{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,13]],"date-time":"2026-11-13T09:59:05Z","timestamp":1794563945955,"version":"4.9.1"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T00:00:00Z","timestamp":1558051200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T00:00:00Z","timestamp":1558051200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Fluorescent <jats:italic>in situ<\/jats:italic> hybridization (FISH) assays to detect gene amplification such as HER2 or MET in tumors are used for prognosis evaluation and selection of targeted therapies. Although FISH guidelines recommended 4~6 \u03bcm FFPE sections, many laboratories use 2~3 \u03bcm sections, which is a common practice for H&amp;E staining and immunohistochemistry. A former study concluded that section thickness did not affect FISH results. We found, however, that thinner FFPE sections may lead to false negative results for gene amplification. A mathematic model was constructed and cell-line based controls with known gene copy number were prepared, and the model had a reasonable fit with the experimental data. The model revealed that even when counting the apparently full-sized nuclear images, many of them have partial volumes, which leads to under-estimation of gene copy number. Therefore, improperly thinner sections are prone to give false negative results, and thicker sections give a better approximation to the true value. The discrepancy between this and the former study was discussed. In summary, the model applies generally to FISH\/ISH detection of gene copy number, and section thickness is an important parameter to control for precision medicine research, assay development, clinical trials and daily practice in pathology laboratory.<\/jats:p>","DOI":"10.1038\/s41598-019-44015-7","type":"journal-article","created":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T10:04:37Z","timestamp":1558087477000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["A model for the impact of FFPE section thickness on gene copy number measurement by FISH"],"prefix":"10.1038","volume":"9","author":[{"given":"Jiyan","family":"Yu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pu","family":"Xue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juanfen","family":"Mo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liangye","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manxiang","family":"Yin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yueyan","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yi","family":"Bao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Ding","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,5,17]]},"reference":[{"key":"44015_CR1","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.5858\/arpa.2016-0331-CP","volume":"140","author":"AN Bartley","year":"2016","unstructured":"Bartley, A. N. et al. HER2 Testing and Clinical Decision Making in Gastroesophageal Adenocarcinoma: Guideline From the College of American Pathologists, American Society for Clinical Pathology, and American Society of Clinical Oncology. Arch Pathol Lab Med 140, 1345\u20131363, https:\/\/doi.org\/10.5858\/arpa.2016-0331-CP (2016).","journal-title":"Arch Pathol Lab Med"},{"key":"44015_CR2","doi-asserted-by":"publisher","first-page":"3997","DOI":"10.1200\/JCO.2013.50.9984","volume":"31","author":"AC Wolff","year":"2013","unstructured":"Wolff, A. C. et al. Recommendations for human epidermal growth factor receptor 2 testing in breast cancer: American Society of Clinical Oncology\/College of American Pathologists clinical practice guideline update. J Clin Oncol 31, 3997\u20134013, https:\/\/doi.org\/10.1200\/JCO.2013.50.9984 (2013).","journal-title":"J Clin Oncol"},{"key":"44015_CR3","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1200\/JCO.2006.09.2775","volume":"25","author":"AC Wolff","year":"2007","unstructured":"Wolff, A. C. et al. American Society of Clinical Oncology\/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. J Clin Oncol 25, 118\u2013145, https:\/\/doi.org\/10.1200\/JCO.2006.09.2775 (2007).","journal-title":"J Clin Oncol"},{"key":"44015_CR4","doi-asserted-by":"publisher","first-page":"2105","DOI":"10.1200\/JCO.2018.77.8738","volume":"36","author":"AC Wolff","year":"2018","unstructured":"Wolff, A. C. et al. Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology\/College of American Pathologists Clinical Practice Guideline Focused Update. J Clin Oncol 36, 2105\u20132122, https:\/\/doi.org\/10.1200\/JCO.2018.77.8738 (2018).","journal-title":"J Clin Oncol"},{"key":"44015_CR5","doi-asserted-by":"publisher","first-page":"1681","DOI":"10.1093\/annonc\/mdu145","volume":"25","author":"KM Kerr","year":"2014","unstructured":"Kerr, K. M. et al. Second ESMO consensus conference on lung cancer: pathology and molecular biomarkers for non-small-cell lung cancer. Ann Oncol 25, 1681\u20131690, https:\/\/doi.org\/10.1093\/annonc\/mdu145 (2014).","journal-title":"Ann Oncol"},{"key":"44015_CR6","doi-asserted-by":"publisher","first-page":"298","DOI":"10.1093\/annonc\/mdn635","volume":"20","author":"F Cappuzzo","year":"2009","unstructured":"Cappuzzo, F. et al. MET increased gene copy number and primary resistance to gefitinib therapy in non-small-cell lung cancer patients. Ann Oncol 20, 298\u2013304, https:\/\/doi.org\/10.1093\/annonc\/mdn635 (2009).","journal-title":"Ann Oncol"},{"key":"44015_CR7","doi-asserted-by":"publisher","first-page":"1667","DOI":"10.1200\/JCO.2008.19.1635","volume":"27","author":"F Cappuzzo","year":"2009","unstructured":"Cappuzzo, F. et al. Increased MET gene copy number negatively affects survival of surgically resected non-small-cell lung cancer patients. J Clin Oncol 27, 1667\u20131674, https:\/\/doi.org\/10.1200\/JCO.2008.19.1635 (2009).","journal-title":"J Clin Oncol"},{"key":"44015_CR8","doi-asserted-by":"publisher","first-page":"e59","DOI":"10.1016\/j.jtho.2015.12.102","volume":"11","author":"Y Zhang","year":"2016","unstructured":"Zhang, Y. et al. Response to Crizotinib Observed in Lung Adenocarcinoma with MET Copy Number Gain but without a High-Level MET\/CEP7 Ratio, MET Overexpression, or Exon 14 Splicing Mutations. J Thorac Oncol 11, e59\u2013e62, https:\/\/doi.org\/10.1016\/j.jtho.2015.12.102 (2016).","journal-title":"J Thorac Oncol"},{"key":"44015_CR9","doi-asserted-by":"publisher","first-page":"1061","DOI":"10.1002\/cncr.30437","volume":"123","author":"DV Catenacci","year":"2017","unstructured":"Catenacci, D. V. et al. MET tyrosine kinase receptor expression and amplification as prognostic biomarkers of survival in gastroesophageal adenocarcinoma. Cancer 123, 1061\u20131070, https:\/\/doi.org\/10.1002\/cncr.30437 (2017).","journal-title":"Cancer"},{"key":"44015_CR10","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.humpath.2017.04.002","volume":"64","author":"WY Kim","year":"2017","unstructured":"Kim, W. Y. et al. The gene copy number of c-MET has a significant impact on progression-free survival in Korean patients with ovarian carcinoma. Hum Pathol 64, 98\u2013105, https:\/\/doi.org\/10.1016\/j.humpath.2017.04.002 (2017).","journal-title":"Hum Pathol"},{"key":"44015_CR11","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1097\/JTO.0000000000000442","volume":"10","author":"F Cappuzzo","year":"2015","unstructured":"Cappuzzo, F. et al. Phase II study of afatinib, an irreversible ErbB family blocker, in EGFR FISH-positive non-small-cell lung cancer. J Thorac Oncol 10, 665\u2013672, https:\/\/doi.org\/10.1097\/JTO.0000000000000442 (2015).","journal-title":"J Thorac Oncol"},{"key":"44015_CR12","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/S1470-2045(17)30694-0","volume":"19","author":"RS Herbst","year":"2018","unstructured":"Herbst, R. S. et al. Cetuximab plus carboplatin and paclitaxel with or without bevacizumab versus carboplatin and paclitaxel with or without bevacizumab in advanced NSCLC (SWOG S0819): a randomised, phase 3 study. Lancet Oncol 19, 101\u2013114, https:\/\/doi.org\/10.1016\/S1470-2045(17)30694-0 (2018).","journal-title":"Lancet Oncol"},{"key":"44015_CR13","doi-asserted-by":"publisher","first-page":"1221","DOI":"10.1097\/01.pas.0000165528.78945.95","volume":"29","author":"E Downs-Kelly","year":"2005","unstructured":"Downs-Kelly, E. et al. The influence of polysomy 17 on HER2 gene and protein expression in adenocarcinoma of the breast: a fluorescent in situ hybridization, immunohistochemical, and isotopic mRNA in situ hybridization study. Am J Surg Pathol 29, 1221\u20131227 (2005).","journal-title":"Am J Surg Pathol"},{"key":"44015_CR14","doi-asserted-by":"publisher","first-page":"4393","DOI":"10.1158\/1078-0432.CCR-04-2256","volume":"11","author":"Y Ma","year":"2005","unstructured":"Ma, Y. et al. Polysomy 17 in HER-2\/neu status elaboration in breast cancer: effect on daily practice. Clin Cancer Res 11, 4393\u20134399, https:\/\/doi.org\/10.1158\/1078-0432.CCR-04-2256 (2005).","journal-title":"Clin Cancer Res"},{"key":"44015_CR15","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1136\/jcp.2007.050336","volume":"61","author":"CL Hyun","year":"2008","unstructured":"Hyun, C. L. et al. The effect of chromosome 17 polysomy on HER-2\/neu status in breast cancer. J Clin Pathol 61, 317\u2013321, https:\/\/doi.org\/10.1136\/jcp.2007.050336 (2008).","journal-title":"J