Journal of Molecular Diagnostics最新文献

{"title":"Harmonization of Reporting of ALK Genetic Alterations in Neuroblastoma","authors":"Alexandra Saint-Charles ,&nbsp;Julien Masliah-Planchon ,&nbsp;Elnaz Saberi-Ansari ,&nbsp;Angela Bellini ,&nbsp;Marie Bernkopf ,&nbsp;Jaime Font de Mora ,&nbsp;Rosa Noguera ,&nbsp;Nadine Van Roy ,&nbsp;Angharad Goodman ,&nbsp;Ales Vicha ,&nbsp;Valery Attignon ,&nbsp;Valérie Combaret ,&nbsp;Klaus Beiske ,&nbsp;Tommy Martinsson ,&nbsp;Jacqueline Schoumans ,&nbsp;Maria Rossing ,&nbsp;Bastiaan Tops ,&nbsp;Frank Westermann ,&nbsp;Sophie Cotteret ,&nbsp;Matthias Fischer ,&nbsp;Gudrun Schleiermacher","doi":"10.1016/j.jmoldx.2025.09.007","DOIUrl":"10.1016/j.jmoldx.2025.09.007","url":null,"abstract":"<div><div>In high-risk neuroblastoma, identification of <em>ALK</em> activating genetic alterations is considered for clinical decision-making at relapse or more recently in frontline treatment. The accurate diagnosis of genetic alterations requires harmonization of molecular techniques and reporting, especially when these concern inclusion criteria for clinical trials. Analysis and validation of 14 DNA samples harboring distinct <em>ALK</em> alterations were performed across the 21 SIOPEN (International Society of Paediatric Oncology Europe Neuroblastoma) molecular diagnostic laboratories. These included <em>ALK</em> mutations at or outside hotspots in the tyrosine kinase domain with variant allele frequencies (VAFs) of 1% to 91% or <em>ALK</em> genomic amplification. Each laboratory used their own techniques: <em>ALK</em> amplifications were detected by pan-genomic copy number techniques or fluorescence <em>in situ</em> hybridization, and <em>ALK</em> mutations were characterized by next-generation sequencing techniques. All laboratories correctly identified high-level <em>ALK</em> amplification and <em>ALK</em> mutations within the known hotspots with VAF &gt;5%, with the exception of two cases. Differences in interpretation and reporting were apparent for samples harboring mutations with a VAF &lt;5% or outside known hotspots. These results highlight the importance of standard operating procedures, standardized reporting, and the robustness of <em>ALK</em> genetic testing in the SIOPEN laboratories, and the need for expert discussions regarding atypical <em>ALK</em> alterations, to validate eligibility for ALK targeted treatment in clinical trials.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"28 1","pages":"Pages 27-38"},"PeriodicalIF":3.4,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145330832","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 Utility of Multitissue Genomic Arrays in Diagnosing Pigmentary Mosaicism Associated with Neurodevelopmental Delay","authors":"Yanca G. Oliveira ,&nbsp;Marilia M. Montenegro ,&nbsp;Vanessa T. Almeida ,&nbsp;Eder A. Moura ,&nbsp;Amom M. Nascimento ,&nbsp;Gleyson Francisco da Silva Carvalho ,&nbsp;Evelin A. Zanardo ,&nbsp;Samar N. Chehimi ,&nbsp;Beatriz M. Wolff ,&nbsp;Lucas L. Vieira ,&nbsp;Mariana R. Costa Siemann ,&nbsp;Rafaela da Silva Mendes ,&nbsp;Lissandro de Sousa Rolim ,&nbsp;Karina M. Nascimento ,&nbsp;Chong Ae Kim ,&nbsp;Leslie D. Kulikowski","doi":"10.1016/j.jmoldx.2025.09.002","DOIUrl":"10.1016/j.jmoldx.2025.09.002","url":null,"abstract":"<div><div>Genomic mosaicism is underdiagnosed owing to its variable tissue distribution and the limitations of single-tissue testing. Cytogenomic techniques applied across multiple tissues can uncover clinically actionable variants and clarify genotype-phenotype relationships. DNA from 21 patients (14 females and 7 males) with pigmentary mosaicism and global developmental delay was analyzed. Each patient underwent G-band karyotyping and array (Infinium CytoSNP-850K) on peripheral blood, skin fibroblasts, and buccal mucosa samples. Pathogenic or likely pathogenic variants were found in 13 of 21 patients (62%). Of these 13 patients, 10 (77%) exhibited mosaicism, with variant allele fractions as low as 15%. On the basis of tissue distribution, 3 cases were classified as germline events and 10 as somatic mosaicism. Patients with positive findings were subdivided into: i) mosaic numerical chromosomal alterations (<em>n</em> = 6), ii) pathogenic copy number variations (<em>n</em> = 5), and iii) structural rearrangements (<em>n</em> = 2). Notably, several mosaic variants—particularly aneuploidies—were detected exclusively in fibroblast DNA, underlining the added diagnostic yield of multitissue sampling. In this cohort, a multitissue cytogenomic approach achieved a 62% overall diagnostic rate and identified mosaicism in 77% of positive cases. These results support the routine incorporation of genomic arrays with multisample analysis into diagnostic workflows for rare developmental disorders, enhancing detection sensitivity and enabling precise genotype-phenotype correlations.