Lower respiratory tract (LRT) infections represent a major cause of mortality, particularly among critically ill patients. Molecular diagnostic tests have improved the detection of respiratory pathogens; however, most co...Lower respiratory tract (LRT) infections represent a major cause of mortality, particularly among critically ill patients. Molecular diagnostic tests have improved the detection of respiratory pathogens; however, most commercial assays are validated exclusively in upper RT (URT) specimens, limiting their applicability in LRT samples, which better reflect disease severity. This study evaluated the diagnostic performance of two commercially available assays, the BioFire Respiratory Panel 2.1 Plus and the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay, on bronchoalveolar lavage (BAL) specimens, using the Allplex Respiratory Panel 1/2/3 and the Allplex SARS-CoV-2 assay as reference methods validated for both matrices. Overall, 132 BAL samples were analyzed. BioFire identified more positives than Allplex, particularly for human rhinovirus/enterovirus (HRV/EV), human parainfluenza virus (HPIV), and non-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The overall agreement was fair (κ = 0.237), and pathogen-specific concordance was almost perfect for SARS-CoV-2 (κ = 0.841), influenza A/B (κ = 0.808), and HPIV (κ = 0.884). The Panther assay showed substantial agreement with Allplex (κ = 0.719) and near-perfect concordance for SARS-CoV-2 and influenza viruses, while BioFire and Panther exhibited almost perfect interassay agreement (κ = 0.903). These findings demonstrate that assays validated for URT specimens can perform reliably on BAL samples, underlining the diagnostic potential of LRT matrices and the need for expanded validation of molecular respiratory panels across specimen types.
Gene-specific variant interpretation guidelines are constantly being published to refine variant classification. The development, implementation, and benefit of such guidelines require careful assessment. This study eval...Gene-specific variant interpretation guidelines are constantly being published to refine variant classification. The development, implementation, and benefit of such guidelines require careful assessment. This study evaluates the utility of these guidelines on variant interpretation. All actionable genes listed in American College of Medical Genetics and Genomics-Secondary findings version 3.3 genes with available Clinical Genome Resource (ClinGen) Variant Curation Expert Panel criteria specifications were analyzed. A total of 1223 variants in these genes were classified using the American College of Medical Genetics and Genomics/Association for Molecular Pathology criteria and revised according to the Variant Curation Expert Panel specifications. Reclassification outcomes were compared using high-confidence variants. Application of the revised guidelines resulted in score changes in 63.1% of variants, although most did not cross classification thresholds. Reclassification occurred in 20.3% of cases, predominantly as downgrades and improved concordance with ClinVar by 5.8%, particularly for benign classifications. Of 622 variants of uncertain significance (VUSs), 25.1% were resolved, with the highest resolution rates in BRCA1, BRCA2, and PALB2, whereas LDLR and TPM1 remained largely unchanged. No consistent correlation was found between the extent of criteria modification for each guideline and VUS resolution. The utility of the guidelines was shown to be variable and gene dependent. Although most reduced VUS rates and refined benign classifications, in some, only a minor impact was achieved, suggesting standardization and calibration of future guidelines are necessary.
Carta MG, Tögel L, Hölsken A
… +9 more, Schubart C, Sticht H, Stöhr R, Spoerl S, Meidenbauer N, Hartmann A, Magni P, Haller F, Ferrazzi F
J Mol Diagn
· 2026 Jun · PMID 41936821
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Accurate and reproducible interpretation of somatic variants is fundamental for therapy decision-making in patients with cancer. To harmonize and automate oncogenicity classification, Oncogenicity Variant Interpreter (On...Accurate and reproducible interpretation of somatic variants is fundamental for therapy decision-making in patients with cancer. To harmonize and automate oncogenicity classification, Oncogenicity Variant Interpreter (OncoVI), an open-source, Python-based implementation of the Clinical Genome Resource/Cancer Genomics Consortium/Variant Interpretation for Cancer Consortium oncogenicity guidelines, was developed. For each of the guideline criteria, the textual descriptions were interpreted, and publicly available resources were identified to be used as reference. Starting from the genomic coordinates of a variant, OncoVI automatically performs functional annotation, collects relevant evidence from the integrated resources, evaluates each criterion, and provides a final oncogenicity classification. OncoVI achieved an accuracy of 80% on a gold standard set of 93 somatic variants provided by the guidelines, with a sensitivity of 88% for oncogenic/likely oncogenic variants. When applied to a real-world set of 7802 variants from 557 participants previously evaluated by the Molecular Tumor Board (MTB) Erlangen, OncoVI showed 79% concordance with the prior MTB assessment of variant impact on protein function. In addition, expert reassessment of 135 MTB variants, conducted in accordance with the oncogenicity guidelines, further confirmed both the validity of OncoVI implementation and the appropriateness of the identified resources. Taken together, OncoVI provides significant support for the harmonized and reproducible oncogenicity classification of somatic variants across institutions.
