Validation of Histopathology-Based Deep Learning Algorithms for Detection of Actionable Non-Small Cell Lung Cancer Biomarkers

Validation of Histopathology-Based Deep Learning Algorithms for Detection of Actionable Non-Small Cell Lung Cancer Biomarkers | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Validation of Histopathology-Based Deep Learning Algorithms for Detection of Actionable Non-Small Cell Lung Cancer Biomarkers Christian Rolfo, Efrat Ofek, Yoash Barak, Jonathan Weidenfeld, and 19 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-6675282/v1 This work is licensed under a CC BY 4.0 License Status: Published Journal Publication published 20 Jan, 2026 Read the published version in npj Precision Oncology → Version 1 posted 15 You are reading this latest preprint version Abstract Non-small cell lung cancer (NSCLC) patient management relies on molecular analysis to determine eligibility for targeted therapy. Furthermore, neoadjuvant immunotherapy is primarily suitable in the absence of specific genomic alterations. However, significant challenges such as suboptimal molecular testing and patients not receiving the most appropriate treatment remain. Here, we present AI classifiers for the identification of EGFR , ALK , BRAF and MET alterations directly from H&E-stained tissue using CanvOI 1.1, a digital pathology foundation model. Their performance was evaluated on an independent validation dataset of 968 NSCLC samples. The classifiers achieved AUCs of 0.87 for EGFR , 0.96 for ALK , 0.88 for BRAF and 0.83 for MET . Moreover, they demonstrated high accuracy in identifying cases lacking alterations. Our results highlight the potential of deep-learning tools for the detection of NSCLC biomarkers and specifically the identification of tumors without EGFR or ALK driver alterations, supporting more informed clinical decision-making. Health sciences/Biomarkers Health sciences/Molecular medicine Health sciences/Oncology Full Text Additional Declarations Competing interest reported. C.R. reports personal fees for advisory board membership from Novocure; institutional fees for advisory board membership from AstraZeneca, Imagene, MedStar, Amgem, Boeringer-Ingelheim , Hoffmann-La Roche Ltd, Janssen Pharmaceutical, NeoGenomics , Pfizer, Inc. and Regeneron; Research collaboration non remunerated: Guardant, Foundation One; institutional fees as an invited speaker from COR2ED, HPM education IDEOlogy Merck and Roche, OneCell Dx; non-renumerated leadership roles as a scientific board member for the European School of Oncology (ESO), Past Chair on the educational committee for the International Association for Study of Lung Cancer (IASLC), President for the International Society of Liquid Biopsy (ISLB) and Educational Chair for the Oncology Latin American Association (OLA); a renumerated role as Editor in Chief for Critical Reviews in Oncology Hematology (CROH); a non-renumerated role as ESMO Faculty Group/Speciality and Faculty Coordinator for metastatic non-small cell lung cancer for European Society for Medical Oncology (ESMO); non-renumerated roles as : Scientific Board Member at ESO (European School of Oncology), External advisor Board member of Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), External Advisor of the School of Public Health, University of Granada, Spain, Scientific Committee of the Fondazione Siciliana di Oncologia, and non-renumerated analysis of liquid biopsies in a lung cancer trial for Guardant Health. N.P. is advisor for Imagene and has stock options as well as an advisor and has honorarium and research with AstraZeneca, Bayer, Boehringer Ingelheim, Bristol-Myers Squibb, Eli Lilly, Imagine, Gaurdant360, Merck, MSD, Novartis, Pfizer, Roche, Renium and Takeda. D.U. declares consulting services for Medison Pharma, Amgen GmBH, Merck Sharp & Dohme, and declares honoraria for Merck Sharp & Dohme, AstraZeneca, Pfizer, Megaphram, BMS, Roche, Takeda and J-C Healthcare. J.B. declared receiving research funding from Immunai, OncoHost, MSD, AstraZeneca, Roche and AbbVie, consulting services for AbbVie, Amgen, AstraZeneca, Bayer, Beigene, Janssen, MSD, Merck-Serono, Medison, Roche and Takeda, honoraria from BMS, Medison and Pfizer and holding roles in Committee IASLC and Lung Ambition Israel leadership. D.R.B received research support from Imagene, C.M. was reimbursed by Imagene AI for attending a conference. D.H. received payment to institution for lectures from AstraZeneca, MSD, Merck, Roche, Medison, BMS and Sanofi. J.Z. is a cofounder and a stockholder of Imagene, A.A., N.P.Y., A.D., I.G. are currently, or were formerly, employees