Journal of Molecular Diagnostics最新文献

Molecular profiling of solid tumors is increasingly essential in oncology practice, guiding diagnosis-prognosis and providing patients with access to molecularly matched therapies that can improve outcomes. In this study, we evaluated 554 patients with advanced solid tumors through the POWER (Precision Oncology at Western University) study, first of its kind Canadian study, designed to prospectively assess clinical impact of expanded Pan-cancer NGS panel testing on patient management, in real-world oncology practice and evaluate the overall health system impact. Our findings reveal that 79% of patients had clinically relevant variants, and nearly 28% experienced changes in treatment eligibility due to the identification of novel druggable mutations. Additionally, our analysis shows that a Pan-cancer NGS panel significantly impacted patient management, with 18% of patients receiving access to clinical trials and off-label therapy with expected better outcomes and 19% (31/162) patients previously tested by tumor-specific panels, experienced management changes when tested through POWER. This study also highlights the broader health system impact: access to safer treatment options (14.5%), change in management (17.6%), treatment sequence changed (17.3%), MOH (Ministry of Health) formulary treatment saved (12.5%).These results underscore the benefits of expanded NGS testing over tumor-specific panels in guiding personalized treatment decisions, optimizing patient care, and enhancing healthcare delivery in oncology.

Acquired TERT promoter (TERTp) variants are found in the blood of patients with telomere biology disorders (TBDs) and carry diagnostic and prognostic significance. Detection of these variants is challenging due to low variant allele frequencies (VAFs) and high GC content. We tested the sensitivity of long-read amplicon sequencing with deepSNV analysis, referred to as LR-deep AmpSeq, for TERTp variant detection. Among 47 patients with TBD features, we achieved an average depth of coverage of 7,943x and detected seven TERTp variants in six individuals (13%) with VAFs ranging from 0.006-0.33. Our results demonstrate that LR-deep AmpSeq is a sensitive, cost-effective method to detect low VAF TERTp variants.

Myelofibrosis (MF) is a hematologic malignancy with a highly heterogeneous clinical course. Copy-neutral loss of heterozygosity (CN-LOH) may contribute to disease progression by promoting mutation homozygosity. Although single-nucleotide polymorphism (SNP) arrays are the gold standard for CN-LOH detection, Optical Genome Mapping (OGM) has emerged as a promising alternative. In this multicenter study, we assessed the capability of OGM to detect CN-LOH in 78 patients with MF. OGM data were analyzed using both de novo (DN) and guided assembly pipelines (GA), followed by re-analysis of CN-LOH-positive cases with the VIA software. Results were validated with SNP arrays. Compared to 45% for GA and 37% for DN, VIA demonstrated the highest concordance, confirming 90% (46/51) of CN-LOH events found by SNP arrays. While VIA maintained a high concordance (90%) for all event sizes, GA (70%) and DN (61%) showed improved concordance for larger events (≥25 Mb). VIA also identified six CN-LOH events in 9p involving JAK2 gene that were missed by DN and GA. Among 19 CN-LOH events detected by all three pipelines, 89% were confirmed by SNP arrays. Events ≥25 Mb exhibited greater concordance across platforms. These findings demonstrate that OGM, particularly when analyzed with VIA, is a sensitive and reliable method for CN-LOH detection in MF. However, in the absence of broader validation, confirmation with orthogonal methods remains necessary.

Cytomegalovirus, Epstein-Barr virus, BK virus, and adenovirus cause significant morbidity and mortality in immunocompromised individuals, especially those undergoing solid organ and hematopoietic stem cell transplant. Quantitative viral load testing is essential to the monitoring and treatment of disease associated with these viruses in the post-transplant period. In this review, the current guidelines for viral load monitoring are described, highlighting the differences in testing recommendations by virus and transplant type. The state of commercially available, Food and Drug Administration-cleared quantitative viral load assays are also reviewed and the ongoing challenges associated with quantitative viral load testing in the clinical laboratory are described.

