Journal of Molecular Diagnostics最新文献

{"title":"Performance Evaluation of a PCR/Nanopore Assay for Carrier Screening for Cystic Fibrosis, Spinal Muscular Atrophy, and Fragile X Syndrome.","authors":"Kendall E Martin, Fernanda Sábato, Jesse Lynch, Andrea Ferreira-Gonzalez, Elizabeth S Barrie","doi":"10.1016/j.jmoldx.2026.03.003","DOIUrl":"10.1016/j.jmoldx.2026.03.003","url":null,"abstract":"<p><p>Cystic fibrosis, spinal muscular atrophy, and fragile X syndrome are among the most common inherited genetic disorders, making carrier screening essential for identifying at-risk couples. Traditional screening often involves multiple workflows and may miss rare variants. Comprehensive sequencing offers broader variant detection across diverse populations. This study validated a PCR/Nanopore-based assay for comprehensive assessment of CFTR, SMN1/2, and FMR1. Samples included anonymized DNA from: whole blood (archival clinical samples; n = 53), cell lines (n = 19), and residual College of American Pathology proficiency testing material (n = 3). Using the AmplideX Nanopore Carrier Plus reagents, gene-specific PCR was performed, followed by barcoding and sequencing on MinION flow cells. Data were analyzed using the AmplideX One Reporter software. Results for SMN1/2 and FMR1 showed 100% concordance with orthogonal methods (PCR/fragment analysis laboratory-developed tests) and 97% for CFTR. These results were reproducible between interrun and intrarun repeats. Here, it is shown that the PCR/Nanopore-based assay is accurate and reproducible for identifying pathogenic variants and poly-T size in CFTR; SMN1/2 copy number and single-nucleotide polymorphism detection; and FMR1 CGG repeat sizes and AGG interruptions. The assay was also able to detect mosaicism as low as 10% for FMR1. This single workflow enables accurate, reproducible screening for multiple disorders, with the ability to identify more CFTR variants than traditional genotyping panels.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147576468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Diagnostic Utility of Single Nucleotide Polymorphism Microarray in Evaluating Pancreaticobiliary Brushing Specimens in Conjunction with Conventional Cytology.","authors":"Ahmet Alptekin, Ashis K Mondal, Ashutosh Vashisht, Vishakha Vashisht, Harmanpreet Singh, Daley Morera, Pankaj Ahluwalia, Jaspreet Farmaha, Sravankumar Kavuri, Nikhil Patel, Luis A Velasquez Zarate, Subbaramiah Sridhar, Viveksandeep T Chandrasekar, Ravindra Kolhe","doi":"10.1016/j.jmoldx.2026.03.002","DOIUrl":"10.1016/j.jmoldx.2026.03.002","url":null,"abstract":"<p><p>Bile duct brushings are noninvasive samplings of cells from the biliary tract for cytologic evaluation and are useful to diagnose pancreaticobiliary malignancies. Although specificity of cytology is satisfactory, sensitivity is inherently low because of challenging or absent morphologic features. Using molecular markers by incorporating fluorescence in situ hybridization has significantly improved sensitivity and diagnosis. To further advance the use of molecular markers, OncoScan microarray was used, which has genome-wide coverage and significantly higher resolution compared with fluorescence in situ hybridization. This study tested 128 pancreaticobiliary brushing specimens with OncoScan and compared them with cytology while using the biopsy of these patients as a reference. OncoScan was able to detect more malignant cases compared with cytology. In addition, the study identified potential molecular markers that have not been previously studied or reported. This study demonstrates that OncoScan is a useful additional diagnostic tool with cytology for pancreaticobiliary brushing specimens by improving the sensitivity to detect malignancies.