of Imagene and have stock options. E.O., Y.B., J.W., R.I.H., F.D., Y.M., A.L., J.S.C., R.Y. and C.A., declare no conflict of interest. Cite Share Download PDF Status: Published Journal Publication published 20 Jan, 2026 Read the published version in npj Precision Oncology → Version 1 posted Editorial decision: Revision requested 08 Sep, 2025 Reviews received at journal 28 Aug, 2025 Reviews received at journal 26 Aug, 2025 Reviewers agreed at journal 25 Aug, 2025 Reviews received at journal 20 Aug, 2025 Reviewers agreed at journal 20 Aug, 2025 Reviewers agreed at journal 20 Aug, 2025 Reviews received at journal 16 Aug, 2025 Reviewers agreed at journal 31 Jul, 2025 Reviewers agreed at journal 31 Jul, 2025 Reviewers agreed at journal 31 Jul, 2025 Reviewers invited by journal 10 Jun, 2025 Editor assigned by journal 10 Jun, 2025 Submission checks completed at journal 20 May, 2025 First submitted to journal 15 May, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-6675282","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":469410225,"identity":"aaf71f0f-8da0-4cd2-b981-45f4f00f1d14","order_by":0,"name":"Christian 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C.R. reports personal fees for advisory board membership from Novocure; institutional fees for advisory board membership from AstraZeneca, Imagene, MedStar, Amgem, Boeringer-Ingelheim , Hoffmann-La Roche Ltd, Janssen Pharmaceutical, NeoGenomics , Pfizer, Inc. and Regeneron; Research collaboration non remunerated: Guardant, Foundation One; institutional fees as an invited speaker from COR2ED, HPM education IDEOlogy Merck and Roche, OneCell Dx; non-renumerated leadership roles as a scientific board member for the European School of Oncology (ESO), Past Chair on the educational committee for the International Association for Study of Lung Cancer (IASLC), President for the International Society of Liquid Biopsy (ISLB) and Educational Chair for the Oncology Latin American Association (OLA); a renumerated role as Editor in Chief for Critical Reviews in Oncology Hematology (CROH); a non-renumerated role as ESMO Faculty Group/Speciality and Faculty Coordinator for metastatic non-small cell lung cancer for European Society for Medical Oncology (ESMO); non-renumerated roles as : Scientific Board Member at ESO (European School of Oncology), External advisor Board member of Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), External Advisor of the School of Public Health, University of Granada, Spain, Scientific Committee of the Fondazione Siciliana di Oncologia, and non-renumerated analysis of liquid biopsies in a lung cancer trial for Guardant Health.\nN.P. is advisor for Imagene and has stock options as well as an advisor and has honorarium and research with AstraZeneca, Bayer, Boehringer Ingelheim, Bristol-Myers Squibb, Eli Lilly, Imagine, Gaurdant360, Merck, MSD, Novartis, Pfizer, Roche, Renium and Takeda. D.U. declares consulting services for Medison Pharma, Amgen GmBH, Merck Sharp \u0026 Dohme, and declares honoraria for Merck Sharp \u0026 Dohme, AstraZeneca, Pfizer, Megaphram, BMS, Roche, Takeda and J-C Healthcare. J.B. declared receiving research funding from Immunai, OncoHost, MSD, AstraZeneca, Roche and AbbVie, consulting services for AbbVie, Amgen, AstraZeneca, Bayer, Beigene, Janssen, MSD, Merck-Serono, Medison, Roche and Takeda, honoraria from BMS, Medison and Pfizer and holding roles in Committee IASLC and Lung Ambition Israel leadership. D.R.B received research support from Imagene, C.M. was reimbursed by Imagene AI for attending a conference. D.H. received payment to institution for lectures from AstraZeneca, MSD, Merck, Roche, Medison, BMS and Sanofi. J.Z. is a cofounder and a stockholder of Imagene, A.A., N.P.Y., A.D., I.G. are currently, or were formerly, employees of Imagene and have stock options. E.O., Y.B., J.W., R.I.H., F.D., Y.M., A.L., J.S.C., R.Y. and C.A., declare no conflict of interest.","formattedTitle":"Validation of Histopathology-Based Deep Learning Algorithms for Detection of Actionable Non-Small Cell Lung Cancer Biomarkers","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"npj-precision-oncology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"npjprecisiononcology","sideBox":"Learn more about [npj Precision Oncology](http://www.nature.com/npjprecisiononcology/)","snPcode":"41698","submissionUrl":"https://submission.springernature.com/new-submission/41698/3","title":"npj Precision Oncology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"NPJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-6675282/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-6675282/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eNon-small