A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
Publication Date
April 17, 2014
Journal
PLOS Genetics
Authors
Jared O'connell, Deepti Gurdasani, Olivier Delaneau, Nicola Pirastu, et al
Volume
10
Issue
4
Pages
e1004234
DOI
http://doi.org/10.1371/journal.pgen.1004234
Publisher URL
http://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1004234
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24743097
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3990520
Europe PMC
http://europepmc.org/abstract/MED/24743097
Web of Science
000335499600016
Scopus
84901370399
Mendeley
http://www.mendeley.com/research/general-approach-haplotype-phasing-across-full-spectrum-relatedness
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Mendeley | Further Information

{"title"=>"A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness", "type"=>"journal", "authors"=>[{"first_name"=>"Jared", "last_name"=>"O'Connell", "scopus_author_id"=>"26325004500"}, {"first_name"=>"Deepti", "last_name"=>"Gurdasani", "scopus_author_id"=>"24401522500"}, {"first_name"=>"Olivier", "last_name"=>"Delaneau", "scopus_author_id"=>"15062248800"}, {"first_name"=>"Nicola", "last_name"=>"Pirastu", "scopus_author_id"=>"22635433900"}, {"first_name"=>"Sheila", "last_name"=>"Ulivi", "scopus_author_id"=>"24598313400"}, {"first_name"=>"Massimiliano", "last_name"=>"Cocca", "scopus_author_id"=>"51763347100"}, {"first_name"=>"Michela", "last_name"=>"Traglia", "scopus_author_id"=>"35173670400"}, {"first_name"=>"Jie", "last_name"=>"Huang", "scopus_author_id"=>"55857939800"}, {"first_name"=>"Jennifer E.", "last_name"=>"Huffman", "scopus_author_id"=>"26654219700"}, {"first_name"=>"Igor", "last_name"=>"Rudan", "scopus_author_id"=>"7007138278"}, {"first_name"=>"Ruth", "last_name"=>"McQuillan", "scopus_author_id"=>"6701394821"}, {"first_name"=>"Ross M.", "last_name"=>"Fraser", "scopus_author_id"=>"14048248200"}, {"first_name"=>"Harry", "last_name"=>"Campbell", "scopus_author_id"=>"7202318417"}, {"first_name"=>"Ozren", "last_name"=>"Polasek", "scopus_author_id"=>"8232027400"}, {"first_name"=>"Gershim", "last_name"=>"Asiki", "scopus_author_id"=>"12752430200"}, {"first_name"=>"Kenneth", "last_name"=>"Ekoru", "scopus_author_id"=>"25930326000"}, {"first_name"=>"Caroline", "last_name"=>"Hayward", "scopus_author_id"=>"35369845200"}, {"first_name"=>"Alan F.", "last_name"=>"Wright", "scopus_author_id"=>"35402433000"}, {"first_name"=>"Veronique", "last_name"=>"Vitart", "scopus_author_id"=>"56920729200"}, {"first_name"=>"Pau", "last_name"=>"Navarro", "scopus_author_id"=>"8724895200"}, {"first_name"=>"Jean Francois", "last_name"=>"Zagury", "scopus_author_id"=>"7007164424"}, {"first_name"=>"James F.", "last_name"=>"Wilson", "scopus_author_id"=>"56920724500"}, {"first_name"=>"Daniela", "last_name"=>"Toniolo", "scopus_author_id"=>"7007056058"}, {"first_name"=>"Paolo", "last_name"=>"Gasparini", "scopus_author_id"=>"22634397400"}, {"first_name"=>"Nicole", "last_name"=>"Soranzo", "scopus_author_id"=>"55800239500"}, {"first_name"=>"Manjinder S.", "last_name"=>"Sandhu", "scopus_author_id"=>"7004012378"}, {"first_name"=>"Jonathan", "last_name"=>"Marchini", "scopus_author_id"=>"56359523500"}], "year"=>2014, "source"=>"PLoS Genetics", "identifiers"=>{"issn"=>"15537404", "scopus"=>"2-s2.0-84901370399", "pui"=>"373162845", "doi"=>"10.1371/journal.pgen.1004234", "isbn"=>"1553-7404 (Electronic)\\n1553-7390 (Linking)", "sgr"=>"84901370399", "pmid"=>"24743097"}, "id"=>"6e2e69b7-0ea5-3641-b450-c5fbab15b94f", "abstract"=>"Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations, we have investigated the performance of different phasing methods designed for nominally 'unrelated' individuals. We find that SHAPEIT2 produces much lower switch error rates in all cohorts compared to other methods, including those designed specifically for isolated populations. In particular, when large amounts of IBD sharing is present, SHAPEIT2 infers close to perfect haplotypes. Based on these results we have developed a general strategy for phasing cohorts with any level of implicit or explicit relatedness between individuals. First SHAPEIT2 is run ignoring all explicit family information. We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. This allows the correction of switch errors, detection of recombination events and genotyping errors. We