{"id":"https://openalex.org/W2016016428","doi":"https://doi.org/10.1186/1756-0500-5-117","title":"Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue","display_name":"Interpretation of genome-wide infinium methylation data from ligated DNA in formalin-fixed, paraffin-embedded paired tumor and normal tissue","publication_year":2012,"publication_date":"2012-02-22","ids":{"openalex":"https://openalex.org/W2016016428","doi":"https://doi.org/10.1186/1756-0500-5-117","mag":"2016016428","pmid":"https://pubmed.ncbi.nlm.nih.gov/22357164"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0500-5-117","doi":"https://doi.org/10.1186/1756-0500-5-117","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0500-5-117","pdf_url":"https://bmcresnotes.biomedcentral.com/counter/pdf/10.1186/1756-0500-5-117","source":{"id":"https://openalex.org/S100014455","display_name":"BMC Research Notes","issn_l":"1756-0500","issn":["1756-0500"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Research Notes","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcresnotes.biomedcentral.com/counter/pdf/10.1186/1756-0500-5-117","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072005435","display_name":"Farzana Jasmine","orcid":"https://orcid.org/0000-0002-5980-1174","observed_orcids":["https://orcid.org/0000-0002-5980-1174"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Farzana Jasmine","raw_affiliation_strings":["Department of Health Studies, The University of Chicago, Chicago, IL 60637, USA","Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL 60637, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085571988","display_name":"Ronald O. Rahaman","orcid":"https://orcid.org/0000-0002-8917-8934","observed_orcids":["https://orcid.org/0000-0002-8917-8934"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ronald Rahaman","raw_affiliation_strings":["Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103526717","display_name":"Shantanu Roy","orcid":"https://orcid.org/0000-0003-4007-5704","observed_orcids":["https://orcid.org/0000-0003-4007-5704"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shantanu Roy","raw_affiliation_strings":["Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091873980","display_name":"Maruf Raza","orcid":"https://orcid.org/0000-0003-0251-4518","observed_orcids":["https://orcid.org/0000-0003-0251-4518"]},"institutions":[{"id":"https://openalex.org/I201969901","display_name":"Bangladesh Medical University","ror":"https://ror.org/042mrsz23","country_code":"BD","type":"education","lineage":["https://openalex.org/I201969901"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Maruf Raza","raw_affiliation_strings":["Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, 1000, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, 1000, Bangladesh","institution_ids":["https://openalex.org/I201969901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088824179","display_name":"Rupash Paul","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I201969901","display_name":"Bangladesh Medical University","ror":"https://ror.org/042mrsz23","country_code":"BD","type":"education","lineage":["https://openalex.org/I201969901"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Rupash Paul","raw_affiliation_strings":["Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, 1000, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, 1000, Bangladesh","institution_ids":["https://openalex.org/I201969901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074024163","display_name":"Muhammad Rakibuz\u2010Zaman","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I4210144957","display_name":"University of Chicago Research Bangladesh","ror":"https://ror.org/04bzg5466","country_code":"BD","type":"facility","lineage":["https://openalex.org/I4210144957"]}],"countries":["BD","US"],"is_corresponding":false,"raw_author_name":"Muhammad Rakibuz-Zaman","raw_affiliation_strings":["University of Chicago Research Office in Bangladesh, Dhaka, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Chicago Research Office in Bangladesh, Dhaka, Bangladesh","institution_ids":["https://openalex.org/I40347166","https://openalex.org/I4210144957"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088912437","display_name":"Rachelle Paul-Brutus","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rachelle Paul-Brutus","raw_affiliation_strings":["Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071232435","display_name":"Charlotte Dodsworth","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charlotte Dodsworth","raw_affiliation_strings":["Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103397870","display_name":"Mohammed Kamal","orcid":"https://orcid.org/0000-0001-8430-2628","observed_orcids":["https://orcid.org/0000-0001-8430-2628"]},"institutions":[{"id":"https://openalex.org/I201969901","display_name":"Bangladesh Medical University","ror":"https://ror.org/042mrsz23","country_code":"BD","type":"education","lineage":["https://openalex.org/I201969901"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Mohammed Kamal","raw_affiliation_strings":["Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, 1000, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, 