{"id":"https://openalex.org/W4361904558","doi":"https://doi.org/10.1158/1078-0432.22447449.v1","title":"Supplementary Methods from Expression Profiling of Archival Tumors for Long-term Health Studies","display_name":"Supplementary Methods from Expression Profiling of Archival Tumors for Long-term Health Studies","publication_year":2023,"publication_date":"2023-03-31","ids":{"openalex":"https://openalex.org/W4361904558","doi":"https://doi.org/10.1158/1078-0432.22447449.v1"},"language":"en","primary_location":{"id":"doi:10.1158/1078-0432.22447449.v1","doi":"https://doi.org/10.1158/1078-0432.22447449.v1","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/1078-0432.22447449.v1","pdf_url":"https://aacr.figshare.com/articles/journal_contribution/Supplementary_Methods_from_Expression_Profiling_of_Archival_Tumors_for_Long-term_Health_Studies/22447449/1/files/39898485.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"},"volume":null,"type":"supplementary-materials","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://aacr.figshare.com/articles/journal_contribution/Supplementary_Methods_from_Expression_Profiling_of_Archival_Tumors_for_Long-term_Health_Studies/22447449/1/files/39898485.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052283192","display_name":"Levi Waldron","orcid":"https://orcid.org/0000-0003-2725-0694","observed_orcids":["https://orcid.org/0000-0003-2725-0694"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Levi Waldron","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076818447","display_name":"Shuji Ogino","orcid":"https://orcid.org/0000-0002-3909-2323","observed_orcids":["https://orcid.org/0000-0002-3909-2323"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shuji Ogino","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007607351","display_name":"Yujin Hoshida","orcid":"https://orcid.org/0000-0001-9430-1426","observed_orcids":["https://orcid.org/0000-0001-9430-1426"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yujin Hoshida","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004733324","display_name":"Kaori Shima","orcid":"https://orcid.org/0000-0002-5556-3236","observed_orcids":["https://orcid.org/0000-0002-5556-3236"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kaori Shima","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091623014","display_name":"Amy E. McCart Reed","orcid":"https://orcid.org/0000-0001-5387-2791","observed_orcids":["https://orcid.org/0000-0001-5387-2791"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Amy E. McCart Reed","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033259635","display_name":"Peter T. Simpson","orcid":"https://orcid.org/0000-0002-4816-8289","observed_orcids":["https://orcid.org/0000-0002-4816-8289"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Peter T. Simpson","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101184836","display_name":"Yoshifumi Baba","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yoshifumi Baba","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057394943","display_name":"Katsuhiko Nosho","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Katsuhiko Nosho","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068576885","display_name":"Nicola Segata","orcid":"https://orcid.org/0000-0002-1583-5794","observed_orcids":["https://orcid.org/0000-0002-1583-5794"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicola Segata","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004851303","display_name":"Ana Cristina Vargas","orcid":"https://orcid.org/0000-0003-3798-5088","observed_orcids":["https://orcid.org/0000-0003-3798-5088","https://orcid.org/0000-0002-9424-2080"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ana Cristina Vargas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091112717","display_name":"Margaret C. Cummings","orcid":"https://orcid.org/0000-0002-7657-0240","observed_orcids":["https://orcid.org/0000-0002-7657-0240"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Margaret C. Cummings","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047329745","display_name":"Sunil R. Lakhani","orcid":"https://orcid.org/0000-0003-4067-2760","observed_orcids":["https://orcid.org/0000-0003-4067-2760","https://orcid.org/0000-0003-1879-2555"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sunil R. Lakhani","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011491566","display_name":"Gregory John