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "haplotypes", "Genetics of disease", "genomics", "Genome complexity", "Structural genomics", "Population biology", "epidemiology", "Disease informatics", "read-depth", "algorithm", "assigning", "copy-number", "fcgr", "population-specific", "tagging"], "article_id"=>694470, "categories"=>["Biological Sciences"], "users"=>["Hoang tan Nguyen", "Tony R. Merriman", "Michael A. Black"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0063219.s001", "https://dx.doi.org/10.1371/journal.pone.0063219.s002", "https://dx.doi.org/10.1371/journal.pone.0063219.s003", "https://dx.doi.org/10.1371/journal.pone.0063219.s004", "https://dx.doi.org/10.1371/journal.pone.0063219.s005", "https://dx.doi.org/10.1371/journal.pone.0063219.s006", "https://dx.doi.org/10.1371/journal.pone.0063219.s007", "https://dx.doi.org/10.1371/journal.pone.0063219.s008", "https://dx.doi.org/10.1371/journal.pone.0063219.s009", "https://dx.doi.org/10.1371/journal.pone.0063219.s010", "https://dx.doi.org/10.1371/journal.pone.0063219.s011", "https://dx.doi.org/10.1371/journal.pone.0063219.s012", "https://dx.doi.org/10.1371/journal.pone.0063219.s013", "https://dx.doi.org/10.1371/journal.pone.0063219.s014"], "stats"=>{"downloads"=>53, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/CNVrd_a_Read_Depth_Algorithm_for_Assigning_Copy_Number_at_the_FCGR_Locus_Population_Specific_Tagging_of_Copy_Number_Variation_at_FCGR3B_/694470", "title"=>"CNVrd, a Read-Depth Algorithm for Assigning Copy-Number at the FCGR Locus: Population-Specific Tagging of Copy Number Variation at <i>FCGR3B</i>", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-04-30 01:14:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/1049252"], "description"=>"<p>(*are 1000 Genomes samples downloaded in September 2012).</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene duplication", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "haplotypes", "Genetics of disease", "genomics", "Genome complexity", "Structural genomics", "Population biology", "epidemiology", "Disease informatics", "frequencies", "hapmap"], "article_id"=>694466, "categories"=>["Biological Sciences"], "users"=>["Hoang tan Nguyen", "Tony R. Merriman", "Michael A. Black"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0063219.t001", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotype_frequencies_in_HapMap_sample_sets_/694466", "title"=>"Genotype frequencies in HapMap sample sets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-04-30 01:14:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/1049246"], "description"=>"<p>(14), CNVnator and CNVrd. 0/1 is deletion, 2 is CN = 2 and 3/4 is duplication.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene duplication", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "haplotypes", "Genetics of disease", "genomics", "Genome complexity", "Structural genomics", "Population biology", "epidemiology", "Disease informatics", "hollox", "et"], "article_id"=>694460, "categories"=>["Biological Sciences"], "users"=>["Hoang tan Nguyen", "Tony R. Merriman", "Michael A. Black"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0063219.g002", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concordance_of_the_three_methods_Hollox_et_al_/694460", "title"=>"Concordance of the three methods: Hollox et al.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:14:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/1049251"], "description"=>"<p>The x-axis is microarray CN assignments (35) and the y-axis CNVrd CN assignments. No clear CNVrd clusters were seen for <i>CNTNAP3</i> or <i>IGLL5.</i> Window sizes were: <i>RHD</i> (2000 bp), <i>UGT2B17</i> (50 0 bp), <i>GSTT1</i> (1000 bp), <i>IGLL3P</i> (1000 bp), <i>SMN2</i> (1000 bp), <i>GSTM1</i> (200 bp), <i>CFHR1</i> (500 bp), <i>CNTNAP3</i> (2000 bp) and <i>IGLL5</i> (1000 bp).</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene duplication", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "haplotypes", "Genetics of disease", "genomics", "Genome complexity", "Structural genomics", "Population biology", "epidemiology", "Disease informatics", "cnvrd", "microarray", "calls", "cnv"], "article_id"=>694465, "categories"=>["Biological Sciences"], "users"=>["Hoang tan Nguyen", "Tony R. Merriman", "Michael A. Black"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0063219.g005", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Concordance_between_CNVrd_and_microarray_calls_35_for_9_CNV_loci_/694465", "title"=>"Concordance between CNVrd and microarray calls (35) for 9 CNV loci.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:14:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/1049249"], "description"=>"<p>Segmentation scores at <i>FCGR3A</i> and <i>FCGR3B</i> derived from DNAcopy (23).</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene duplication", "population genetics", "Genetic polymorphism", "Evolutionary biology", "genetics", "haplotypes", "Genetics of disease", "genomics", "Genome complexity", "Structural genomics", "Population biology", "epidemiology", "Disease informatics", "scores", "derived", "dnacopy"], "article_id"=>694463, "categories"=>["Biological Sciences"], "users"=>["Hoang tan Nguyen", "Tony R. Merriman", "Michael A. Black"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0063219.g004", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Segmentation_scores_at_FCGR3A_and_FCGR3B_derived_from_DNAcopy_23_/694463", "title"=>"Segmentation scores at <i>FCGR3A</i> and <i>FCGR3B</i> derived from DNAcopy (23).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-04-30 01:14:23"}

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"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"6", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"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"=>"8"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[295, 511, 651, 775, 882, 992, 1100, 1201, 1304, 1400, 1486, 1570, 1650]}, {"subject_area"=>"/Biology and life sciences/Developmental biology", "average_usage"=>[275, 472, 605, 720, 822, 921, 1013, 1106, 1200, 1289, 1378, 1459, 1531]}]}
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