1000, Bangladesh","institution_ids":["https://openalex.org/I201969901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003374278","display_name":"Habibul Ahsan","orcid":"https://orcid.org/0000-0001-9808-377X","observed_orcids":["https://orcid.org/0000-0001-9808-377X"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I4390039251","display_name":"University of Chicago Medicine Comprehensive Cancer Center","ror":"https://ror.org/042wftp98","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I4210087865","https://openalex.org/I4390039251"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Habibul Ahsan","raw_affiliation_strings":["Department of Comprehensive Cancer Center, The University of Chicago, Chicago, IL, 60637, USA","Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA","Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Comprehensive Cancer Center, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166","https://openalex.org/I4390039251"]},{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081425275","display_name":"Muhammad Ghulam Kibriya","orcid":"https://orcid.org/0000-0001-9784-6958","observed_orcids":["https://orcid.org/0000-0001-9784-6958"]},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Muhammad G Kibriya","raw_affiliation_strings":["Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Studies, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081425275"],"corresponding_institution_ids":["https://openalex.org/I40347166"],"apc_list":{"value":1690,"currency":"USD","value_usd":1690},"apc_paid":{"value":1690,"currency":"USD","value_usd":1690},"fwci":1.3933,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.79512875,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"5","issue":"1","first_page":"117","last_page":"117"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9980000257492065,"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":0.9980000257492065,"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/T10885","display_name":"Gene expression and cancer classification","score":0.0003000000142492354,"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":0.9160000085830688},{"id":"https://openalex.org/keywords/formalin-fixed-paraffin-embedded-tissue","display_name":"formalin-fixed paraffin-embedded tissue","score":0.9819999933242798},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"colorectal cancer","score":0.8539999723434448},{"id":"https://openalex.org/keywords/differentially-methylated-loci","display_name":"differentially methylated loci","score":0.9570000171661377},{"id":"https://openalex.org/keywords/fresh-frozen-tissue-comparison","display_name":"fresh frozen tissue comparison","score":0.8119999766349792},{"id":"https://openalex.org/keywords/snp-genotyping","display_name":"SNP genotyping","score":0.5720000267028809}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6748076677322388},{"id":"https://openalex.org/C160798450","wikidata":"https://www.wikidata.org/wiki/Q4230870","display_name":"Concordance","level":2,"score":0.6378517746925354},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5879435539245605},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5822604894638062},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.48482954502105713},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47350531816482544},{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.45099353790283203},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.39757198095321655},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3382485508918762},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3317209482192993},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.23638367652893066},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23222309350967407},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11181378364562988}],"mesh":[{"descriptor_ui":"D003106","descriptor_name":"Colon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003106","descriptor_name":"Colon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003106","descriptor_name":"Colon","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003106","descriptor_name":"Colon","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D003106","descriptor_name":"Colon","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D003106","descriptor_name":"Colon","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005557","descriptor_name":"Formaldehyde","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005557","descriptor_name":"Formaldehyde","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005557","descriptor_name":"Formaldehyde","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005629","descriptor_name":"Frozen Sections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005629","descriptor_name":"Frozen Sections","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005629","descriptor_name":"Frozen