A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses
Publication Date
February 27, 2014
Journal
PLOS Computational Biology
Authors
Frederick A. Matsen Iv, Christopher T. Small, Khanh Soliven, Gregory A. Engel, et al
Volume
10
Issue
2
Pages
e1003493
DOI
https://dx.plos.org/10.1371/journal.pcbi.1003493
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003493
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24586139
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3937129
Europe PMC
http://europepmc.org/abstract/MED/24586139
Web of Science
000332016700027
Scopus
84895734576
Mendeley
http://www.mendeley.com/research/novel-bayesian-method-detection-apobec3mediated-hypermutation-application-zoonotic-transmission-simi
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Mendeley | Further Information

{"title"=>"A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses", "type"=>"journal", "authors"=>[{"first_name"=>"Frederick A.", "last_name"=>"Matsen IV", "scopus_author_id"=>"55620556600"}, {"first_name"=>"Christopher T.", "last_name"=>"Small", "scopus_author_id"=>"55753770800"}, {"first_name"=>"Khanh", "last_name"=>"Soliven", "scopus_author_id"=>"26649027100"}, {"first_name"=>"Gregory A.", "last_name"=>"Engel", "scopus_author_id"=>"7102354118"}, {"first_name"=>"Mostafa M.", "last_name"=>"Feeroz", "scopus_author_id"=>"6507516709"}, {"first_name"=>"Xiaoxing", "last_name"=>"Wang", "scopus_author_id"=>"55753907900"}, {"first_name"=>"Karen L.", "last_name"=>"Craig", "scopus_author_id"=>"55753003100"}, {"first_name"=>"M. Kamrul", "last_name"=>"Hasan", "scopus_author_id"=>"55057478400"}, {"first_name"=>"Michael", "last_name"=>"Emerman", "scopus_author_id"=>"7006862840"}, {"first_name"=>"Maxine L.", "last_name"=>"Linial", "scopus_author_id"=>"7103138036"}, {"first_name"=>"Lisa", "last_name"=>"Jones-Engel", "scopus_author_id"=>"7801517374"}], "year"=>2014, "source"=>"PLoS Computational Biology", "identifiers"=>{"pui"=>"372548701", "isbn"=>"1553-7358 (Electronic)\\r1553-734X (Linking)", "issn"=>"15537358", "doi"=>"10.1371/journal.pcbi.1003493", "scopus"=>"2-s2.0-84895734576", "pmid"=>"24586139", "sgr"=>"84895734576"}, "id"=>"fff9747a-2982-33c9-a6f0-7ecdbbbe4f5c", "abstract"=>"<title>Author Summary</title><p>Simian Foamy Virus (SFV) is a very common retrovirus in monkeys. When an infected monkey bites a human it can transmit the virus to the human; however, there are no documented cases of human to human transmission. There also appear to be significant differences between infection in monkey and human hosts. The reason for these differences in the two hosts is not completely understood. In this paper we show that a family of host defense enzymes called APOBEC3 may prevent replication of SFV in humans. They do this by changing the genome of the virus so that it cannot replicate. Although this same process also happens in monkeys, it appears to happen less than in humans, and the changes that the monkey APOBEC3 enzymes make are less likely to prevent the virus from replicating. We are able to make these inferences by seeing characteristic types of mutations in a collection of virus DNA sequences sampled in Bangladesh. We develop new statistical methodology to do this analysis.</p>", "link"=>"http://www.mendeley.com/research/novel-bayesian-method-detection-apobec3mediated-hypermutation-application-zoonotic-transmission-simi", "reader_count"=>26, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>1, "Librarian"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>10, "Student > Postgraduate"=>1, "Student > Master"=>2, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Biochemistry, Genetics and Molecular Biology"=>4, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>2, "Immunology and Microbiology"=>4}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>4}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>4}, "Unspecified"=>{"Unspecified"=>3}}, "reader_count_by_country"=>{"United States"=>1, "Brazil"=>1}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1402002"], "description"=>"<p>The ratio of the mean squared error (MSE) of the RR estimate to that of the MAP estimator is plotted for each simulation parameter set. Points are grouped into lines and colored by control context mutation probability. The x-axis shows the relative probability ratio used for simulation. MSE ratio values greater than one indicate parameter regimes where MAP estimator does better than the RR or the mid-P estimator. Note that because RR isn't necessarily well-defined when one of the counts is zero, pseudocounts were added (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003493#s4\" target=\"_blank\">Materials and Methods</a>). Arrows label simulations in the parameter regime of the indicated study.