Madurai LS, Reddy K, Nair S
… +3 more, Manivannan B, Pillay K, Mahomed S
J Mol Diagn
· 2026 Jun · PMID 41936820
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Pediatric HIV-1 viral load monitoring is often limited by the small blood volumes that can be safely obtained from infants and young children. Standard assays typically require 0.5 to 0.7 mL of plasma, which can pose cha...Pediatric HIV-1 viral load monitoring is often limited by the small blood volumes that can be safely obtained from infants and young children. Standard assays typically require 0.5 to 0.7 mL of plasma, which can pose challenges in these settings. This study evaluated a modified low-volume protocol using 100 μL of plasma, diluted for use with the Hologic Aptima HIV-1 Quant Dx assay, to determine whether performance was equivalent to the standard 700 μL protocol. An analytical validation was conducted by using de-identified EDTA plasma samples spanning a wide range of HIV-1 RNA concentrations. Each specimen was tested by using both protocols on the Panther system. Agreement between methods was assessed by using log differences, correlation analysis, and Bland-Altman analysis; within-run and between-run precision was evaluated by using replicate testing of negative, low-positive, and high-positive samples. The 100 μL protocol displayed excellent concordance with the standard method, with a mean log difference of approximately 0.00 and a maximum difference of 0.12 log copies/mL. No false-positive or false-negative results were observed among 30 fully suppressed samples. Precision analyses showed minimal variability, with all results within predefined acceptability criteria. These findings indicate that the low-volume Aptima protocol provides accurate and reliable HIV-1 RNA quantification and can expand access to viral load testing in pediatric patients and other clinical settings in which plasma volume is limited.
Reliable quantification of cell-free DNA (cfDNA) in liquid biopsy diagnostics critically depends on unbiased and reproducible isolation workflows. Fragment-length-dependent recovery during isolation represents a major so...Reliable quantification of cell-free DNA (cfDNA) in liquid biopsy diagnostics critically depends on unbiased and reproducible isolation workflows. Fragment-length-dependent recovery during isolation represents a major source of pre-analytical bias. This variability limits method validation, interlaboratory comparability, and the reliability of cfDNA measurements in clinical and research laboratories. However, certified reference materials (CRMs) specifically designed to evaluate cfDNA isolation recovery are currently lacking. In this study, two synthetic cfDNA CRMs were developed to enable fragment-length-resolved assessment of isolation recovery. TÜBİTAK National Metrology Institute (UME) CRM 3022 comprises 80- and 240-bp double-stranded DNA fragments, whereas UME CRM 3024 includes fragments of 80, 120, 160, and 240 bp. The materials were prepared gravimetrically and characterized using optimized duplex and multiplex droplet digital PCR assays. Homogeneity, short-term stability, and long-term stability were evaluated. Certified copy number concentrations with stated measurement uncertainties were assigned for each fragment. Applicability in a plasma matrix was demonstrated to support practical workflow integration. These CRMs provide a traceable, fragment-resolved framework for recovery-based standardization of cfDNA isolation, supporting improved analytical reliability in liquid biopsy applications.
Alptekin A, Mondal AK, Vashisht A
… +11 more, Vashisht V, Singh H, Morera D, Ahluwalia P, Farmaha J, Kavuri S, Patel N, Velasquez Zarate LA, Sridhar S, Chandrasekar VT, Kolhe R
J Mol Diagn
· 2026 Jun · PMID 41905556
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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, sensiti...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.
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 invo...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.
