{"id":"https://openalex.org/W2541245055","doi":"https://doi.org/10.3791/54131","title":"Methyl-binding DNA capture Sequencing for Patient Tissues","display_name":"Methyl-binding DNA capture Sequencing for Patient Tissues","publication_year":2016,"publication_date":"2016-10-31","ids":{"openalex":"https://openalex.org/W2541245055","doi":"https://doi.org/10.3791/54131","mag":"2541245055","pmid":"https://pubmed.ncbi.nlm.nih.gov/27842364","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/5203769"},"language":"en","primary_location":{"id":"doi:10.3791/54131","doi":"https://doi.org/10.3791/54131","is_oa":false,"landing_page_url":"https://doi.org/10.3791/54131","pdf_url":null,"source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5203769","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012971026","display_name":"Rohit R. Jadhav","orcid":"https://orcid.org/0000-0002-2999-6329","observed_orcids":["https://orcid.org/0000-0002-2999-6329"]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rohit R. Jadhav","raw_affiliation_strings":["Department of Molecular Medicine, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063643571","display_name":"Yao V. Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yao V. Wang","raw_affiliation_strings":["Department of Molecular Medicine, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101626874","display_name":"Ya\u2010Ting Hsu","orcid":"https://orcid.org/0000-0001-7649-2812","observed_orcids":["https://orcid.org/0000-0001-7649-2812"]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ya-Ting Hsu","raw_affiliation_strings":["Department of Molecular Medicine, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023687478","display_name":"Joseph K. Liu","orcid":"https://orcid.org/0000-0001-6656-6240","observed_orcids":["https://orcid.org/0000-0001-6656-6240"]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph Liu","raw_affiliation_strings":["Department of Molecular Medicine, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113085591","display_name":"Dawn K. Garcia","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dawn Garcia","raw_affiliation_strings":["Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015534740","display_name":"Zhao Lai","orcid":"https://orcid.org/0000-0002-3543-5376","observed_orcids":["https://orcid.org/0000-0002-3543-5376"]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhao Lai","raw_affiliation_strings":["Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049119185","display_name":"Tim H.\u2010M. Huang","orcid":"https://orcid.org/0000-0001-5985-9176","observed_orcids":["https://orcid.org/0000-0001-5985-9176"]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tim H. M. Huang","raw_affiliation_strings":["Department of Molecular Medicine, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066355670","display_name":"Victor X. Jin","orcid":"https://orcid.org/0000-0002-8765-3471","observed_orcids":["https://orcid.org/0000-0002-8765-3471"]},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Victor X. Jin","raw_affiliation_strings":["Department of Molecular Medicine, University of Texas Health Science Center at San Antonio; jinv@uthscsa.edu","Department of Molecular Medicine, University of Texas Health Science Center at San Antonio"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine, University of Texas Health Science Center at San Antonio; jinv@uthscsa.edu","institution_ids":["https://openalex.org/I165951966"]},{"raw_affiliation_string":"Department of Molecular Medicine, University of Texas Health Science Center at San Antonio","institution_ids":["https://openalex.org/I165951966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I165951966"],"apc_list":null,"apc_paid":null,"fwci":0.1424,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.54708005,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":"116","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.8270000219345093},{"id":"https://openalex.org/keywords/affinity-enrichment","display_name":"affinity enrichment","score":0.7720000147819519},{"id":"https://openalex.org/keywords/epigenetics","display_name":"epigenetics","score":0.6949999928474426},{"id":"https://openalex.org/keywords/bioinformatics-pipeline","display_name":"bioinformatics