Kirkner","orcid":"https://orcid.org/0009-0005-0386-5223","observed_orcids":["https://orcid.org/0009-0005-0386-5223"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gregory J. Kirkner","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038373228","display_name":"Edward L. Giovannucci","orcid":"https://orcid.org/0000-0002-6123-0219","observed_orcids":["https://orcid.org/0000-0002-6123-0219","https://orcid.org/0009-0003-9117-569X"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Edward Giovannucci","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084245470","display_name":"John F Quackenbush","orcid":"https://orcid.org/0000-0002-2702-5879","observed_orcids":["https://orcid.org/0000-0002-2702-5879","https://orcid.org/0009-0005-2193-1829"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"John Quackenbush","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001449157","display_name":"Todd R. Golub","orcid":"https://orcid.org/0000-0003-0113-2403","observed_orcids":["https://orcid.org/0000-0003-0113-2403"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Todd R. Golub","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049314303","display_name":"Charles S. Fuchs","orcid":"https://orcid.org/0000-0003-1582-9842","observed_orcids":["https://orcid.org/0000-0003-1582-9842"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Charles S. Fuchs","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050977500","display_name":"Giovanni Parmigiani","orcid":"https://orcid.org/0000-0002-8783-5961","observed_orcids":["https://orcid.org/0000-0002-8783-5961"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Giovanni Parmigiani","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5008844345","display_name":"Curtis Huttenhower","orcid":"https://orcid.org/0000-0002-1110-0096","observed_orcids":["https://orcid.org/0000-0002-1110-0096"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Curtis Huttenhower","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.5845000147819519,"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/T10885","display_name":"Gene expression and cancer classification","score":0.5845000147819519,"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/T10183","display_name":"Breast Cancer Treatment Studies","score":0.20000000298023224,"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"}},{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.051899999380111694,"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/gene-expression-profiling","display_name":"gene expression profiling","score":0.9340000152587891},{"id":"https://openalex.org/keywords/long-term-health-effects","display_name":"long-term health effects","score":0.8180000185966492},{"id":"https://openalex.org/keywords/cancer-survivors","display_name":"cancer survivors","score":0.7419999837875366},{"id":"https://openalex.org/keywords/tumor-markers","display_name":"tumor markers","score":0.38100001215934753}],"concepts":[{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.7143099308013916},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.540747880935669},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.4335938096046448},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39132508635520935},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.3565090298652649},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35392874479293823},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2959885001182556},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25331151485443115},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.12499591708183289},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11896449327468872},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1158/1078-0432.22447449.v1","doi":"https://doi.org/10.1158/1078-0432.22447449.v1","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/1078-0432.22447449.v1","pdf_url":"https://aacr.figshare.com/articles/journal_contribution/Supplementary_Methods_from_Expression_Profiling_of_Archival_Tumors_for_Long-term_Health_Studies/22447449/1/files/39898485.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"},{"id":"pmh:oai:figshare.com:article/22447449","doi":null,"is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Supplementary_Methods_from_Expression_Profiling_of_Archival_Tumors_for_Long-term_Health_Studies/22447449","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1158/1078-0432.22447449.v1","doi":"https://doi.org/10.1158/1078-0432.22447449.v1","is_oa":true,"landing_page_url":"http://dx.doi.org/10.1158/1078-0432.22447449.v1","pdf_url":"https://aacr.figshare.com/articles/journal_contribution/Supplementary_Methods_from_Expression_Profiling_of_Archival_Tumors_for_Long-term_Health_Studies/22447449/1/files/39898485.