Identifying the molecular causes of hereditary sensorineural hearing loss is essential for effective prevention and control. Current prenatal diagnostic methods are primarily invasive and carry significant risks. While n...Identifying the molecular causes of hereditary sensorineural hearing loss is essential for effective prevention and control. Current prenatal diagnostic methods are primarily invasive and carry significant risks. While noninvasive prenatal testing for common aneuploidies has become widespread over the past decade, noninvasive prenatal testing for monogenic hereditary disorders remains limited by complex procedures, low detection accuracy, and the need for prior knowledge of parental genotypes or haplotypes. This study aimed to address these limitations. A noninvasive prenatal testing method for hereditary sensorineural hearing loss using next-generation sequencing based on single-molecule counting technology was developed. In a validation experiment involving 50 patients with singleton pregnancies at risk for fetal sensorineural hearing loss, the consistency and accuracy of allele detection for diagnosis were 99.67% and 96%, respectively. Single-molecule counting technology enabled relatively accurate identification of maternal and fetal genotypes from cell-free DNA. However, due to the limited sample size, reliable false-negative and false-positive rates could not be established. Thus, this study serves only as preliminary proof of concept for this detection method.
The Idylla GeneFusion Assay detects gene fusions with fusion-specific and expression imbalance methods. The purpose of this study was to evaluate the diagnostic utility of detecting fusions with expression imbalance alon...The Idylla GeneFusion Assay detects gene fusions with fusion-specific and expression imbalance methods. The purpose of this study was to evaluate the diagnostic utility of detecting fusions with expression imbalance alone in non-small-cell lung cancer. Results of ALK, ROS1, and RET fusion detection with expression imbalance were compared with results of orthogonal testing. Of 1982 cases reviewed from October 2022 through August 2024, 63 (3.2%) had fusions detected with the expression imbalance method alone, including 47 ALK, 10 ROS1, and 7 RET fusions. One case had ALK and RET fusions. Fluorescence in situ hybridization (FISH) confirmation for 51 cases revealed 8 positive (15.7%), 3 equivocal (5.9%), and 40 negative (78.4%) results. Anaplastic lymphoma kinase (ALK) immunohistochemistry performed for 22 ALK-detected cases revealed 3 positive (13.6%) and 19 negative (86.4%) results that were concordant with ALK FISH results. The positive predictive value of expression imbalance detection alone varied by gene (12.5% for ALK, 16.7% for ROS1, and 33.3% for RET). RNA next-generation sequencing results for seven select cases (three ALK, two ROS1, and two RET) showed six novel fusions (eg, STRN::ALK, SQSTM1::ROS1, and ERC1::RET) and had 100% concordance with FISH results. One case showed an NOL10::ALK out-of-frame fusion with negative ALK immunohistochemistry and equivocal ALK FISH results. Because the expression imbalance method can detect novel fusions, its implementation with confirmation testing is recommended.
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 con...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 P < 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 >90% reduction in sequencing failures, lowering the failure rate from 4.2% to 0.3% (P < 0.001), with significant improvements for high-risk samples. This approach also reduced projected costs by 257 RMB (Renminbi; Chinese Yuan) per sample, saving >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.
Nuño MM, Murray MJ, Lafin JT
… +16 more, Scarpini CG, Wang Z, Gagan J, Jia L, Lewis CM, Murray S, Smitham J, Giannikou K, Jamieson C, Margulis V, Woldu SL, Coleman N, Amatruda JF, Klosterkemper L, Frazier AL, Bagrodia A
J Mol Diagn
· 2026 May · PMID 41759576
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Previous work has shown that circulating miR-371a-3p has higher sensitivity and specificity than current biomarkers for malignant germ cell tumors (MGCTs). Herein, the performance of two methods commonly used to measure...Previous work has shown that circulating miR-371a-3p has higher sensitivity and specificity than current biomarkers for malignant germ cell tumors (MGCTs). Herein, the performance of two methods commonly used to measure miR-371a-3p levels was compared: quantitative RT-PCR (RT-qPCR) and droplet digital PCR (ddPCR). Samples from the University of Texas Southwestern Medical Center (Dallas, TX) and the University of Cambridge (Cambridge, UK) were evaluated using both RT-qPCR and ddPCR, as per current protocols (RT-qPCR) or standard manufacturer's recommendations (ddPCR). Data were available for 70 individuals: 36 patients with MGCT and 34 control participants (nonmalignant GCT, non-GCT cancer, and noncancer). The performance of the two assays was compared using receiver operating characteristic curves and the area under the curve. Raw miR-371a-3p Cq values (RT-qPCR) were generally lower (ie, miR-371a-3p was more abundant) and the number of positive droplets (ddPCR) higher for patients with MGCT compared with control participants. The area under the curve (95% CI) was 0.94 (0.90-0.99) and 0.82 (0.70-0.93) when using RT-qPCR and ddPCR, respectively. Thus, RT-qPCR had better classification performance compared with ddPCR in the present cohort, supporting the continued use of RT-qPCR in standard clinical practice. Further investigation is required to optimize ddPCR before it should be considered for clinical adoption.