pipeline","score":0.7260000109672546}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.818246603012085},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.768734872341156},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6370418071746826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6015549302101135},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5380020141601562},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5276916027069092},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5038151144981384},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.41872429847717285},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39632368087768555},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37824714183807373},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1476401388645172}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.3791/54131","doi":"https://doi.org/10.3791/54131","is_oa":false,"landing_page_url":"https://doi.org/10.3791/54131","pdf_url":null,"source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"},{"id":"doi:10.3791/54131-v","doi":"https://doi.org/10.3791/54131-v","is_oa":false,"landing_page_url":"https://doi.org/10.3791/54131-v","pdf_url":null,"source":{"id":"https://openalex.org/S199738284","display_name":"Journal of Visualized Experiments","issn_l":"1940-087X","issn":["1940-087X","2834-8400"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320416","host_organization_name":"MyJOVE","host_organization_lineage":["https://openalex.org/P4310320416"],"host_organization_lineage_names":["MyJOVE"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Visualized Experiments","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:5203769","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5203769","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Vis Exp","raw_type":"Text"},{"id":"pmid:27842364","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27842364","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of visualized experiments : JoVE","raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5203769","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5203769","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"J Vis Exp","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.8371999859809875,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G7030894098","display_name":"Omics analysis of three-dimensional transcriptional regulation","funder_award_id":"R01GM114142","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320314011","display_name":"William and Ella Owens Medical Research Foundation","ror":"https://ror.org/0101ppd69"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W2000225203","https://openalex.org/W2014039097","https://openalex.org/W2041612371","https://openalex.org/W2062039251","https://openalex.org/W2076628461","https://openalex.org/W2107457596","https://openalex.org/W2110128489","https://openalex.org/W2111465765","https://openalex.org/W2120437661","https://openalex.org/W2134337220","https://openalex.org/W2135814599","https://openalex.org/W2146404065","https://openalex.org/W2154242091","https://openalex.org/W2155605783","https://openalex.org/W2156780274","https://openalex.org/W2289178372"],"related_works":["https://openalex.org/W2315362456","https://openalex.org/W2605715346","https://openalex.org/W2111465765","https://openalex.org/W7099712585","https://openalex.org/W4393076482","https://openalex.org/W7027387409","https://openalex.org/W2014039097","https://openalex.org/W2774037863","https://openalex.org/W3139518338","https://openalex.org/W2164732672"],"abstract_inverted_index":{"Methylation":[0],"is":[1,12,34],"one":[2,46],"of":[3,18,26,31,38,47,76,98,107],"the":[4,9,15,36,48,108],"essential":[5],"epigenetic":[6],"modifications":[7],"to":[8,58,86,95],"DNA,":[10],"which":[11],"responsible":[13],"for":[14,21,67],"precise":[16],"regulation":[17],"genes":[19],"required":[20],"stable":[22],"development":[23],"and":[24,64],"differentiation":[25],"different":[27],"tissue":[28],"types.":[29],"Dysregulation":[30],"this":[32,77],"process":[33],"often":[35],"hallmark":[37],"various":[39,62,101],"diseases":[40],"like":[41],"cancer.":[42],"Here,":[43],"we":[44],"outline":[45],"recent":[49],"sequencing":[50,55],"techniques,":[51],"Methyl-Binding":[52],"DNA":[53],"Capture":[54],"(MBDCap-seq),":[56],"used":[57,94],"quantify":[59],"methylation":[60],"in":[61],"normal":[63],"disease":[65],"tissues":[66],"large":[68],"patient":[69],"cohorts.":[70],"We":[71],"describe":[72],"a":[73,83,105],"detailed":[74],"protocol":[75],"affinity":[78],"enrichment":[79],"approach":[80],"along":[81],"with":[82],"bioinformatics":[84],"pipeline":[85],"achieve":[87],"optimal":[88],"quantification.":[89],"This":[90],"technique":[91],"has":[92],"been":[93],"sequence":[96],"hundreds":[97],"patients":[99],"across":[100],"cancer":[102],"types":[103],"as":[104],"part":[106],"1,000":[109],"methylome":[110],"project":[111],"(Cancer":[112],"Methylome":[113],"System).":[114]},"counts_by_year":[{"year":2018,"cited_by_count":1}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-11-04T00:00:00"}