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{"title"=>"Characterization of within-host plasmodium falciparum diversity using next-generation sequence data", "type"=>"journal", "authors"=>[{"first_name"=>"Sarah", "last_name"=>"Auburn", "scopus_author_id"=>"25521147500"}, {"first_name"=>"Susana", "last_name"=>"Campino", "scopus_author_id"=>"14827794400"}, {"first_name"=>"Olivo", "last_name"=>"Miotto", "scopus_author_id"=>"8840256300"}, {"first_name"=>"Abdoulaye A.", "last_name"=>"Djimde", "scopus_author_id"=>"6603275857"}, {"first_name"=>"Issaka", "last_name"=>"Zongo", "scopus_author_id"=>"15842711900"}, {"first_name"=>"Magnus", "last_name"=>"Manske", "scopus_author_id"=>"25723615000"}, {"first_name"=>"Gareth", "last_name"=>"Maslen", "scopus_author_id"=>"6602079261"}, {"first_name"=>"Valentina", "last_name"=>"Mangano", "scopus_author_id"=>"23480303800"}, {"first_name"=>"Daniel", "last_name"=>"Alcock", "scopus_author_id"=>"25924190200"}, {"first_name"=>"Bronwyn", "last_name"=>"MacInnis", "scopus_author_id"=>"6603896940"}, {"first_name"=>"Kirk A.", "last_name"=>"Rockett", "scopus_author_id"=>"7003949633"}, {"first_name"=>"Taane G.", "last_name"=>"Clark", "scopus_author_id"=>"7403216793"}, {"first_name"=>"Ogobara K.", "last_name"=>"Doumbo", "scopus_author_id"=>"7005026392"}, {"first_name"=>"Jean Bosco", "last_name"=>"Ouédraogo", "scopus_author_id"=>"7003494281"}, {"first_name"=>"Dominic P.", "last_name"=>"Kwiatkowski", "scopus_author_id"=>"7102780531"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84857678104", "doi"=>"10.1371/journal.pone.0032891", "pui"=>"364355288", "issn"=>"19326203", "pmid"=>"22393456", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84857678104"}, "id"=>"54dfca9c-bb1f-3cab-82b7-cd420ab1a6ba", "abstract"=>"Our understanding of the composition of multi-clonal malarial infections and the epidemiological factors which shape their diversity remain poorly understood. Traditionally within-host diversity has been defined in terms of the multiplicity of infection (MOI) derived by PCR-based genotyping. Massively parallel, single molecule sequencing technologies now enable individual read counts to be derived on genome-wide datasets facilitating the development of new statistical approaches to describe within-host diversity. In this class of measures the F(WS) metric characterizes within-host diversity and its relationship to population level diversity. Utilizing P. falciparum field isolates from patients in West Africa we here explore the relationship between the traditional MOI and F(WS) approaches. F(WS) statistics were derived from read count data at 86,158 SNPs in 64 samples sequenced on the Illumina GA platform. MOI estimates were derived by PCR at the msp-1 and -2 loci. Significant correlations were observed between the two measures, particularly with the msp-1 locus (P = 5.92×10(-5)). The F(WS) metric should be more robust than the PCR-based approach owing to reduced sensitivity to potential locus-specific artifacts. Furthermore the F(WS) metric captures information on a range of parameters which influence out-crossing risk including the number of clones (MOI), their relative proportions and genetic divergence. This approach should provide novel insights into the factors which correlate with, and shape within-host diversity.", "link"=>"http://www.mendeley.com/research/characterization-withinhost-plasmodium-falciparum-diversity-using-nextgeneration-sequence-data", "reader_count"=>96, "reader_count_by_academic_status"=>{"Researcher"=>31, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>5, "Student > Master"=>14, "Other"=>6, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Researcher"=>31, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>5, "Student > Master"=>14, "Other"=>6, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Mathematics"=>2, "Medicine and Dentistry"=>8, "Agricultural and Biological Sciences"=>65, "Business, Management and Accounting"=>1, "Social Sciences"=>1, "Computer Science"=>2, "Immunology and Microbiology"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Social Sciences"=>{"Social Sciences"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>65}, "Computer Science"=>{"Computer Science"=>2}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Mathematics"=>{"Mathematics"=>2}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Burkina Faso"=>1, "United States"=>2, "Tanzania"=>1, "Brazil"=>1, "Denmark"=>1, "United Kingdom"=>7, "Mexico"=>1, "Kenya"=>1, "France"=>1, "India"=>1}, "group_count"=>6}

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• http://doi.org/10.1016/S1995-7645(13)60102-9
• http://doi.org/10.1111/1574-6976.12032
• http://doi.org/10.1186/s12936-018-2322-5
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• http://doi.org/10.1038/s41467-018-03807-7
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• http://doi.org/10.1021/acsinfecdis.5b00049
• http://doi.org/10.1016/j.ijpara.2016.08.006