Betensley A, Vandervest K, Ross DJ
… +16 more, Ragalie WS, Presberg KW, Dolan S, Haasler G, Mason D, Biller JA, North P, Ryan GD, Sultan S, Bhorade S, Demko Z, Prewett A, Simpson P, Dasgupta M, Tomita-Mitchell A, Mitchell ME
Lung allografts are susceptible to myriad injury types, including acute rejection (AR), infectious disease (ID), baseline lung allograft dysfunction (BLAD), and chronic lung allograft dysfunction (CLAD), that affect outc...Lung allografts are susceptible to myriad injury types, including acute rejection (AR), infectious disease (ID), baseline lung allograft dysfunction (BLAD), and chronic lung allograft dysfunction (CLAD), that affect outcomes. Donor-derived cell-free DNA (dd-cfDNA) is validated for detecting AR after lung transplantation (LT). However, data are limited regarding the ability of dd-cfDNA or total cell-free DNA (TcfDNA) to detect or differentiate other clinical conditions. This study stratified patients into Stable, AR, CLAD, and ID cohorts. Stable double LT recipients were further stratified into BLAD and non-BLAD over different periods posttransplantation. dd-cfDNA and TcfDNA results were associated with the various cohorts. cfDNA was measured in 354 plasma samples from 66 LT recipients. Median dd-cfDNA was elevated in AR (2.08%; P = 0.014) and ID (1.19%; P = 0.065) versus Stable (0.60%) but not CLAD; TcfDNA was only elevated in the ID cohort (P = 0.0078). dd-cfDNA was analyzed before and after treatment of eight episodes of AR, during which the median dd-cfDNA fraction decreased from 2.41% to 0.80% (P = 0.004). No differences were observed during early time points for BLAD versus non-BLAD, whereas median TcfDNA, but not dd-cfDNA, was elevated for BLAD beyond 12 months (13,843 vs 7768 cp/mL; P = 0.005). Overall, this was the first study that explored dd-cfDNA and TcfDNA levels across AR, ID, BLAD, and CLAD cohorts. These data suggest that cfDNA-based biomarkers have value in assessing allograft dysfunction beyond AR.
Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder with extensive allelic heterogeneity. Although RNA-based assays can increase sensitivity, their cost and complexity limit their routine use. A DNA-on...Neurofibromatosis type 1 (NF1) is a common autosomal dominant disorder with extensive allelic heterogeneity. Although RNA-based assays can increase sensitivity, their cost and complexity limit their routine use. A DNA-only tiered diagnostic approach was evaluated in 1917 unrelated Korean individuals with clinically suspected NF1. The process began with targeted sequencing of blood-derived genomic DNA, followed by reflex multiplex ligation-dependent probe amplification for copy number variants and a lesional tissue test for suspected mosaicism. Initial targeted sequencing of the NF1 gene established a diagnostic yield of 74.0%. The addition of reflex multiplex ligation-dependent probe amplification and tissue testing increased the cumulative yield to 79.2%. Subsequent post-report variant reclassification and whole-genome sequencing further increased the overall diagnostic yield to 81.6%. Among 901 distinct pathogenic variants identified-81.4% of which were private-truncating variants were predominant (79.0%). Notably, several variants enriched in European cohorts and with established genotype-phenotype correlations (eg, p.Arg1809Cys, p.Met992del, and p.Arg1276Gln) were rare in this cohort, highlighting population-specific differences. Individuals with large deletions were referred at younger ages, suggesting potential genotype-phenotype associations. These data demonstrate that a stepwise, DNA-only strategy delivers high yield and scalability for routine NF1 diagnostics, while delineating a Korean-specific mutational landscape. This practical workflow offers a robust alternative to RNA-based approaches in real-world clinical settings.