In November 2023, our Canadian tertiary care facility implemented optical genome mapping (OGM) as a first-line diagnostic test for adults with newly diagnosed acute leukemias. Here, the analytical performance and clinical utility of OGM alongside karyotype, fluorescence in situ hybridization (FISH), and next-generation sequencing are reported. During test validation, OGM demonstrated robust analytical performance, reproducibility, and limits of detection, revealing 100% specificity, 96.1% sensitivity, and 98.0% accuracy. After implementation, clinical reports from the entire cytogenetic and molecular genetic workflow were prospectively compiled from the first 200 cases to evaluate concordance with parallel karyotype/FISH and added yield of OGM. A total of 640 reportable variants were detected by OGM and stratified on the basis of clinical significance, classified as tier 1A (25%), tier 1B (3%), tier 2 (2%), or tier 3A (70%). Of these, 64 variants were missed by karyotype and FISH, 3 KMT2A partial tandem duplications were missed by next-generation sequencing, and 9 cases with failed karyotype were rescued by OGM: overall impacting 35 cases (18%) by altering diagnostic classification (n = 12) and/or risk stratification (n = 31). Despite comprehensive pre-existing diagnostic workflows, implementation of OGM has revealed diagnostically and prognostically significant alterations in cases otherwise cryptic or failed by karyotype, demonstrating strong clinical utility and supporting its use as a first-tier diagnostic test for hematolymphoid malignancies.

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 guidelines. Overall, a genetic diagnosis was achieved for 68.53% of the families in the cohort; 35 causative genes were identified, predominantly ABCA4 and USH2A. 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 ABCA4 (NM_000350.2): c.1299A > G mutation through the functional assay of a minigene. Furthermore, the genes FAM161A and GUCY2D 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.

Pathogenic POLE mutations (pPOLE) undermine mismatch error correction by polymerase ε during DNA replication, and the resulting somatic ultramutation predicts response to immunotherapy. Beyond frequently recurrent alleles, historical pPOLE classification has been largely based on exonuclease domain localization. A POLE-specific phenotypic classification model was developed, encompassing tumor mutational burden (TMB), mutational signatures, germline frequency, and consideration of comutation with other POLE mutations to identify pPOLE. This model was applied to >490,000 samples and identified 29 predicted pPOLE, including 16 not previously reported. A total of 748 tumors (0.2%) had one or more pPOLE, most commonly in endometrial and colorectal cancers, although pPOLE were observed in many additional cancer types. pPOLE were associated with ultramutation [median TMB, 186.3 mutations per megabase (mut/Mb)] across tumor types. Concurrent pPOLE and microsatellite instability were more common than previously appreciated and produced a synergistic TMB impact, with medians of 135.7 mut/Mb for pPOLE/microsatellite stable samples compared with 325.6 mut/Mb for pPOLE/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. pPOLE 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 pPOLE.

In this multilaboratory validation study of 145 ovarian cancer samples, the SOPHiA DDM HRD Solution was compared with the regulatory-approved Myriad myChoice HRD assay to assess clinical comparability for class 3 in-house in vitro diagnostic medical device companion diagnostic use. BRCA1/2 mutation status showed 100% concordance, and genomic instability (GI) measurements demonstrated strong linear agreement, absence of bias, and high analytical precision. Receiver operating characteristic analysis suggested a threshold adjustment from 0 to -1.5, improving overall accuracy to 91.2% when combined with BRCA mutation status to assign homologous recombination deficiency (HRD) status. Approximately 6% of samples were excluded because of inconclusive results, whereas GI classification discordance was concentrated near the clinical threshold. Neither inconclusiveness nor discordance was associated with sample-related factors. These findings indicate that the SOPHiA HRD assay can provide results broadly interchangeable with Myriad myChoice, although caution is warranted when assigning HRD status to borderline GI values.