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"American Association for Cancer Research","raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.9391000270843506,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4361904558.pdf","grobid_xml":"https://content.openalex.org/works/W4361904558.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1965301144","https://openalex.org/W1971804207","https://openalex.org/W1976974072","https://openalex.org/W1981293025","https://openalex.org/W1987745928","https://openalex.org/W2009671859","https://openalex.org/W2010446139","https://openalex.org/W2012908693","https://openalex.org/W2017727119","https://openalex.org/W2026349620","https://openalex.org/W2046257690","https://openalex.org/W2064854706","https://openalex.org/W2110065044","https://openalex.org/W2110546638","https://openalex.org/W2137211337","https://openalex.org/W2141009231","https://openalex.org/W2144366590","https://openalex.org/W2144458108","https://openalex.org/W2146457336"],"related_works":["https://openalex.org/W7098372797","https://openalex.org/W3014721553","https://openalex.org/W4361950421","https://openalex.org/W2135973238","https://openalex.org/W6884881085","https://openalex.org/W2467804754","https://openalex.org/W4244406655","https://openalex.org/W2129346062","https://openalex.org/W2504900032","https://openalex.org/W7098064605"],"abstract_inverted_index":{"Methods":[0],"Patient":[1],"SamplesFor":[2],"the":[3,75,82,91,110,118,193],"NHS/HPFS":[4,76],"CRC":[5,77],"study,":[6],"we":[7],"collected":[8],"paraffin-embedded":[9],"tissue":[10],"blocks":[11],"from":[12,117],"hospitals":[13],"where":[14],"participants":[15],"underwent":[16],"tumor":[17,27,85,107,205],"resections(1).Tissue":[18],"microarray":[19],"(TMA)":[20],"was":[21],"constructed":[22],"as":[23,44,159,165],"previously":[24],"described(2).Analyses":[25],"of":[26,84,104,115,122,178,202],"characteristics":[28],"(protein":[29],"expression":[30],"by":[31,167],"immunohistochemistry,":[32],"IHC":[33],"or":[34],"DNA":[35],"methylation":[36],"and":[37,62,141,154,171,184,206,215],"microsatellite":[38,64],"instability":[39,65],"(MSI)":[40],"analyses)":[41],"were":[42,99,145,189,209],"described":[43],"follows:":[45],"CCND1(3);":[46],"CDX2(4);":[47],"CHFR(5);":[48],"FASN(6);":[49],"HIC1(5);":[50],"HIF1A(7);":[51],"IGF2":[52],"differentially":[53],"methylated":[54],"region":[55],"(DMR0)":[56],"methylation(8);":[57],"IGFBP3(5);":[58],"MGMT":[59],"promoter":[60],"hypermethylation(9)":[61],"IHC(10);":[63],"(MSI)(11);":[66],"MLH1(9);":[67],"MSH2(12);":[68],"PTGER2(13);":[69],"PTGS2(14);":[70],"SIRT1(15);":[71],"VDR(16);":[72],"WRN(5).Similarly":[73],"to":[74],"samples,":[78,199],"a":[79,102,150,155,168,200],"pathologist":[80],"supervised":[81],"enrichment":[83],"cells":[86],"via":[87],"manual":[88],"micro-dissection":[89],"for":[90,101],"BC/A":[92],"series.The":[93],"Illumina":[94],"DASL\u00ae":[95],"HumanRef8":[96],"v3":[97],"chips":[98],"used":[100],"series":[103,177],"9":[105],"archival":[106],"samples":[108,116,144],"termed":[109],"'Autopsy'":[111],"set,":[112],"which":[113],"consists":[114],"following":[119],"organs":[120],"(year":[121],"embedding":[123],"in":[124,147,175,211,219],"parenthesis);":[125],"liver":[126],"(1972,":[127],"1981),":[128],"lymph":[129,186],"node":[130,187],"(1981),":[131,140],"lung":[132],"(1981,":[133],"1989,":[134],"1993),":[135],"chest":[136],"wall":[137],"(1960),":[138],"breast":[139,182],"spleen":[142],"(1981).These":[143],"run":[146,191,210,218],"duplicate,":[148,212],"with":[149,213],"duplicate":[151],"negative":[152,214],"control":[153],"positive":[156,160,216],"(internally":[157],"regarded":[158],"based":[161],"on":[162,192],"previous":[163],"success":[164],"determined":[166],"high":[169],"P95Grn":[170],"corresponding":[172],"probe":[173],"success)":[174],"triplicate.A":[176],"primary":[179],"invasive":[180],"lobular":[181],"cancers":[183],"matched":[185,204],"metastases":[188],"also":[190],"same":[194],"chips.Of":[195],"these":[196],"66":[197],"patient":[198],"sub-series":[201],"12":[203],"metastasis":[207],"pairs":[208],"controls":[217],"triplicate.":[220]},"counts_by_year":[],"updated_date":"2026-11-01T11:40:01.658920","created_date":"2023-04-05T00:00:00"}