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147576387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allele, Diplotype, and Phenotype Frequency Distribution of CYP2B6, CYP2C19, and CYP2D6 in the Han Population in North China","authors":"Yueyao Luan ,&nbsp;Qixuan Sun ,&nbsp;Yiyuan Wang ,&nbsp;Binliang Tong ,&nbsp;Liguang Duan ,&nbsp;Jiaqi Wang ,&nbsp;Yuhang Yan ,&nbsp;Chaoli Chen ,&nbsp;Yang Lun ,&nbsp;Jing Yu ,&nbsp;Yuanyuan Zhao ,&nbsp;Mengqiang Zhao ,&nbsp;Chunhua Zhou","doi":"10.1016/j.jmoldx.2025.11.007","DOIUrl":"10.1016/j.jmoldx.2025.11.007","url":null,"abstract":"<div><div>This large-scale retrospective study investigated the allele, diplotype, and phenotype frequencies of <em>CYP2B6</em>, <em>CYP2C19</em>, and <em>CYP2D6</em> in a Han Chinese population (<em>N</em> &gt; 10,000), using real-world genetic data from The First Hospital of Hebei Medical University, assessed between March 2021 and April 2025. Single-nucleotide polymorphism genotyping was performed using the Agena MassARRAY assay. <em>CYP2D6</em> copy number variation (CNV) was analyzed by TaqMan real-time quantitative PCR. The sample sizes were 9729 for <em>CYP2B6</em>, 11,479 for <em>CYP2C19</em>, and 11,315 for <em>CYP2D6</em>, all from the Han Chinese population. The high frequencies of alleles were <em>CYP2B6∗6</em> (16.19%), <em>CYP2C19∗2</em> (30.36%), and <em>CYP2D6∗10</em> (41.67%), with the most common diplotypes being <em>CYP2B6 ∗1/∗6</em> (23.65%), <em>CYP2C19 ∗1/∗2</em> (37.62%), and <em>CYP2D6 ∗1/∗10</em> (16.05%), respectively. At the phenotype level, normal metabolizer was most common for <em>CYP2B6</em> (57.86%) and <em>CYP2D6</em> (60.50%), whereas the intermediate metabolizer phenotype was noted for <em>CYP2C19</em> (44.77%). <em>CYP2D6</em> CNVs included zero copies (0.43%), one copy (13.64%), two copies (83.79%), three copies (2.11%), and more than three copies (0.03%). This large-scale, real-world study of a Northern Han Chinese cohort provides a valuable pharmacogenomic reference and demonstrates the necessity of integrating CNV analysis with single-nucleotide polymorphism genotyping to ensure accurate clinical phenotyping of <em>CYP2D6</em>.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 252-263"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenotypic POLE Variant Classification Identifies Patients Who May Have Favorable Prognosis and Benefit from Immunotherapy","authors":"Rachel B. Keller-Evans ,&nbsp;Zoe Fleischmann ,&nbsp;Smruthy Sivakumar ,&nbsp;Radwa Sharaf ,&nbsp;Erik A. Williams ,&nbsp;Benjamin Kaplan ,&nbsp;Ethan S. Sokol ,&nbsp;Alexa B. Schrock ,&nbsp;Hanna Tukachinsky ,&nbsp;Douglas A. Mata ,&nbsp;Tyler Janovitz ,&nbsp;Douglas I. Lin ,&nbsp;Lei Zhong ,&nbsp;Lyle Lopez ,&nbsp;Nimesh R. Patel ,&nbsp;Garrett M. Frampton ,&nbsp;Geoffrey R. Oxnard ,&nbsp;Julia A. Elvin ,&nbsp;Brennan Decker","doi":"10.1016/j.jmoldx.2025.12.004","DOIUrl":"10.1016/j.jmoldx.2025.12.004","url":null,"abstract":"<div><div>Pathogenic <em>POLE</em> mutations (p<em>POLE</em>) undermine mismatch error correction by polymerase ε during DNA replication, and the resulting somatic ultramutation predicts response to immunotherapy. Beyond frequently recurrent alleles, historical p<em>POLE</em> classification has been largely based on exonuclease domain localization. A <em>POLE</em>-specific phenotypic classification model was developed, encompassing tumor mutational burden (TMB), mutational signatures, germline frequency, and consideration of comutation with other <em>POLE</em> mutations to identify p<em>POLE</em>. This model was applied to &gt;490,000 samples and identified 29 predicted p<em>POLE</em>, including 16 not previously reported. A total of 748 tumors (0.2%) had one or more p<em>POLE</em>, most commonly in endometrial and colorectal cancers, although p<em>POLE</em> were observed in many additional cancer types. p<em>POLE</em> were associated with ultramutation [median TMB, 186.3 mutations per megabase (mut/Mb)] across tumor types. Concurrent p<em>POLE</em> and microsatellite instability