Sections","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":"D006801","descriptor_name":"Humans","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":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008297","descriptor_name":"Male","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012737","descriptor_name":"Sex Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012737","descriptor_name":"Sex Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012737","descriptor_name":"Sex Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013048","descriptor_name":"Specimen Handling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013048","descriptor_name":"Specimen Handling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013048","descriptor_name":"Specimen Handling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013048","descriptor_name":"Specimen Handling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D013048","descriptor_name":"Specimen Handling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D013048","descriptor_name":"Specimen Handling","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D016612","descriptor_name":"Paraffin Embedding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016612","descriptor_name":"Paraffin Embedding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016612","descriptor_name":"Paraffin Embedding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016707","descriptor_name":"Tissue Fixation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016707","descriptor_name":"Tissue Fixation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016707","descriptor_name":"Tissue Fixation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1186/1756-0500-5-117","doi":"https://doi.org/10.1186/1756-0500-5-117","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0500-5-117","pdf_url":"https://bmcresnotes.biomedcentral.com/counter/pdf/10.1186/1756-0500-5-117","source":{"id":"https://openalex.org/S100014455","display_name":"BMC Research Notes","issn_l":"1756-0500","issn":["1756-0500"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Research Notes","raw_type":"journal-article"},{"id":"pmid:22357164","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22357164","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":"BMC research notes","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2316794","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3309956","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3309956","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3309956","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Res Notes","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:93204beb1e314bb4bee09031649e508c","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/93204beb1e314bb4bee09031649e508c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Research Notes, Vol 5, Iss 1, p 117 (2012)","raw_type":"article"},{"id":"doi:10.60692/a53aa-0vh93","doi":"https://doi.org/10.60692/a53aa-0vh93","is_oa":true,"landing_page_url":"https://doi.org/10.60692/a53aa-0vh93","pdf_url":null,"source":{"id":"https://openalex.org/S7407051682","display_name":"Greater South Information System","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"},{"id":"doi:10.60692/f65xf-08p65","doi":"https://doi.org/10.60692/f65xf-08p65","is_oa":true,"landing_page_url":"https://doi.org/10.60692/f65xf-08p65","pdf_url":null,"source":{"id":"https://openalex.org/S7407051682","display_name":"Greater South Information System","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/1756-0500-5-117","doi":"https://doi.org/10.1186/1756-0500-5-117","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0500-5-117","pdf_url":"https://bmcresnotes.biomedcentral.com/counter/pdf/10.1186/1756-0500-5-117","source":{"id":"https://openalex.org/S100014455","display_name":"BMC Research Notes","issn_l":"1756-0500","issn":["1756-0500"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","poland-70","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Research Notes","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.9391000270843506,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"sustainable_development_goals_aurora":[{"score":0.5699999928474426,"display_name":"No poverty","id":"https://metadata.un.org/sdg/1"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G125515613","display_name":null,"funder_award_id":"R01 CA 107431","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1749530826","display_name":"Genetic Susceptibility to Arsenic-induced Skin Cancer","funder_award_id":"R01CA102484","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1945244547","display_name":null,"funder_award_id":"P30-CA014599","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3148195175","display_name":null,"funder_award_id":"P42ES010349","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G6027852047","display_name":null,"funder_award_id":"U01CA122171","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G9000099858","display_name":null,"funder_award_id":"P30 CA 014599","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000105455","display_name":null,"funder_award_id":"U01 CA122171","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000178561","display_name":null,"funder_award_id":"R01 CA 107431","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000307092","display_name":null,"funder_award_id":"P42 ES010349","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2016016428.pdf","grobid_xml":"https://content.openalex.org/works/W2016016428.