show that the method detects numbers of recombination events that align very well with expectations based on genetic maps, and that it infers far fewer spurious recombination events than Merlin. The method can also detect genotyping errors and infer recombination events in otherwise uninformative families, such as trios and duos. The detected recombination events can be used in association scans for recombination phenotypes. The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics.", "link"=>"http://www.mendeley.com/research/general-approach-haplotype-phasing-across-full-spectrum-relatedness", "reader_count"=>301, "reader_count_by_academic_status"=>{"Unspecified"=>6, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>99, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>101, "Student > Postgraduate"=>9, "Student > Master"=>32, "Other"=>6, "Student > Bachelor"=>18, "Lecturer"=>2, "Professor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>6, "Professor > Associate Professor"=>10, "Librarian"=>1, "Researcher"=>99, "Student > Doctoral Student"=>9, "Student > Ph. D. Student"=>101, "Student > Postgraduate"=>9, "Student > Master"=>32, "Other"=>6, "Student > Bachelor"=>18, "Lecturer"=>2, "Professor"=>8}, "reader_count_by_subject_area"=>{"Unspecified"=>20, "Agricultural and Biological Sciences"=>168, "Chemistry"=>1, "Computer Science"=>12, "Engineering"=>4, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>53, "Materials Science"=>1, "Mathematics"=>9, "Medicine and Dentistry"=>17, "Neuroscience"=>3, "Physics and Astronomy"=>2, "Psychology"=>4, "Social Sciences"=>4, "Immunology and Microbiology"=>1, "Linguistics"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>17}, "Social Sciences"=>{"Social Sciences"=>4}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>4}, "Mathematics"=>{"Mathematics"=>9}, "Unspecified"=>{"Unspecified"=>20}, "Environmental Science"=>{"Environmental Science"=>1}, "Engineering"=>{"Engineering"=>4}, "Chemistry"=>{"Chemistry"=>1}, "Neuroscience"=>{"Neuroscience"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>168}, "Computer Science"=>{"Computer Science"=>12}, "Linguistics"=>{"Linguistics"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>53}}, "reader_count_by_country"=>{"New Zealand"=>2, "Greece"=>1, "Canada"=>1, "Austria"=>1, "Netherlands"=>1, "United States"=>11, "Norway"=>1, "United Kingdom"=>10, "Italy"=>1, "Germany"=>3}, "group_count"=>18}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1469445"], "description"=>"<p>The mean number of switches occurring (excluding ) found by the Viterbi path through our four state HMM for SHAPEIT2 and Beagle maximum likelihood haplotypes for chromosome 10 for paternal (P) and maternal (M) duos. SHAPEIT2 has very few impossible transitions ( and ) and the number possible recombinations () are much closer to the genetic length of chromosome 10 than Beagle. The 2002 deCODE map gives the chromosome 10 genetic length as 1.34 and 2.18 Morgans for males and females respectively.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "duohmm", "transitions"], "article_id"=>1003264, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.t003", "stats"=>{"downloads"=>3, "page_views"=>23, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_DuoHMM_state_transitions_for_each_cohort_/1003264", "title"=>"Summary of DuoHMM state transitions for each cohort.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469443"], "description"=>"<p>All individuals not explicitly related in the defined pedigrees were phased. We calculate overall SE rate (All), for chromosome 10 (this is not possible for SLRP) as well as SE rates within (IBD) and outside (no IBD) SLRP detected IBD regions. SHAPEIT2 consistently produces the most accurate haplotypes. Chip abbreviations: 370K - Illumina HumanHap 370CNV. 300K - Illumina HumanHap 300, 2.5S - Illumina Omni 2.5S.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "rates", "samples", "containing", "nominally", "unrelated"], "article_id"=>1003262, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.t001", "stats"=>{"downloads"=>5, "page_views"=>93, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Switch_error_rates_for_samples_containing_nominally_unrelated_individuals_/1003262", "title"=>"Switch error rates for samples containing nominally unrelated individuals.