were more common than previously appreciated and produced a synergistic TMB impact, with medians of 135.7 mut/Mb for p<em>POLE</em>/microsatellite stable samples compared with 325.6 mut/Mb for p<em>POLE</em>/microsatellite instability-high samples. Comutation analysis in endometrial and colorectal cancers highlighted associations with homologous recombination pathway gene mutations that were predominantly monoallelic passengers that are unlikely to predict response to therapies targeting DNA repair deficiencies. p<em>POLE</em> have been incorporated into treatment guidelines for several malignancies and are an important predictor of immunotherapy response. This study provides biological insight to guide classification and clinical management of patients with tumors harboring p<em>POLE</em>.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 264-281"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145901471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Piloting an Interpretive External Quality Assurance Model for Genomic Testing for Childhood Syndromes and Intellectual Disability","authors":"Ben Lundie ,&nbsp;Sze Yee Chai ,&nbsp;Alicia B. Byrne ,&nbsp;Dimitar Azmanov ,&nbsp;John Christodoulou ,&nbsp;Matilda A. Haas ,&nbsp;Karin S. Kassahn ,&nbsp;Sebastian Lunke ,&nbsp;Ami Stott ,&nbsp;Bryony A. Thompson ,&nbsp;Tony Badrick ,&nbsp;Bruce Bennetts","doi":"10.1016/j.jmoldx.2025.11.006","DOIUrl":"10.1016/j.jmoldx.2025.11.006","url":null,"abstract":"<div><div>Few external quality assurance programs adequately address the complexity of largescale human genome or exome analysis. To bridge this gap, Australian Genomics and the Royal College of Pathologists of Australasia Quality Assurance Programs (QAP) developed a pilot interpretive module focused on genomic testing for childhood syndromes and intellectual disabilities. The program assessed laboratories' proficiency in interpreting complex genomic data for pediatric disorders. Six clinically accredited laboratories analyzed standardized genomic, phenotypic, and referral data. Reports were evaluated using a rubric adapted from the European Molecular Genetics Quality Network model, covering genotyping, variant classification, interpretation, and report content. Feedback included comparative performance results and individual recommendations. All laboratories correctly identified and classified target variants, but variation was observed in report structure, inclusion of genetic counseling advice, and application of the American College of Medical Genetics and Genomics/Association for Molecular Pathology classification framework. Participants noted that data-sharing limitations and differences in local reporting practices contributed to scoring inconsistencies. The pilot demonstrated the feasibility of a disease-specific interpretive QAP for complex pediatric genomic testing. Future rounds will address logistical challenges, refine scoring criteria, and strengthen standardization, supporting broader implementation. This initiative lays the groundwork for integrating specialized QAP modules into routine practice to improve diagnostic accuracy and consistency across laboratories.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 227-237"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical Exome Sequencing","authors":"Pilar Barberán-Martínez ,&nbsp;Mar Balanzá ,&nbsp;Belén García-Bohórquez ,&nbsp;Sofia Escobar-Parra ,&nbsp;Romana García-Gil ,&nbsp;Anselmo Feliciano-Sánchez ,&nbsp;Teresa Jaijo ,&nbsp;Elena Aller ,&nbsp;Gema García-García ,&nbsp;José M. Millán","doi":"10.1016/j.jmoldx.2025.11.008","DOIUrl":"10.1016/j.jmoldx.2025.11.008","url":null,"abstract":"<div><div>Inherited retinal dystrophies (IRDs) represent a diverse group of rare pathologies affecting vision, with significant genetic and clinical variability. Clinical exome sequencing was performed on 143 families clinically diagnosed