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "mid-p", "rr", "estimates", "mutation", "simulations", "600", "bp", "1200"], "article_id"=>947360, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_MAP_to_mid_P_and_RR_effect_size_estimates_based_on_mutation_count_simulations_of_600_bp_A_and_1200_bp_B_length_sequences_/947360", "title"=>"Comparison of MAP to mid-P and RR effect size estimates based on mutation count simulations of 600 bp (A) and 1200 bp (B) length sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402009"], "description"=>"<p>These counts are only for core strains. Additionally, since both monkeys and humans are frequently infected with more than one strain, the host counts for a given strain represent the total number of animals infected with that strain, even if infected with other strains as well.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "presented"], "article_id"=>947367, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.t002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hypermutation_activity_by_strain_presented_on_both_a_sequence_by_sequence_and_host_by_host_basis_/947367", "title"=>"Hypermutation activity by strain, presented on both a sequence by sequence and host by host basis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402008"], "description"=>"<p>The rows show a variety of different statistical cutoffs, and columns show a variety of relative probability ratios. The rejection frequency of our method is closer to the cutoff under the null hypothesis, and is more frequently able to find a difference when one exists. These simulations were based on simulated sequences of 1200 bp, with 1/16 of sequence positions in the focus context, and 3/16 in a control context, and with a background (control context) G to A mutation probability of 0.008.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "fisher", "mid-p", "methodology", "simulated", "probability"], "article_id"=>947366, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.t001", "stats"=>{"downloads"=>1, "page_views"=>46, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_positive_rate_of_Fisher_test_before_mid_P_test_between_and_our_methodology_after_under_various_simulated_relative_probability_ratios_/947366", "title"=>"The positive rate of Fisher test (before/), mid-P test (between/), and our methodology (after/) under various simulated relative probability ratios.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402005"], "description"=>"<p>Box and whisker plots are shown as in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003493#pcbi-1003493-g003\" target=\"_blank\">Figure 3</a>. The strongest hypermutation signal is observed in the human sequences.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "gg", "hypermutation", "buccal"], "article_id"=>947363, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.g005", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_GG_context_hypermutation_signal_in_human_blood_monkey_blood_and_monkey_buccal_sequences_/947363", "title"=>"Comparison of GG context hypermutation signal in human blood, monkey blood and monkey buccal sequences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402004"], "description"=>"<p>Box and whisker plots on the same data are overlaid, where the thick horizontal bar shows the median value of the observations and the rectangle spans the first and third quartiles; points are randomly “jittered” horizontally within a species to avoid superimposed points. Panels labeled by target context using IUPAC degenerate notation, thus “R” designates A or G, and “M” designates A or C.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "sequences", "hypermutation", "profiles", "congruent", "observed"], "article_id"=>947362, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.g004", "stats"=>{"downloads"=>4, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Viral_sequences_show_distinct_hypermutation_profiles_in_the_two_host_species_congruent_with_activity_observed_in_other_studies_/947362", "title"=>"Viral sequences show distinct hypermutation profiles in the two host species, congruent with activity observed in other studies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402013", "https://ndownloader.figshare.com/files/1402014", "https://ndownloader.figshare.com/files/1402015", "https://ndownloader.figshare.com/files/1402016", "https://ndownloader.figshare.com/files/1402017", "https://ndownloader.figshare.com/files/1402018", "https://ndownloader.figshare.com/files/1402019", "https://ndownloader.figshare.com/files/1402020"], "description"=>"<div><p>Simian Foamy Virus (SFV) can be transmitted from non-human primates (NHP) to humans. However, there are no documented cases of human to human transmission, and significant differences exist between infection in NHP and human hosts. The mechanism for these between-host differences is not completely understood. In this paper we develop a new Bayesian approach to the detection of APOBEC3-mediated hypermutation, and use it to compare SFV sequences from human and NHP hosts living in close proximity in Bangladesh. We find that human APOBEC3G can induce genetic changes that may prevent SFV replication in infected humans in vivo.