{
    "abstract": "The advent of novel therapeutic agents has advanced biomarker characterization in non-small-cell lung cancer (NSCLC), driving increased adoption of next-generation sequencing (NGS) technologies for molecular testing. However, comprehensive data addressing the clinical utility of different NGS platforms for NSCLC remains limited.\nThis retrospective study analyzed real-world data from 478 Taiwanese NSCLC patients over five years, using the Oncomine Focus Assay (OFA) to assess genetic alterations. The evaluation focused on assay accuracy, limit of detection (LoD), sequencing performance, and the genetic landscape of NSCLC.\nThe OFA achieved an NGS success rate of 80.5% (385/478), with tumor cell percentage, specimen source and FFPE block age identified as key factors affecting success. Quality metrics demonstrated robust sequencing performance, including 97.0 \u00b1\u20099.6% on-target alignment, 94.7 \u00b1\u20096.4% uniformity, and \u2265\u2009500 \u00d7\u2009coverage for 98.0 \u00b1\u20096.6% of amplicons. Among the 385 patients analyzed, 86.8% (334/385) were found to harbor pathogenic or likely pathogenic variants, of which 78.4% (262/334) were SNVs/Indels, 41.6% (139/334) were CNVs, 2.7% (9/334) were exon skipping alterations, and 10.2% (34/334) were gene fusions. Actionable driver mutations included EGFR mutations (46.2%, 178/385), KRAS mutations (9.4%, 36/385), ERBB2 mutations (6.8%, 26/385), ALK fusions (4.4%, 17/385), MET exon 14 skipping (2.3%, 9/385), BRAF mutations (2.3%, 9/385), ROS1 and RET fusions (1.8%, 7/385 each), and NTRK1 fusions (0.5%, 2/385). Notably, KRAS G12 C mutation was detected in 2.8% (11/385) of cases.\nThis study demonstrates the robust performance of the OFA in identifying clinically relevant genetic alterations in NSCLC. The findings support its clinical utility in precision oncology and provide valuable insights into the genetic landscape of Asian NSCLC, enhancing personalized treatment strategies for lung cancer patients.",
    "authors": [
        {
            "affiliation": "Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan.\nDepartment of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.",
            "firstname": "Fang-Yu",
            "initials": "FY",
            "lastname": "Wang"
        },
        {
            "affiliation": "Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan.\nSchool of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.",
            "firstname": "Yi-Chen",
            "initials": "YC",
            "lastname": "Yeh"
        },
        {
            "affiliation": "Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan.",
            "firstname": "Shin-Ying",
            "initials": "SY",
            "lastname": "Lin"
        },
        {
            "affiliation": "Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan.",
            "firstname": "Shu-Ying",
            "initials": "SY",
            "lastname": "Wang"
        },
        {
            "affiliation": "Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan.",
            "firstname": "Paul Chih-Hsueh",
            "initials": "PC",
            "lastname": "Chen"
        },
        {
            "affiliation": "Department of Pathology and Precision Medicine Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan.",
            "firstname": "Teh-Ying",
            "initials": "TY",
            "lastname": "Chou"
        },
        {
            "affiliation": "Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, 201, Section 2, Shipai Road, Taipei, 11217, Taiwan. hlho5@vghtpe.gov.tw.\nDepartment of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan. hlho5@vghtpe.gov.tw.",
            "firstname": "Hsiang-Ling",
            "initials": "HL",
            "lastname": "Ho"
        }
    ],
    "conclusions": null,
    "copyrights": "\u00a9 2025. The Author(s).",
    "doi": "10.1186/s12885-025-14016-z",
    "journal": "BMC cancer",
    "keywords": [
        "Actionable driver mutations",
        "Non-small-cell lung cancer",
        "Real-world application",
        "Targeted next-generation sequencing"
    ],
    "methods": null,
    "publication_date": "2025-04-18",
    "pubmed_id": "40247220\n38230766\n27861270\n31378236\n29364287\n33316418\n34985916\n39121882\n34385702\n27184599\n35877212\n26936516\n39063150\n28161563\n34856311\n32445813\n34597339\n38100106\n38457233\n37612335\n38730622\n39947926\n29228562\n30105577\n29154853\n32669854\n38893636\n27993330\n34704312\n35629172\n30192857\n28812131\n33030786\n26222067\n29429887",
    "results": "The OFA achieved an NGS success rate of 80.5% (385/478), with tumor cell percentage, specimen source and FFPE block age identified as key factors affecting success. Quality metrics demonstrated robust sequencing performance, including 97.0 \u00b1\u20099.6% on-target alignment, 94.7 \u00b1\u20096.4% uniformity, and \u2265\u2009500 \u00d7\u2009coverage for 98.0 \u00b1\u20096.6% of amplicons. Among the 385 patients analyzed, 86.8% (334/385) were found to harbor pathogenic or likely pathogenic variants, of which 78.4% (262/334) were SNVs/Indels, 41.6% (139/334) were CNVs, 2.7% (9/334) were exon skipping alterations, and 10.2% (34/334) were gene fusions. Actionable driver mutations included EGFR mutations (46.2%, 178/385), KRAS mutations (9.4%, 36/385), ERBB2 mutations (6.8%, 26/385), ALK fusions (4.4%, 17/385), MET exon 14 skipping (2.3%, 9/385), BRAF mutations (2.3%, 9/385), ROS1 and RET fusions (1.8%, 7/385 each), and NTRK1 fusions (0.5%, 2/385). Notably, KRAS G12 C mutation was detected in 2.8% (11/385) of cases.",
    "title": "Real-world application of targeted next-generation sequencing for identifying molecular variants in Asian non-small-cell lung cancer.",
    "xml": "<Element 'PubmedArticle' at 0x788504155cb0>"
}