with IRDs. The obtained variants were filtered and classified according to the American College of Medical Genetics and Genomics guidelines. Overall, a genetic diagnosis was achieved for 68.53% of the families in the cohort; 35 causative genes were identified, predominantly <em>ABCA4</em> and <em>USH2A</em>. A total of 170 clinically relevant variants were identified, 45 (26.47%) of which were novel, with missense variants being the most common type (40.59%). This study reported aberrant splicing generated by the <em>ABCA4</em> (NM_000350.2): c.1299A&gt;G mutation through the functional assay of a minigene. Furthermore, the genes <em>FAM161A</em> and <em>GUCY2D</em> were associated with IRDs that are not typically linked to these genes. Consequently, this study expands the current understanding of IRDs and supports the use of clinical exome sequencing as an effective strategy for the genetic diagnosis of these pathologies.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 211-226"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145919058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dideoxy Sequencing Enhances Detection of KIT Mutations in Gastrointestinal Stromal Tumors Initially Evaluated by Next-Generation Sequencing Hotspot Panels","authors":"Lisa Robinson,&nbsp;Sharleen Rapp,&nbsp;Weiwei Zhang,&nbsp;Jaclyn Pope,&nbsp;Allison M. Cushman-Vokoun","doi":"10.1016/j.jmoldx.2025.11.005","DOIUrl":"10.1016/j.jmoldx.2025.11.005","url":null,"abstract":"<div><div>Gastrointestinal stromal tumors (GISTs) are predominantly characterized by mutations in <em>KIT</em> or <em>PDGFRA</em>. Mutation detection is important for optimal therapy. Next-generation sequencing (NGS) panels are useful in GIST assessment as they allow for simultaneous evaluation of multiple genes. However, inherent to use of NGS with short-read sequences on formalin-fixed specimens is the potential to miss larger insertion or deletion variants. Over 9 years, GIST testing was performed on specimens from 55 patients by amplicon-based, semiconductor NGS using the Ion AmpliSeq Cancer Hotspot Panel version 2, a Cancer Hotspot Panel version 2–based GIST panel, or the Oncomine Precision Assay. Negative cases were evaluated by dideoxy sequencing for detection of mutations in <em>KIT</em> and <em>PDGFRA,</em> as per the clinical protocol. Before reflexive sequencing, of 55 completed analyses, 47 (85%) were positive for <em>KIT</em> or <em>PDGFRA</em> mutations by NGS. Three cases were attributed to positivity for pathogenic variants in other genes. Of the five cases evaluated by dideoxy sequencing, all five (9% of all specimens) were positive for pathogenic or likely pathogenic <em>KIT</em> mutations. A total of 12% of <em>KIT</em> mutations required dideoxy sequencing for identification. Mutations were 12 to 39 nucleotide deletion or duplication variants. The results suggest that short-read, amplicon-based NGS assays may miss a significant number of clinically actionable <em>KIT</em> mutations and that follow-up of <em>KIT</em> and <em>PDGFRA</em> NGS-negative cases by alternative testing modalities should be considered.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 238-251"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"REVIEWER ACKNOWLEDGMENT","authors":"","doi":"10.1016/j.jmoldx.2026.01.001","DOIUrl":"10.1016/j.jmoldx.2026.01.001","url":null,"abstract":"","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 321-322"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147413197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Laboratory-Adaptive Dynamic Quality Control Framework Reduces Targeted Capture Sequencing Failure in Solid Tumors by >90%","authors":"Jiang Wu ,&nbsp;Jie Zhao ,&nbsp;Xiaofeng Wang ,&nbsp;Yifan Shen ,&nbsp;Xin Liao ,&nbsp;Zihan Yang ,&nbsp;Shan Jiang ,&nbsp;Fan Li ,&nbsp;Wei Cheng ,&nbsp;Lixue Chen ,&nbsp;Xueping