Lin J, Opoku KB, Litzow MR
… +7 more, Paietta E, Pui CH, Jeha S, Roberts KG, Mullighan CG, Alexander TB, Wang JR
J Mol Diagn
· 2026 May · PMID 41679504
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Long-read whole-transcriptome sequencing (WTS) has the potential to precisely characterize fusion oncogenes that drive leukemia and other cancers. Although there is a variety of general-purpose fusion detection algorithm...Long-read whole-transcriptome sequencing (WTS) has the potential to precisely characterize fusion oncogenes that drive leukemia and other cancers. Although there is a variety of general-purpose fusion detection algorithms that use modern long-read sequencing data, they show poor sensitivity for precision diagnostics in B-cell acute lymphoblastic leukemia (B-ALL) and do not robustly assess technical and analytical parameters (eg, sequencing depth) to reliably detect fusion transcripts. FUSILLI (FUSions In Leukemia Long-read sequencing Investigator) is a novel long-read fusion detection algorithm, with a focus on targeted genomic subtyping in B-ALL. FUSILLI was evaluated against extant methods using nanopore WTS from 51 pediatric B-ALL samples sequenced at high depth and 68 at low depth (mean of 11.2 and 1.4 million reads, respectively). In the high-depth cohort, FUSILLI demonstrated increased sensitivity (0.81) compared with FusionSeeker, JAFFAL, and LongGF (0.63, 0.76, and 0.70, respectively), while maintaining high specificity (0.92). At lower sequencing depth, FUSILLI showed correspondingly lower sensitivity (0.27) but still outperformed the other fusion callers (sensitivities ranging from 0.09 to 0.16). Computational down sampling suggests that 10 million reads is sufficient to sensitively detect B-ALL-relevant fusions using this approach. FUSILLI detects B-ALL fusions with high sensitivity at modest sequencing depth, supporting implementation of nanopore WTS as a low-cost and globally accessible sequencing-based molecular diagnostic platform for pediatric B-ALL and other fusion-driven cancers.
Kirchner RE, Pereira ML, Peterson MM
… +2 more, Berres ME, Churpek JE
J Mol Diagn
· 2026 Apr · PMID 41654254
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Acquired TERT promoter (TERTp) variants are found in the blood of patients with telomere biology disorders and carry diagnostic and prognostic significance. Detection of these variants is challenging because of low varia...Acquired TERT promoter (TERTp) variants are found in the blood of patients with telomere biology disorders and carry diagnostic and prognostic significance. Detection of these variants is challenging because of low variant allele frequencies (VAFs) and high GC content. The sensitivity of long-read amplicon sequencing with deepSNV analysis, referred to as LR-deep AmpSeq, for TERTp variant detection was tested. Among 47 patients with telomere biology disorder features, an average depth of coverage of 7943× was achieved, and seven TERTp variants were detected in six individuals (13%) with VAFs ranging from 0.006 to 0.33. These results demonstrate that LR-deep AmpSeq is a sensitive, cost-effective method to detect low VAF TERTp variants.
Bhai P, Turowec JP, Pickard LA
… +23 more, Haghshenas S, Karim K, McConkey H, Santos S, Kerkhof J, Black M, Breadner D, Cecchini M, Howlett C, Schenkel L, Lalonde E, Panuganty V, Raphael J, Lohmann AE, Winquist E, Lenehan J, Stewart P, Tsvetkova E, Vincent M, Fernandes R, Bauman G, Welch S, Sadikovic B
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...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, 554 patients with advanced solid tumors were evaluated through the POWER (Precision Oncology at Western University) study, a first of its kind Canadian study, designed to prospectively assess the clinical impact of expanded pan-cancer next-generation sequencing (NGS) panel testing on patient management, in real-world oncology practice and evaluate the overall health system impact. The findings reveal that 79% of patients had clinically relevant variants, and nearly 28% experienced changes in treatment eligibility because of the identification of novel druggable mutations. Additionally, the 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, experiencing 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%), and Ministry of Health formulary treatment saved (12.5%). These results underline the benefits of expanded NGS testing over tumor-specific panels in guiding personalized treatment decisions, optimizing patient care, and enhancing health care delivery in oncology.
Díaz-González Á, Mora E, Garrote M
… +20 more, Carreño-Tarragona G, Salido M, Pastor-Galán I, Stuckey R, Uresandi-Iruin N, Avetisyan G, Orellana C, Roselló M, García-Ruiz C, Torres-Hernández N, Martínez-Campuzano D, Berenguer-Rubio A, Liquori A, Villamón E, Espinet B, Cervera J, Rubia J, Álvarez-Larrán A, Hernández-Boluda JC, Such E
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...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, the capability of OGM to detect CN-LOH in 78 patients with MF was assessed. 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 Variant Intelligence Applications (VIA) software. Results were validated with SNP arrays. Compared with 45% for GA and 37% for DN, VIA demonstrated the highest concordance, confirming 90% (46/51) of CN-LOH events found by SNP arrays. Although 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 the 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.