Background Investigating the safe range of orthodontic tooth movement is essential for maintaining oral and maxillofacial stability posttreatment. Although clear aligners rely on pretreatment digital models, their effect on periodontal hard tissues remains uncertain. By integrating cone beam computed tomography–derived cervical and root data with crown data from digital intraoral scans, a 3D fusion model may enhance precision and safety. Objective This study aims to construct a 3D fusion model based on artificial intelligence software that matches cone beam computed tomography and intraoral scanning data using the Andrews’ Six Element standard. The model will be used to assess the 3D effects of clear aligners on tooth movement, to provide a reference for the design of pretreatment target positions. Methods Between May 2022 and May 2024, a total of 320 patients who completed clear aligner therapy at our institution were screened; 136 patients (aged 13-35 years, fully erupted permanent dentition and periodontal pocket depth <3 mm) met the criteria. Baseline (“simulation”) and posttreatment (“fusion”) models were compared. Outcomes included upper core discrepancy (UCD), upper incisors anteroposterior discrepancy (UAP), lower Spee curve deep discrepancy (LSD), upper anterior teeth width discrepancy (UAW), upper canine width discrepancy (UCW), upper molar width discrepancy (UMW), and total scores. Subanalyses examined sex, age stage (adolescent vs adult), and treatment method (extraction vs nonextraction). Results The study was funded in May 2022, with data collection beginning the same month and continuing until May 2024. Of 320 initial participants, 136 met the inclusion criteria. Data analysis is ongoing, and final results are expected by late 2024. Among the 136 participants, 90 (66%) were female, 46 (34%) were male, 64 (47%) were adolescents, 72 (53%) were adults, 38 (28%) underwent extraction, and 98 (72%) did not. Total scores did not differ significantly by sex (mean difference 0.01, 95% CI –0.13 to 0.15; P=.85), age stage (mean difference 0.03, 95% CI –0.10 to 0.17; P=.60), or treatment method (mean difference 0.07, 95% CI –0.22 to 0.07; P=.32). No significant differences were found in UCD (mean difference 0.001, 95% CI –0.02 to 0.01; P=.90) or UAP (mean difference 0.01, 95% CI –0.03 to 0.00; P=.06) by treatment method. However, adolescents exhibited smaller differences in UCD, UAW, UCW, and UMW yet larger differences in UAP and LSD (df=134; P<.001). Extraction cases showed smaller LSD, UAW, and UCW but larger UMW differences compared with nonextraction (df=134; P<.001). Conclusions The 3D fusion model provides a reliable clinical reference for target position design and treatment outcome evaluation in clear aligner systems. The construction and application of a 3D fusion model in clear aligner orthodontics represent a significant leap forward, offering substantial clinical benefits while establishing a new standard for precision, personalization, and evidence-based treatment planning in the field. Trial Registration Chinese Clinical Trial Registry ChiCTR2400094304, https://www.chictr.org.cn/hvshowproject.html?id=266090&v=1.0
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