Chen","doi":"10.1016/j.jmoldx.2025.12.003","DOIUrl":"10.1016/j.jmoldx.2025.12.003","url":null,"abstract":"<div><div>High failure rates in targeted capture sequencing of solid tumors—especially from formalin-fixed, paraffin-embedded samples—limit the clinical application of next-generation sequencing. Current wet-laboratory quality control (QC) relies on rigid, predefined thresholds, which are not adaptable to the heterogeneity of clinical samples and contribute significantly to sequencing failures. Retrospective analysis of QC parameters from 1146 tumor samples (425-gene panel; 2021 to 2023) identified five independent predictors of failure: total DNA amount, nucleic acid quality, DNA input, prelibrary total DNA, and prelibrary input (all <em>P</em> &lt; 0.05). On the basis of these findings, the first laboratory-adaptive dynamic QC framework was developed to utilize sample-specific QC metrics for real-time adjustment of wet-laboratory workflows. Prospective validation in 2687 consecutive samples (March 2023 to the present) demonstrated a &gt;90% reduction in sequencing failures, lowering the failure rate from 4.2% to 0.3% (<em>P</em> &lt; 0.001), with significant improvements for high-risk samples. This approach also reduced projected costs by 257 RMB (Renminbi; Chinese Yuan) per sample, saving &gt;230,000 RMB annually. By replacing static cutoffs with a dynamic, sample-specific strategy, this framework offers a scalable and cost-efficient solution, providing a paradigm shift in wet-laboratory QC for heterogeneous clinical specimens.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 308-320"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147318797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and Clinical Validation of OncCNV","authors":"Stephanie A. Smoley ,&nbsp;Gopinath Sivasankaran ,&nbsp;Mallika Gandham ,&nbsp;Beth A. Pitel ,&nbsp;Shannon M. Knight ,&nbsp;Stefan W. Nelson ,&nbsp;Nipun A. Mistry ,&nbsp;Katherine B. Geiersbach ,&nbsp;Sounak Gupta ,&nbsp;Kevin C. Halling ,&nbsp;Robert B. Jenkins ,&nbsp;Hussam Al-Kateb","doi":"10.1016/j.jmoldx.2025.12.001","DOIUrl":"10.1016/j.jmoldx.2025.12.001","url":null,"abstract":"<div><div>Large-scale tumor molecular profiling has enabled the discovery of diagnostic, prognostic, and therapeutic biomarkers, and expanded the clinical utility of alterations such as gene amplifications (GAMPs), homozygous deletions (HMZ-Dels), and biallelic inactivation (BI) of tumor suppressor genes. Comprehensive clinical detection of these events is essential for optimal patient management. Illumina's TruSight Oncology 500 (TSO500) kit detects multiple biomarkers, including GAMPs for select genes, but does not assess HMZ-Del or BI events. To address this gap, OncCNV, a genome-wide copy number analysis and visualization pipeline that integrates both on-target and off-target probe data from TSO500 sequencing, was developed. Performance optimization evaluated copy number calling tools, on-target and off-target probe selection strategies, off-target bin sizes, and panel-of-normal configurations. Clinical validation was conducted using 132 unique solid tumors characterized by a clinically validated microarray assay. OncCNV showed &gt;96% positive percentage agreement, &gt;99% negative percentage agreement, and &gt;99% accuracy at the assay's established limit of detection (40 ng DNA at 40% tumor content). Sensitivity for HMZ-Del and BI detection decreased to 62%–70% at tumor content of 20%–39% in <em>in silico</em> dilution experiments; however, intrarun, interrun, and interanalyst precision remained &gt;99%. OncCNV extends the analytical capabilities of TSO500 by enabling robust and precise detection of GAMP, HMZ-Del, and BI events, enhancing solid tumor comprehensive molecular profiling.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 3","pages":"Pages 282-293"},"PeriodicalIF":3.4,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}