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W186096183","https://openalex.org/W1504303645","https://openalex.org/W1505543021","https://openalex.org/W1570006151","https://openalex.org/W1965262464","https://openalex.org/W1965301144","https://openalex.org/W1970149181","https://openalex.org/W1971937022","https://openalex.org/W1994322947","https://openalex.org/W1994473465","https://openalex.org/W2007470097","https://openalex.org/W2020413417","https://openalex.org/W2040257851","https://openalex.org/W2041140837","https://openalex.org/W2061623083","https://openalex.org/W2062421371","https://openalex.org/W2067959916","https://openalex.org/W2074526425","https://openalex.org/W2078727419","https://openalex.org/W2092075890","https://openalex.org/W2098442878","https://openalex.org/W2099892743","https://openalex.org/W2101170994","https://openalex.org/W2106816824","https://openalex.org/W2107972234","https://openalex.org/W2121308112","https://openalex.org/W2132148197","https://openalex.org/W2133766123","https://openalex.org/W2137846548","https://openalex.org/W2158774461","https://openalex.org/W2163125553","https://openalex.org/W2169903102","https://openalex.org/W2170029176","https://openalex.org/W2314185483"],"related_works":["https://openalex.org/W2214376880","https://openalex.org/W3212149434","https://openalex.org/W2073893804","https://openalex.org/W2291484187","https://openalex.org/W2902329290","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744","https://openalex.org/W2024490794"],"abstract_inverted_index":{"BACKGROUND:":[0],"Formalin-fixed,":[1],"paraffin-embedded":[2],"(FFPE)":[3],"samples":[4],"are":[5,316],"a":[6,35,192,305],"highly":[7],"desirable":[8],"resource":[9],"for":[10,45,108,277],"epigenetic":[11],"studies,":[12],"but":[13,310],"there":[14],"is":[15,335],"no":[16],"suitable":[17],"platform":[18],"to":[19,41,164,175,211,297],"assay":[20,302],"genome-wide":[21,300],"methylation":[22,48,59,301],"in":[23,157,208,214,227,320],"these":[24],"widely":[25],"available":[26],"resources.":[27],"Recently,":[28],"Thirlwell":[29],"et":[30],"al.":[31],"(2010)":[32],"have":[33,54],"reported":[34],"modified":[36,140],"ligation-based":[37,271],"DNA":[38,44,137,295,334],"repair":[39],"protocol":[40],"prepare":[42],"FFPE":[43,71,117,136,161,200,218,247,294,333,340],"the":[46,56,126,130,135,177,223,241,251,267,270,274,298,311,325],"Infinium":[47,104,275,299],"assay.":[49],"In":[50],"this":[51,63],"study,":[52],"we":[53,204,265],"tested":[55],"accuracy":[57],"of":[58,87,94,111,116,129,151,181,195,222,243,256,269,284,293,308,313,327],"data":[60],"obtained":[61],"with":[62,345],"modification":[64,272],"by":[65],"comparing":[66],"paired":[67,158],"fresh-frozen":[68],"(FF)":[69],"and":[70,75,85,113,121,146,160,199,217,220,248,332,337],"colon":[72,128],"tissue":[73,118,124,185,213],"(normal":[74,187],"tumor)":[76],"from":[77,119,125,339],"colorectal":[78],"cancer":[79],"patients.":[80],"We":[81,101,190],"report":[82],"locus-specific":[83],"correlation":[84,150,242,260],"concordance":[86,326],"tumor-specific":[88],"differentially":[89],"methylated":[90],"loci":[91,156,226,245,257,315],"(DML),":[92],"both":[93,144,215,228],"which":[95,286],"were":[96,232],"not":[97],"previously":[98],"assessed.":[99],"METHODS:":[100],"used":[102],"Illumina's":[103],"Methylation":[105],"27K":[106],"chip":[107],"12":[109,114],"pairs":[110,115],"FF":[112,159,198,216,249,321,331],"tumor":[120,145,209],"surrounding":[122],"healthy":[123],"resected":[127],"same":[131],"individual,":[132],"after":[133],"repairing":[134],"using":[138],"Thirlwell's":[139],"protocol.":[141],"RESULTS:":[142],"For":[143],"normal":[147,212],"tissue,":[148],"overall":[149],"\u03b2":[152],"values":[153],"between":[154,197,246,330],"all":[155],"was":[162,173],"comparable":[163],"previous":[165],"studies.":[166],"Tissue":[167],"storage":[168],"type":[169,186],"(FF":[170],"or":[171,188],"FFPE)":[172],"found":[174,191],"be":[176,343],"most":[178],"significant":[179],"source":[180],"variation":[182],"rather":[183],"than":[184,254,319],"tumor).":[189],"large":[193],"number":[194,307],"DML":[196,207,328,338],"DNA.":[201],"Using":[202],"ANOVA,":[203],"also":[205,287],"identified":[206],"compared":[210],"samples,":[219,285],"out":[221],"top":[224],"50":[225],"groups":[229],"only":[230],"7":[231],"common,":[233],"indicating":[234],"poor":[235,289],"concordance.":[236],"Likewise,":[237],"while":[238],"looking":[239],"at":[240],"individual":[244],"across":[250],"patients,":[252],"less":[253],"10%":[255],"showed":[258,288],"strong":[259],"(r":[261],"\u2265":[262],"0.6).":[263],"Finally,":[264],"checked":[266],"effect":[268],"on":[273,280],"chemistry":[276],"SNP":[278],"genotyping":[279],"an":[281],"independent":[282],"set":[283],"performance.":[290],"CONCLUSION:":[291],"Ligation":[292],"prior":[296],"may":[303],"detect":[304],"reasonable":[306],"loci,":[309],"numbers":[312],"detected":[314,329],"much":[317],"fewer":[318],"samples.":[322],"More":[323],"importantly,":[324],"suboptimal,":[336],"tissues":[341],"should":[342],"interpreted":[344],"great":[346],"caution.":[347]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2025-10-10T00:00:00"}