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/344569", "https://ndownloader.figshare.com/files/344614", "https://ndownloader.figshare.com/files/344640"], "description"=>"<div><p>Our understanding of the composition of multi-clonal malarial infections and the epidemiological factors which shape their diversity remain poorly understood. Traditionally within-host diversity has been defined in terms of the multiplicity of infection (MOI) derived by PCR-based genotyping. Massively parallel, single molecule sequencing technologies now enable individual read counts to be derived on genome-wide datasets facilitating the development of new statistical approaches to describe within-host diversity. In this class of measures the <em>F_WS</em> metric characterizes within-host diversity and its relationship to population level diversity. Utilizing <em>P. falciparum</em> field isolates from patients in West Africa we here explore the relationship between the traditional MOI and <em>F_WS</em> approaches. <em>F_WS</em> statistics were derived from read count data at 86,158 SNPs in 64 samples sequenced on the Illumina GA platform. MOI estimates were derived by PCR at the <em>msp-1</em> and <em>-2</em> loci. Significant correlations were observed between the two measures, particularly with the <em>msp-1</em> locus (<em>P</em> = 5.92×10⁻⁵). The <em>F_WS</em> metric should be more robust than the PCR-based approach owing to reduced sensitivity to potential locus-specific artifacts. Furthermore the <em>F_WS</em> metric captures information on a range of parameters which influence out-crossing risk including the number of clones (MOI), their relative proportions and genetic divergence. This approach should provide novel insights into the factors which correlate with, and shape within-host diversity.</p> </div>", "links"=>[], "tags"=>["characterization", "within-host", "next-generation"], "article_id"=>128112, "categories"=>["Microbiology", "Cancer", "Genetics", "Biotechnology"], "users"=>["Sarah Auburn", "Susana Campino", "Olivo Miotto", "Abdoulaye A. Djimde", "Issaka Zongo", "Magnus Manske", "Gareth Maslen", "Valentina Mangano", "Daniel Alcock", "Bronwyn MacInnis", "Kirk A. Rockett", "Taane G. Clark", "Ogobara K. Doumbo", "Jean Bosco Ouédraogo", "Dominic P. Kwiatkowski"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032891.s001", "https://dx.doi.org/10.1371/journal.pone.0032891.s002", "https://dx.doi.org/10.1371/journal.pone.0032891.s003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Characterization_of_Within_Host_Plasmodium_falciparum_Diversity_Using_Next_Generation_Sequence_Data/128112", "title"=>"Characterization of Within-Host <em>Plasmodium falciparum</em> Diversity Using Next-Generation Sequence Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-02-29 02:15:12"}
• {"files"=>["https://ndownloader.figshare.com/files/674376"], "description"=>"<p><i>F_WS</i> against MSP1 MOI, MSP2 MOI, and maximum MOI.</p>", "links"=>[], "tags"=>["msp1", "msp2"], "article_id"=>344843, "categories"=>["Microbiology", "Genetics", "Infectious Diseases", "Biotechnology"], "users"=>["Sarah Auburn", "Susana Campino", "Olivo Miotto", "Abdoulaye A. Djimde", "Issaka Zongo", "Magnus Manske", "Gareth Maslen", "Valentina Mangano", "Daniel Alcock", "Bronwyn MacInnis", "Kirk A. Rockett", "Taane G. Clark", "Ogobara K. Doumbo", "Jean Bosco Ouédraogo", "Dominic P. Kwiatkowski"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032891.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_F_WS_against_MSP1_MOI_MSP2_MOI_and_maximum_MOI_/344843", "title"=>"<i>F_WS</i> against MSP1 MOI, MSP2 MOI, and maximum MOI.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-02-29 01:20:43"}
• {"files"=>["https://ndownloader.figshare.com/files/674481"], "description"=>"<p>Summary of MOI and <i>F_WS</i> estimates in Burkina Faso, Mali and the combined (West Africa) population.</p>", "links"=>[], "tags"=>["moi", "estimates", "burkina", "mali"], "article_id"=>344951, "categories"=>["Microbiology", "Genetics", "Infectious Diseases", "Biotechnology"], "users"=>["Sarah Auburn", "Susana Campino", "Olivo Miotto", "Abdoulaye A. Djimde", "Issaka Zongo", "Magnus Manske", "Gareth Maslen", "Valentina Mangano", "Daniel Alcock", "Bronwyn MacInnis", "Kirk A. Rockett", "Taane G. Clark", "Ogobara K. Doumbo", "Jean Bosco Ouédraogo", "Dominic P. Kwiatkowski"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0032891.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_MOI_and_F_WS_estimates_in_Burkina_Faso_Mali_and_the_combined_West_Africa_population_/344951", "title"=>"Summary of MOI and <i>F_WS</i> estimates in Burkina Faso, Mali and the combined (West Africa) population.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-02-29 01:22:31"}

PMC Usage Stats | Further Information

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Relative Metric

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F1000Prime