Clin Pathol"},{"key":"44015_CR16","doi-asserted-by":"publisher","first-page":"12959","DOI":"10.18632\/oncotarget.24430","volume":"9","author":"L Fang","year":"2018","unstructured":"Fang, L. et al. MET amplification assessed using optimized FISH reporting criteria predicts early distant metastasis in patients with non-small cell lung cancer. Oncotarget 9, 12959\u201312970, https:\/\/doi.org\/10.18632\/oncotarget.24430 (2018).","journal-title":"Oncotarget"},{"key":"44015_CR17","doi-asserted-by":"publisher","first-page":"e0181527","DOI":"10.1371\/journal.pone.0181527","volume":"12","author":"S Al-Saad","year":"2017","unstructured":"Al-Saad, S. et al. The impact of MET, IGF-1, IGF1R expression and EGFR mutations on survival of patients with non-small-cell lung cancer. PLoS One 12, e0181527, https:\/\/doi.org\/10.1371\/journal.pone.0181527 (2017).","journal-title":"PLoS One"},{"key":"44015_CR18","doi-asserted-by":"publisher","first-page":"753","DOI":"10.1016\/j.jmoldx.2016.05.008","volume":"18","author":"CJ Lih","year":"2016","unstructured":"Lih, C. J. et al. Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods. J Mol Diagn 18, 753\u2013761, https:\/\/doi.org\/10.1016\/j.jmoldx.2016.05.008 (2016).","journal-title":"J Mol Diagn"},{"key":"44015_CR19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.bdq.2016.02.001","volume":"8","author":"HJ He","year":"2016","unstructured":"He, H. J. et al. Development of NIST standard reference material 2373: Genomic DNA standards for HER2 measurements. Biomol Detect Quantif 8, 1\u20138, https:\/\/doi.org\/10.1016\/j.bdq.2016.02.001 (2016).","journal-title":"Biomol Detect Quantif"},{"key":"44015_CR20","doi-asserted-by":"publisher","first-page":"1307","DOI":"10.1373\/clinchem.2008.120576","volume":"55","author":"Y Xiao","year":"2009","unstructured":"Xiao, Y., Gao, X., Maragh, S., Telford, W. G. & Tona, A. Cell lines as candidate reference materials for quality control of ERBB2 amplification and expression assays in breast cancer. Clin Chem 55, 1307\u20131315, https:\/\/doi.org\/10.1373\/clinchem.2008.120576 (2009).","journal-title":"Clin Chem"},{"key":"44015_CR21","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1016\/j.ymeth.2010.08.012","volume":"52","author":"A Babic","year":"2010","unstructured":"Babic, A. et al. The impact of pre-analytical processing on staining quality for H&E, dual hapten, dual color in situ hybridization and fluorescent in situ hybridization assays. Methods 52, 287\u2013300, https:\/\/doi.org\/10.1016\/j.ymeth.2010.08.012 (2010).","journal-title":"Methods"},{"key":"44015_CR22","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1097\/JTO.0b013e3181ce3d1d","volume":"5","author":"H Go","year":"2010","unstructured":"Go, H. et al. High MET gene copy number leads to shorter survival in patients with non-small cell lung cancer. J Thorac Oncol 5, 305\u2013313, https:\/\/doi.org\/10.1097\/JTO.0b013e3181ce3d1d (2010).","journal-title":"J Thorac Oncol"},{"key":"44015_CR23","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1038\/s41576-018-0063-5","volume":"20","author":"A Buchwalter","year":"2019","unstructured":"Buchwalter, A., Kaneshiro, J. M. & Hetzer, M. W. Coaching from the sidelines: the nuclear periphery in genome regulation. Nat Rev Genet 20, 39\u201350, https:\/\/doi.org\/10.1038\/s41576-018-0063-5 (2019).","journal-title":"Nat Rev Genet"},{"key":"44015_CR24","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1007\/s00418-015-1346-y","volume":"144","author":"C Lemaitre","year":"2015","unstructured":"Lemaitre, C. & Bickmore, W. A. Chromatin at the nuclear periphery and the regulation of genome functions. Histochem Cell Biol 144, 111\u2013122, https:\/\/doi.org\/10.1007\/s00418-015-1346-y (2015).","journal-title":"Histochem Cell Biol"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-44015-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-44015-7","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-44015-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T09:47:39Z","timestamp":1671270459000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-019-44015-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,5,17]]},"references-count":24,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2019,12]]}},"alternative-id":["44015"],"URL":"https:\/\/doi.org\/10.1038\/s41598-019-44015-7","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,17]]},"assertion":[{"value":"11 November 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 May 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"17 May 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing Interests"}}],"article-number":"7518"}}