</p></div>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "bayesian", "detection", "apobec3-mediated", "hypermutation", "zoonotic", "simian", "foamy"], "article_id"=>947371, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003493.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003493.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003493.s003", "https://dx.doi.org/10.1371/journal.pcbi.1003493.s004", "https://dx.doi.org/10.1371/journal.pcbi.1003493.s005", "https://dx.doi.org/10.1371/journal.pcbi.1003493.s006", "https://dx.doi.org/10.1371/journal.pcbi.1003493.s007", "https://dx.doi.org/10.1371/journal.pcbi.1003493.s008"], "stats"=>{"downloads"=>9, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_Novel_Bayesian_Method_for_Detection_of_APOBEC3_Mediated_Hypermutation_and_Its_Application_to_Zoonotic_Transmission_of_Simian_Foamy_Viruses_/947371", "title"=>"A Novel Bayesian Method for Detection of APOBEC3-Mediated Hypermutation and Its Application to Zoonotic Transmission of Simian Foamy Viruses", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402007"], "description"=>"<p>Every sequence found to be hypermutated in our data set has a column (51 of 77 human sequences, and 105 of 1097 monkey blood sequences and 8 of 152 monkey buccal sequences). The top plot represents hypermutation intensity, where the dot shows the Maximum A Posteori (MAP) value for the relative probability ratio and the lower limit of the line shows the 0.05 quantile. Sequences colored by species and sample type (whole blood (WB) or buccal swab (BS)). The call pattern is the context in which the strongest dinucleotide hypermutation signal was found (using IUPAC degenerate nucleotide notation). “Stops” signifies the presence of in frame stop codons.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "sequences"], "article_id"=>947365, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.g006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_sequences_found_to_be_hypermutated_/947365", "title"=>"Overview of sequences found to be hypermutated.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402003"], "description"=>"<p>The distribution of the 8 human whole blood (WB) samples is to the right (towards larger values) compared to the 169 WB and 30 buccal swab (BS) samples from monkeys. The maximum of the relative probability ratio density for monkey WB samples is about 4, but the y axis of this figure was truncated for clarity.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "posteriori", "probability", "ratios", "sequences"], "article_id"=>947361, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Histogram_of_the_Maximum_A_Posteriori_MAP_of_relative_probability_ratios_for_all_sequences_in_the_study_/947361", "title"=>"Histogram of the Maximum A Posteriori (MAP) of relative probability ratios for all sequences in the study.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 04:01:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/1402001"], "description"=>"<p>Top row: starting with a prior distribution and then adding data, we get a posterior distribution of the mutation probability given that data. Bottom row: we can do this in the <i>focus</i> context (a nucleotide context associated with hypermutation) and a <i>control</i> context (one that is not). Taking the ratio of the corresponding random variables gives the posterior on the ratio of the mutation probabilities. Using this distribution we estimate the 0.05 quantile (Q05) and the Maximum A Posteriori (MAP) estimates of the RPR.</p>", "links"=>[], "tags"=>["immunology", "immunity", "Innate immunity", "microbiology", "Virology", "statistics", "overview", "probability"], "article_id"=>947359, "categories"=>["Biological Sciences", "Mathematics"], "users"=>["Frederick A. Matsen IV", "Christopher T. Small", "Khanh Soliven", "Gregory A. Engel", "Mostafa M. Feeroz", "Xiaoxing Wang", "Karen L. Craig", "M. Kamrul Hasan", "Michael Emerman", "Maxine L. Linial", "Lisa Jones-Engel"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003493.g001", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_An_overview_of_calculating_the_relative_probability_ratio_RPR_/947359", "title"=>"An overview of calculating the relative probability ratio (RPR).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-02-27 04:01:03"}

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Relative Metric

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