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469440"], "description"=>"<p>The green values are for a cohort with nominally unrelated individuals and the orange values are for a cohort that has been filtered such that no individuals are closely related (). Left: The ROC curves for recombination detection in uninformative duos for our duo HMM using the SHAPEIT2 haplotypes. Right: The average number of correct detections against the average posterior probability. Setting a high probability threshold ensures a very low false discovery rate.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "detection", "uninformative", "duos", "simulated", "chromosome", "val", "borbera"], "article_id"=>1003259, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.g007", "stats"=>{"downloads"=>2, "page_views"=>42, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Recombination_detection_accuracy_in_uninformative_duos_simulated_from_chromosome_X_data_in_the_Val_Borbera_cohort_/1003259", "title"=>"Recombination detection accuracy in uninformative duos simulated from chromosome X data in the Val Borbera cohort.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469434"], "description"=>"<p>The light and dark purple represent genetic material from the grand-paternal and grand-maternal chromosomes (as inferred by Merlin's Viterbi algorithm), hence changing from light to dark implies a a recombination event. The grey rectangles contain the posterior probability (in black) of recombination from our method. The two methods broadly agree, although Merlin has inferred a number of implausibly small cross over events.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "merlin", "informative", "meioses", "chromosome", "10", "taken", "val", "borbera", "cohort"], "article_id"=>1003253, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.g005", "stats"=>{"downloads"=>4, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Inferred_gene_flow_by_Merlin_purple_and_our_method_grey_for_ten_informative_meioses_on_chromosome_10_taken_from_Val_Borbera_cohort_pedigrees_/1003253", "title"=>"Inferred gene flow by Merlin (purple) and our method (grey) for ten informative meioses on chromosome 10 taken from Val Borbera cohort pedigrees.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469430"], "description"=>"<p>The four possible IBD states (A, B, C, D) are shown using colours pale blue, dark blue, light red and dark red respectively. The left and right panels show the results of the duo HMM applied to the SHAPEIT2 and Beagle haplotypes respectively. Changes between a blue and red colour correspond to a or transition, both of which imply a SE in the child. Changes of colour between light and dark blue or between light and dark red correspond to transitions, which correspond to a change on IBD state in the parent, and could be caused by a recombination or a SE in the parent. The x-axis shows the sex-averaged genetic distance across the chromosome in centiMorgans.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "duo", "hmm", "viterbi", "paths", "50", "father-child", "duos", "val", "borbera", "cohort", "chromosome"], "article_id"=>1003249, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.g003", "stats"=>{"downloads"=>2, "page_views"=>44, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_duo_HMM_Viterbi_paths_for_50_father_child_duos_from_the_Val_Borbera_cohort_on_chromosome_10_/1003249", "title"=>"The duo HMM Viterbi paths for 50 father-child duos from the Val Borbera cohort on chromosome 10.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469428"], "description"=>"<p>In each examples , , and denotes the two parental and child haplotypes and denotes the pattern of gene flow. Top: Correctly inferred haplotypes in a region of a true recombination event that causes a transition in the duo HMM. The other 4 examples in the figure add SEs to these true parental and child haplotypes. Middle left: addition of a SE in the child's haplotypes that causes a transition. Middle right: addition of a SE in the parent's haplotypes that causes a transition. Bottom left: addition of a SE in the parent's haplotypes at the site of the recombination event that causes the transition to be missed. Bottom right: addition of a SE in both the child's and parent's haplotypes at the same position that causes a transition.