{"doi":"10.1093/nar/gkr1042","title":"Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques","abstract":null,"journal":"Nucleic Acids Research","year":2012,"id":589489,"datarank":7.039961277918487,"base_score":4.867534450455582,"endowment":4.867534450455582,"self_citation_contribution":0.7301301675683375,"citation_network_contribution":6.309831110350149,"self_endowment_contribution":0.7301301675683375,"citer_contribution":6.309831110350149,"corpus_percentile":null,"corpus_rank":null,"citation_count":129,"citer_count":119,"citers_with_citation_signal":98,"citers_with_endowment":98,"datacite_reuse_total":8,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":679674,"name":"Gayle K. McEwen","orcid":"0000-0001-5134-1380","position":1,"is_corresponding":false},{"id":1508233,"name":"Thomas Huebsch","orcid":null,"position":2,"is_corresponding":false},{"id":1508234,"name":"Stefanie Palczewski","orcid":null,"position":3,"is_corresponding":false},{"id":1508235,"name":"Sabrina Schulz","orcid":null,"position":4,"is_corresponding":false},{"id":1508236,"name":"Kevin Verstrepen","orcid":null,"position":5,"is_corresponding":false},{"id":1508237,"name":"Eun-Kyung Suk","orcid":null,"position":6,"is_corresponding":false},{"id":608309,"name":"Margret R. Hoehe","orcid":null,"position":7,"is_corresponding":false},{"id":1508232,"name":"Jorge Duitama","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques","abstract":"Determining the underlying haplotypes of individual human genomes is an essential, but currently difficult, step toward a complete understanding of genome function. Fosmid pool-based next-generation sequencing allows genome-wide generation of 40-kb haploid DNA segments, which can be phased into contiguous molecular haplotypes computationally by Single Individual Haplotyping (SIH). Many SIH algorithms have been proposed, but the accuracy of such methods has been difficult to assess due to the lack of real benchmark data. To address this problem, we generated whole genome fosmid sequence data from a HapMap trio child, NA12878, for which reliable haplotypes have already been produced. We assembled haplotypes using eight algorithms for SIH and carried out direct comparisons of their accuracy, completeness and efficiency. Our comparisons indicate that fosmid-based haplotyping can deliver highly accurate results even at low coverage and that our SIH algorithm, ReFHap, is able to efficiently produce high-quality haplotypes. We expanded the haplotypes for NA12878 by combining the current haplotypes with our fosmid-based haplotypes, producing near-to-complete new gold-standard haplotypes containing almost 98% of heterozygous SNPs. This improvement includes notable fractions of disease-related and GWA SNPs. Integrated with other molecular biological data sets, this phase information will advance the emerging field of diploid genomics.","is_dataset_classified":null,"base_score":4.867534450455582,"endowment":4.867534450455582,"datacite_reuse_total":8,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"22102577","pmcid":"PMC3299995","openalex_id":"https://openalex.org/W2122767081","authors":[],"funders":[{"funder_name":"European Research Council","grant_id":"241426","title":null},{"funder_name":"European Commission FP7","grant_id":"FP7_241426","title":null}],"total_grants":2,"fwci":2.6763,"citation_percentile":0.90782706,"influential_citations":0,"citation_trend":[{"year":2012,"count":4},{"year":2013,"count":8},{"year":2014,"count":10},{"year":2015,"count":12},{"year":2016,"count":22},{"year":2017,"count":11},{"year":2018,"count":12},{"year":2019,"count":11},{"year":2020,"count":11},{"year":2021,"count":6},{"year":2022,"count":7},{"year":2023,"count":8},{"year":2024,"count":3},{"year":2025,"count":3},{"year":2026,"count":1}],"oa_status":"gold","license":"cc-by-nc","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/40/5/2041/16804987/gkr1042.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/40/5/2041/16804987/gkr1042.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/40/5/2041/16804987/gkr1042.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkr1042","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/22102577","host_type":"repository"},{"url":"https://lirias.kuleuven.be/handle/123456789/625452","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.271.4616","host_type":""},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3299995","host_type":"repository"},{"url":"http://hdl.handle.net/11858/00-001M-0000-0010-78A2-4","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC3299995","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC3299995?pdf=render","host_type":"Europe_PMC"}],"fields_of_study":["Genomics and Phylogenetic Studies","Gene expression and cancer classification","Genomic variations and chromosomal abnormalities","Algorithms","Genome, Human","Genomics","HapMap Project","Haplotypes","High-Throughput Nucleotide Sequencing","Humans","Polymorphism, Single Nucleotide","Sequence Analysis, DNA"],"mesh_terms":["Algorithms","Haplotypes","Humans","Genome, Human","Sequence Analysis, DNA","Polymorphism, Single Nucleotide","Genomics","High-Throughput Nucleotide Sequencing","HapMap Project"],"keywords":["Haplotype","Fosmid","International HapMap Project","Biology","Haplotype estimation","Genome","Genetics","Computational biology","1000 Genomes Project","Single-nucleotide polymorphism","DNA sequencing","Genomics","Contig","Gene","Genotype"],"sdg_mappings":[],"linked_datasets":[{"doi":"10.6084/m9.figshare.23606845.v1","title":"Additional file 1 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23606845","title":"Additional file 1 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23606851","title":"Additional file 3 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23606851.v1","title":"Additional file 3 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"JournalArticle"},{"doi":"10.6084/m9.figshare.23606848.v1","title":"Additional file 2 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"Dataset"},{"doi":"10.6084/m9.figshare.23606854","title":"Additional file 4 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"Dataset"},{"doi":"10.6084/m9.figshare.23606854.v1","title":"Additional file 4 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"Dataset"},{"doi":"10.6084/m9.figshare.23606848","title":"Additional file 2 of Pairwise comparative analysis of six haplotype assembly methods based on users’ experience","publisher":"figshare","resource_type":"Dataset"}],"clinical_trials":[],"software_tools":[],"database_accessions":[{"name":"gen"},{"name":"igsr"},{"name":"doi"}],"source":"live","citation_network_status":"fetched"},"created_at":"2026-07-23T19:38:20.922268Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}