{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T10:49:59Z","timestamp":1792752599250,"version":"4.5.0"},"reference-count":50,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T00:00:00Z","timestamp":1673913600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":["acsjournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Cancer Cytopathology"],"published-print":{"date-parts":[[2023,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Rather than surgical resection, cytologic specimens are often used as first\u2010line clinical diagnostic procedures due to higher safety, speed, and cost\u2010effectiveness. Archival diagnostic cytology slides containing cancer can be equivalent to tissue biopsies for DNA mutation testing, but the accuracy of transcriptomic profiling by RNA sequencing (RNA\u2010seq) is less understood.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>This study compares the results from whole transcriptome RNA\u2010seq and a targeted RNA\u2010seq assay of stained cytology smears (CS) versus matched tumor tissue samples preserved fresh\u2010frozen (FF) and processed as formalin\u2010fixed paraffin\u2010embedded (FFPE) sections. Cellular cytology scrapes from all 11 breast cancers were fixed and stained using three common protocols: Carnoy's (CS_C) or 95% ethanol (CS_E) fixation and then Papanicolaou stain or air\u2010dried then methanol fixation and DiffQuik stain (CS_DQ). Agreement between samples was assessed using Lin's concordance correlation coefficient.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Library yield for CS_DQ was too low, therefore it was not sequenced. The distributions of concordance correlation coefficient of gene expression levels in comparison to FF were comparable between CS_C and CS_E, but expression of genes enriched in stroma was lower in cytosmear samples than in FF or FFPE. Six signatures showed similar concordance to FF for all methods and two were slightly worse in CS_C and CS_E. Genomic signatures were highly concordant using targeted RNA\u2010seq. The allele fraction of selected mutations calculated on cytosmear specimens was highly correlated with FF tissues using both RNA\u2010seq methods.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>RNA can be reliably extracted from cytology smears and is suitable for transcriptome profiling or mutation detection, except for signatures of tumor stroma.<\/jats:p><\/jats:sec>","DOI":"10.1002\/cncy.22679","type":"journal-article","created":{"date-parts":[[2023,1,17]],"date-time":"2023-01-17T23:20:15Z","timestamp":1673997615000},"page":"289-299","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Assessment of stained direct cytology smears of breast cancer for whole transcriptome and targeted messenger RNA sequencing"],"prefix":"10.1002","volume":"131","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2508-5736","authenticated-orcid":false,"given":"Michal","family":"Marczyk","sequence":"first","affiliation":[{"name":"Yale Cancer Center Yale School of Medicine  New Haven Connecticut USA"},{"name":"Department of Data Science and Engineering Silesian University of Technology  Gliwice Poland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chunxiao","family":"Fu","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"},{"name":"Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rosanna","family":"Lau","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"},{"name":"Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Du","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"},{"name":"Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander J.","family":"Trevarton","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"},{"name":"Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruno V.","family":"Sinn","sequence":"additional","affiliation":[{"name":"Institute of Pathology Charit\u00e9 Universit\u00e4tsmedizin Berlin  Berlin Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebekah E.","family":"Gould","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"},{"name":"Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lajos","family":"Pusztai","sequence":"additional","affiliation":[{"name":"Yale Cancer Center Yale School of Medicine  New Haven Connecticut USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christos","family":"Hatzis","sequence":"additional","affiliation":[{"name":"Yale Cancer Center Yale School of Medicine  New Haven Connecticut USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"William Fraser","family":"Symmans","sequence":"additional","affiliation":[{"name":"Department of Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"},{"name":"Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer Center  Houston Texas USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,1,17]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.21742"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.21476"},{"key":"e_1_2_8_4_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.21771"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.22381"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.21868"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.22134"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1136\/jclinpath\u20102021\u2010207825"},{"issue":"3","key":"e_1_2_8_9_1","first-page":"794","article-title":"The feasibility of using fine needle aspiration from primary breast cancers for cDNA microarray analyses","volume":"8","author":"Assersohn L","year":"2002","journal-title":"Clin Cancer Res"},{"issue":"7","key":"e_1_2_8_10_1","first-page":"2406","article-title":"Gene expression profiles obtained from fine\u2010needle aspirations of breast cancer reliably identify routine prognostic markers and reveal large\u2010scale molecular differences between estrogen\u2010negative and estrogen\u2010positive tumors","volume":"9","author":"Pusztai L","year":"2003","journal-title":"Clin Cancer Res"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncr.11435"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2011.593"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41523\u2010019\u20100111\u20100"},{"key":"e_1_2_8_14_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2016.10"},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u201015\u20101008"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1200\/po.17.00091"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12885\u2010019\u20106363\u20100"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/djr438"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gni054"},{"key":"e_1_2_8_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598\u2010018\u201024781\u20106"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12885\u2010021\u201007814\u20108"},{"key":"e_1_2_8_22_1","unstructured":"AndrewsS.FastQC: A Quality Control tool for High Throughput Sequence Data. Accessed April 30 2019.http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu170"},{"key":"e_1_2_8_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859\u2010016\u20100922\u2010z"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts356"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102105\u201012\u2010323"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms3612"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13058\u2010015\u20100530\u20102"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1158\/1078\u20100432.ccr\u201011\u20100926"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/415530a"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.1186\/gb\u20102010\u201011\u20102\u2010r18"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/jnci\/djj052"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0907011107"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa041588"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471\u20102164\u20109\u2010239"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv693"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp352"},{"key":"e_1_2_8_39_1","article-title":"Umap: Uniform manifold approximation and projection for dimension reduction","author":"McInnes L","year":"2018","journal-title":"arXiv:180203426"},{"key":"e_1_2_8_40_1","doi-asserted-by":"publisher","DOI":"10.2307\/2532051"},{"key":"e_1_2_8_41_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007"},{"key":"e_1_2_8_42_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2018.2858825"},{"key":"e_1_2_8_43_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw1092"},{"key":"e_1_2_8_44_1","doi-asserted-by":"publisher","DOI":"10.1101\/060012"},{"key":"e_1_2_8_45_1","doi-asserted-by":"publisher","DOI":"10.1002\/cncy.21699"},{"key":"e_1_2_8_46_1","doi-asserted-by":"publisher","DOI":"10.1089\/thy.2013.0278"},{"key":"e_1_2_8_47_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0203608"},{"key":"e_1_2_8_48_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jasc.2022.09.003"},{"key":"e_1_2_8_49_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2013.08.008"},{"key":"e_1_2_8_50_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaw0726"},{"key":"e_1_2_8_51_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2019.01.012"}],"container-title":["Cancer Cytopathology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cncy.22679","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/cncy.22679","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/acsjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/cncy.22679","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,12]],"date-time":"2025-10-12T08:53:23Z","timestamp":1760259203000},"score":1,"resource":{"primary":{"URL":"https:\/\/acsjournals.onlinelibrary.wiley.com\/doi\/10.1002\/cncy.22679"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,17]]},"references-count":50,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2023,5]]}},"alternative-id":["10.1002\/cncy.22679"],"URL":"https:\/\/doi.org\/10.1002\/cncy.22679","archive":["Portico"],"relation":{},"ISSN":["1934-662X","1934-6638"],"issn-type":[{"value":"1934-662X","type":"print"},{"value":"1934-6638","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,17]]},"assertion":[{"value":"2022-08-03","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-11-28","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-01-17","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}