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "inferred", "recombination"], "article_id"=>1003247, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.g001", "stats"=>{"downloads"=>3, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_inferred_haplotypes_with_true_recombination_events_and_SEs_/1003247", "title"=>"Examples of inferred haplotypes with true recombination events and SEs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469429"], "description"=>"<p>Left: The proportion of heterozygote sites phased by SLRP for all individuals (pink) and when individuals with close relatives () are removed (blue). Right: The distributions of the average number of “surrogate” parents for each cohort when closely related pairs () are removed.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "ibd", "sharing"], "article_id"=>1003248, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.g002", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_IBD_sharing_in_cohorts_/1003248", "title"=>"Summary of IBD sharing in cohorts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469441"], "description"=>"<p>SHAPEIT2 concordance is the percentage of SHAPEIT2 crossover events that intersected a Merlin crossover event, the proceeding column is vice versa. We also provide the mean number of paternal/maternal recombination events detected for informative meioses by Merlin and SHAPEIT2. For comparison, the frequently cited deCODE 2002 genetic map estimated an average of 42.81 and 25.9 autosomal recombinations per paternal and maternal meioses respectively. SHAPEIT2's estimates are consistently closer to the deCODE values which are considered to be of high quality.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "recombination", "detection", "merlin", "informative", "paternal", "maternal", "meioses"], "article_id"=>1003260, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.t004", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_recombination_detection_using_our_method_and_Merlin_for_all_informative_paternal_P_and_maternal_M_meioses_events_in_each_cohort_/1003260", "title"=>"Comparison of recombination detection using our method and Merlin for all informative paternal (P) and maternal (M) meioses events in each cohort.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469438"], "description"=>"<p>Only duos that were part of an informative pedigree were used. Top: The mean number of recombinations per meiosis (for all informative duos from all cohorts) found for each chromosome against the expected number (from the 2002 deCODE map) for paternal meioses (left) and maternal meioses (right). Merlin's values are substantially inflated whilst SHAPEIT2's are more consistent with the well known deCODE map genetic lengths. Bottom: Q-Q plots for the observed against expected number of recombinations estimated by each method for paternal meioses (left) and maternal meioses (right). For the expected distribution of recombination rates, a Poisson distribution using the genetic lengths from the 2002 deCODE Map was used (with rate parameter 42.81 and 25.9 for maternal and paternal recombinations respectively). SHAPEIT2's rates are less inflated than those of the Merlin.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "crossovers"], "article_id"=>1003256, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.g006", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distributions_of_the_number_of_detected_crossovers_for_all_cohorts_/1003256", "title"=>"Distributions of the number of detected crossovers for all cohorts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469493", "https://ndownloader.figshare.com/files/1469494", "https://ndownloader.figshare.com/files/1469495", "https://ndownloader.figshare.com/files/1469496", "https://ndownloader.figshare.com/files/1469497", "https://ndownloader.figshare.com/files/1469498", "https://ndownloader.figshare.com/files/1469499", "https://ndownloader.figshare.com/files/1469500", "https://ndownloader.figshare.com/files/1469501", "https://ndownloader.figshare.com/files/1469502", "https://ndownloader.figshare.com/files/1469503", "https://ndownloader.figshare.com/files/1469504", "https://ndownloader.figshare.com/files/1469505", "https://ndownloader.figshare.com/files/1469506", "https://ndownloader.figshare.