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DNA assembly\u2010based barcoding and amplification technologies are currently being actively explored for RNA in situ analysis. However, these modular integrated DNA assembly processes are inevitably accompanied with false positive signals caused by unexpected misassembly. Completely avoiding this phenomenon through simple and universal methods is challenging. Here, a novel dual\u2010input to dual\u2010output in situ analysis paradigm is proposed, aiming to improve target specificity through co\u2010recognition (dual\u2010input) and to eliminate false positive misassembly through fluorescent signal co\u2010localization (dual\u2010output). Based on this paradigm, Gemini molecular assembly co\u2010localization (GOAL) in situ imaging system is launched to accurately distinguish the fusion gene subtypes associated with chronic myeloid leukemia (CML), and to precisely report the proportion of minimum residual cancer cells in clinical samples by intelligent co\u2010localization counting and sorting. GOAL achieves highly sensitive and accurate genotyping recognition of 0.01% CML tumor cells and realizes fully automatic rapid diagnosis with a customized Intelligent Cell Image Sorter\u00a0(iCis). iCis\u2010assisted GOAL represents an innovative and versatile molecular toolkit for accurate, rapid, user\u2010friendly, and professional\u2010independent profiling of cancer cells with RNA small fragment aberrances, providing efficient clinical decision support for disease diagnosis.<\/jats:p>","DOI":"10.1002\/smtd.202500194","type":"journal-article","created":{"date-parts":[[2025,4,14]],"date-time":"2025-04-14T07:10:21Z","timestamp":1744614621000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Gemini Molecular Assembly Colocalization (GOAL): Accurate and Efficient Fusion Genotyping for Chronic Myeloid Leukemia Intelligent Diagnosis"],"prefix":"10.1002","volume":"9","author":[{"given":"Yuanyuan","family":"Huang","sequence":"first","affiliation":[{"name":"The Center for Clinical Molecular Medical Detection The First Affiliated Hospital of Chongqing Medical University  Chongqing 400016 P. 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