cell lung cancer (NSCLC) patient management relies on molecular analysis to determine eligibility for targeted therapy. Furthermore, neoadjuvant immunotherapy is primarily suitable in the absence of specific genomic alterations. However, significant challenges such as suboptimal molecular testing and patients not receiving the most appropriate treatment remain. Here, we present AI classifiers for the identification of \u003cem\u003eEGFR\u003c/em\u003e, \u003cem\u003eALK\u003c/em\u003e, \u003cem\u003eBRAF\u003c/em\u003e and \u003cem\u003eMET\u003c/em\u003e alterations directly from H\u0026amp;E-stained tissue using CanvOI 1.1, a digital pathology foundation model. Their performance was evaluated on an independent validation dataset of 968 NSCLC samples. The classifiers achieved AUCs of 0.87 for \u003cem\u003eEGFR\u003c/em\u003e, 0.96 for \u003cem\u003eALK\u003c/em\u003e, 0.88 for \u003cem\u003eBRAF\u003c/em\u003e and 0.83 for \u003cem\u003eMET\u003c/em\u003e. Moreover, they demonstrated high accuracy in identifying cases lacking alterations. Our results highlight the potential of deep-learning tools for the detection of NSCLC biomarkers and specifically the identification of tumors without \u003cem\u003eEGFR\u003c/em\u003e or \u003cem\u003eALK\u003c/em\u003e driver alterations, supporting more informed clinical decision-making.\u003c/p\u003e","manuscriptTitle":"Validation of Histopathology-Based Deep Learning Algorithms for Detection of Actionable Non-Small Cell Lung Cancer Biomarkers","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-06-12 16:23:51","doi":"10.21203/rs.3.rs-6675282/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-09-08T16:10:00+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-28T10:16:33+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-26T14:03:35+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"276606794614624897382574688511742817482","date":"2025-08-25T10:46:12+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-20T11:17:41+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"131063305723599863470452486209146758405","date":"2025-08-20T09:32:09+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"73844614454446743699226046969855345322","date":"2025-08-20T07:14:23+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-08-16T04:51:32+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"5727882844169599588099333937635530653","date":"2025-07-31T18:46:37+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"162929546693983747362280363688754143554","date":"2025-07-31T17:36:40+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"134461092425511386175230266008765907578","date":"2025-07-31T17:28:31+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-06-10T16:23:02+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-06-10T13:34:01+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-05-20T05:54:48+00:00","index":"","fulltext":""},{"type":"submitted","content":"npj Precision Oncology","date":"2025-05-15T19:26:44+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"npj-precision-oncology","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"npjprecisiononcology","sideBox":"Learn more about [npj Precision Oncology](http://www.nature.com/npjprecisiononcology/)","snPcode":"41698","submissionUrl":"https://submission.springernature.com/new-submission/41698/3","title":"npj Precision Oncology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"NPJ","inReviewEnabled":true,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"15a44362-ff08-4fb3-b8a6-41dba4adbb61","owner":[],"postedDate":"June 12th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"published-in-journal","subjectAreas":[{"id":49840403,"name":"Health sciences/Biomarkers"},{"id":49840404,"name":"Health sciences/Molecular medicine"},{"id":49840405,"name":"Health sciences/Oncology"}],"tags":[],"updatedAt":"2026-01-26T16:08:05+00:00","versionOfRecord":{"articleIdentity":"rs-6675282","link":"https://doi.org/10.1038/s41698-025-01267-z","journal":{"identity":"npj-precision-oncology","isVorOnly":false,"title":"npj Precision Oncology"},"publishedOn":"2026-01-20 15:57:02","publishedOnDateReadable":"January 20th, 2026"},"versionCreatedAt":"2025-06-12 16:23:51","video":"","vorDoi":"10.1038/s41698-025-01267-z","vorDoiUrl":"https://doi.org/10.1038/s41698-025-01267-z","workflowStages":[]},"version":"v1","identity":"rs-6675282","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-6675282","identity":"rs-6675282","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}