com/files/1469507", "https://ndownloader.figshare.com/files/1469508", "https://ndownloader.figshare.com/files/1469509", "https://ndownloader.figshare.com/files/1469510", "https://ndownloader.figshare.com/files/1469511", "https://ndownloader.figshare.com/files/1469512", "https://ndownloader.figshare.com/files/1469513", "https://ndownloader.figshare.com/files/1469514", "https://ndownloader.figshare.com/files/1469515", "https://ndownloader.figshare.com/files/1469516", "https://ndownloader.figshare.com/files/1469517", "https://ndownloader.figshare.com/files/1469518", "https://ndownloader.figshare.com/files/1469519", "https://ndownloader.figshare.com/files/1469520", "https://ndownloader.figshare.com/files/1469521", "https://ndownloader.figshare.com/files/1469522", "https://ndownloader.figshare.com/files/1469523", "https://ndownloader.figshare.com/files/1469524", "https://ndownloader.figshare.com/files/1469525", "https://ndownloader.figshare.com/files/1469526", "https://ndownloader.figshare.com/files/1469527", "https://ndownloader.figshare.com/files/1469528", "https://ndownloader.figshare.com/files/1469529"], "description"=>"<div><p>Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations, we have investigated the performance of different phasing methods designed for nominally ‘unrelated’ individuals. We find that SHAPEIT2 produces much lower switch error rates in all cohorts compared to other methods, including those designed specifically for isolated populations. In particular, when large amounts of IBD sharing is present, SHAPEIT2 infers close to perfect haplotypes. Based on these results we have developed a general strategy for phasing cohorts with any level of implicit or explicit relatedness between individuals. First SHAPEIT2 is run ignoring <i>all</i> explicit family information. We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. This allows the correction of switch errors, detection of recombination events and genotyping errors. We show that the method detects numbers of recombination events that align very well with expectations based on genetic maps, and that it infers far fewer spurious recombination events than Merlin. The method can also detect genotyping errors and infer recombination events in otherwise uninformative families, such as trios and duos. The detected recombination events can be used in association scans for recombination phenotypes. The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics.</p></div>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "haplotype", "phasing"], "article_id"=>1003301, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1004234.s001", "https://dx.doi.org/10.1371/journal.pgen.1004234.s002", "https://dx.doi.org/10.1371/journal.pgen.1004234.s003", "https://dx.doi.org/10.1371/journal.pgen.1004234.s004", "https://dx.doi.org/10.1371/journal.pgen.1004234.s005", "https://dx.doi.org/10.1371/journal.pgen.1004234.s006", "https://dx.doi.org/10.1371/journal.pgen.1004234.s007", "https://dx.doi.org/10.1371/journal.pgen.1004234.s008", "https://dx.doi.org/10.1371/journal.pgen.1004234.s009", "https://dx.doi.org/10.1371/journal.pgen.1004234.s010", "https://dx.doi.org/10.1371/journal.pgen.1004234.s011", "https://dx.doi.org/10.1371/journal.pgen.1004234.s012", "https://dx.doi.org/10.1371/journal.pgen.1004234.s013", "https://dx.doi.org/10.1371/journal.pgen.1004234.s014", "https://dx.doi.org/10.1371/journal.pgen.1004234.s015", "https://dx.doi.org/10.1371/journal.pgen.1004234.s016", "https://dx.doi.org/10.1371/journal.pgen.1004234.s017", "https://dx.doi.org/10.1371/journal.pgen.1004234.s018", "https://dx.doi.org/10.1371/journal.pgen.1004234.s019", "https://dx.doi.org/10.1371/journal.pgen.1004234.s020", "https://dx.doi.org/10.1371/journal.pgen.1004234.s021", "https://dx.doi.org/10.1371/journal.pgen.1004234.s022", "https://dx.doi.org/10.1371/journal.pgen.1004234.s023", "https://dx.doi.org/10.1371/journal.pgen.1004234.s024", "https://dx.doi.org/10.1371/journal.pgen.1004234.s025", "https://dx.doi.org/10.1371/journal.pgen.1004234.s026", "https://dx.doi.org/10.1371/journal.pgen.1004234.s027", "https://dx.doi.org/10.1371/journal.pgen.1004234.s028", "https://dx.doi.org/10.1371/journal.pgen.1004234.s029", "https://dx.doi.org/10.1371/journal.pgen.1004234.s030", "https://dx.doi.org/10.1371/journal.pgen.1004234.s031", "https://dx.doi.org/10.1371/journal.pgen.1004234.s032", "https://dx.doi.org/10.1371/journal.pgen.1004234.s033", "https://dx.doi.org/10.1371/journal.pgen.1004234.s034", "https://dx.doi.org/10.1371/journal.pgen.1004234.s035", "https://dx.doi.org/10.1371/journal.pgen.1004234.s036", "https://dx.doi.org/10.1371/journal.pgen.1004234.s037"], "stats"=>{"downloads"=>57, "page_views"=>24, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_General_Approach_for_Haplotype_Phasing_across_the_Full_Spectrum_of_Relatedness_/1003301", "title"=>"A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469432"], "description"=>"<p>Points