Journal of Molecular Diagnostics最新文献

This large-scale retrospective study investigated the allele, diplotype, and phenotype frequencies of CYP2B6, CYP2C19, and CYP2D6 in a Han Chinese population (N > 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. CYP2D6 copy number variation (CNV) was analyzed by TaqMan real-time quantitative PCR. The sample sizes were 9729 for CYP2B6, 11,479 for CYP2C19, and 11,315 for CYP2D6, all from the Han Chinese population. The high frequencies of alleles were CYP2B6∗6 (16.19%), CYP2C19∗2 (30.36%), and CYP2D6∗10 (41.67%), with the most common diplotypes being CYP2B6 ∗1/∗6 (23.65%), CYP2C19 ∗1/∗2 (37.62%), and CYP2D6 ∗1/∗10 (16.05%), respectively. At the phenotype level, normal metabolizer was most common for CYP2B6 (57.86%) and CYP2D6 (60.50%), whereas the intermediate metabolizer phenotype was noted for CYP2C19 (44.77%). CYP2D6 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 CYP2D6.

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.

Gastrointestinal stromal tumors (GISTs) are predominantly characterized by mutations in KIT or PDGFRA. 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 KIT and PDGFRA, as per the clinical protocol. Before reflexive sequencing, of 55 completed analyses, 47 (85%) were positive for KIT or PDGFRA 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 KIT mutations. A total of 12% of KIT 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 KIT mutations and that follow-up of KIT and PDGFRA NGS-negative cases by alternative testing modalities should be considered.

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 >96% positive percentage agreement, >99% negative percentage agreement, and >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 in silico dilution experiments; however, intrarun, interrun, and interanalyst precision remained >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.