are coloured according to what relationship was used by Beagle to phase that individual (red meaning no relationships were used). Left: Beagle using duo/trio phasing versus SHAPEIT2 using no relationships. Centre: Beagle using duo/trio phasing versus SHAPEIT2+duoHMM using no relationships. Right: Beagle using duo/trio phasing versus SHAPEIT2+duoHMM using no relationships when masking loci flagged as probable genotyping errors by the duoHMM. Switch error is reduced for both methods suggesting the masking is sensible.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "rates", "individuals", "pedigrees", "phasing", "pipelines", "european", "cohorts"], "article_id"=>1003251, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.g004", "stats"=>{"downloads"=>2, "page_views"=>55, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Switch_error_rates_for_individuals_in_extended_pedigrees_for_different_phasing_pipelines_across_all_European_cohorts_chromosome_10_/1003251", "title"=>"Switch error rates for individuals in extended pedigrees for different phasing pipelines across all European cohorts (chromosome 10).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-17 03:51:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/1469444"], "description"=>"<p>We evaluate SE for individuals who are members of a complex pedigree (pedigrees that are larger than a parent-child duo and father-mother-child trio). The first row is the number of individuals from each cohort in such pedigrees. The second row shows the yield of SLRP when applied to each cohort. Rows 3–6 show the SE for SHAPEIT2, SLRP, Beagle and HAPI-UR within SLRP detected IBD regions. Rows 7–9 show the SE for SHAPEIT2, Beagle and HAPI-UR outside SLRP detected IBD regions. Rows 10–12 show the overall SE for SHAPEIT2, Beagle and HAPI-UR. Rows 13–15 show the overall SE for SHAPEIT2, Beagle and HAPI-UR haplotypes after correction with the duoHMM method. Row 16 show the overall SE for Beagle applied to pedigrees partitioned into duos and trios where possible. Rows 17–18 show the switch error rate for the SHAPEIT2+duoHMM and Beagle Duo/Trio phasing <i>after</i> masking genotypes flagged as erroneous by the duoHMM.</p>", "links"=>[], "tags"=>["Computational biology", "genome analysis", "Genome-wide association studies", "Evolutionary biology", "population genetics", "haplotypes", "genetics", "Gene identification and analysis", "Genetic screens", "Human genetics", "Genetic association studies", "Animal genetics", "Genetics of disease", "mathematics", "Statistics (mathematics)", "Statistical methods", "rates", "methods", "applied"], "article_id"=>1003263, "categories"=>["Biological Sciences"], "users"=>["Jared O'Connell", "Deepti Gurdasani", "Olivier Delaneau", "Nicola Pirastu", "Sheila Ulivi", "Massimiliano Cocca", "Michela Traglia", "Jie Huang", "Jennifer E. Huffman", "Igor Rudan", "Ruth McQuillan", "Ross M. Fraser", "Harry Campbell", "Ozren Polašek", "Gershim Asiki", "Kenneth Ekoru", "Caroline Hayward", "Alan F. Wright", "Veronique Vitart", "Pau Navarro", "Jean-François Zagury", "James F. Wilson", "Daniela Toniolo", "Paolo Gasparini", "Nicole Soranzo", "Manjinder S. Sandhu", "Jonathan Marchini"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1004234.t002", "stats"=>{"downloads"=>1, "page_views"=>45, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Switch_error_SE_rates_for_different_methods_applied_to_extended_pedigrees_/1003263", "title"=>"Switch error (SE) rates for different methods applied to extended pedigrees.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-17 03:51:01"}

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Relative Metric

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