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1232-1241"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145240189","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":"Developing Consensus for a More Provider-Friendly Next-Generation Sequencing Molecular Biomarker Report","authors":"Jane Gibson ,&nbsp;Hanadi El Achi ,&nbsp;Dana Altenburger ,&nbsp;Noah Brown ,&nbsp;Amy S. Clark ,&nbsp;Joshua Coleman ,&nbsp;Rajyasree Emmadi ,&nbsp;Amber M. Fussell ,&nbsp;Meera Hameed ,&nbsp;Danielle Jordan ,&nbsp;Jennifer Laudadio ,&nbsp;Anthony Provenzano ,&nbsp;Robyn L. Temple-Smolkin ,&nbsp;Christopher G. Suciu","doi":"10.1016/j.jmoldx.2025.08.011","DOIUrl":"10.1016/j.jmoldx.2025.08.011","url":null,"abstract":"<div><div>Despite the increasing availability of next-generation sequencing (NGS) gene panel analysis for cancers, published reports suggest underutilization of testing, citing the shortage of credentialed professionals available to assist with the interpretation of test results among the key barriers. Obtaining a multidisciplinary consensus regarding a shared best practice NGS molecular biomarker reporting section template may facilitate introduction and/or increased testing for institutions that adopt similar report structures by improving report effectiveness and efficiency for both health care providers and laboratory professionals, leading to improved patient care. To address this challenge, the Association for Molecular Pathology convened a multidisciplinary collaborative expert working group to identify and utilize best practices from current reporting guidelines and approaches to develop an NGS biomarker report template to optimally present complex molecular profiling information for efficient use by oncologists and other health care providers. Seventeen non–small-cell lung cancer NGS biomarker reports from public, private, and academic laboratories were reviewed, and specific components (eg, report length, color use, formatting, presentation order of information, specific information included or omitted, tables, and figures) were assessed for their ability to be considered provider friendly. Based on this review, public and stakeholder input, available literature, and cumulative professional experience of the working group members, a guideline-concordant reporting template was developed based on expert opinion consensus and made freely available online with planned implementation assessment.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1123-1136"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187375","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":"Next-Generation Sequencing–Based T-Cell Receptor Gene Rearrangement Analysis in Nodal T Follicular Helper Cell Lymphoma, a Comparison with the EuroClonality/BIOMED-2 Assay","authors":"Ryuko Nakayama ,&nbsp;Leonie I. Kroeze ,&nbsp;Jeroen Luijks ,&nbsp;Avital Amir ,&nbsp;Jos Rijntjes ,&nbsp;Konnie M. Hebeda ,&nbsp;Patricia J.T.A. Groenen","doi":"10.1016/j.jmoldx.2025.08.007","DOIUrl":"10.1016/j.jmoldx.2025.08.007","url":null,"abstract":"<div><div>Nodal T follicular helper cell lymphoma (nTFHL) can be difficult to diagnose because it often shows features of immune dysregulation and can have a low number of neoplastic T cells in involved lymph nodes. The analysis of T-cell receptor (TR) gene rearrangements by next-generation sequencing (NGS) and the conventional EuroClonality/BIOMED-2 were performed to compare their performance on this challenging diagnosis. DNA was extracted from 32 formalin-fixed, paraffin-embedded nTFHL samples from two pathology archives. NGS amplicon-based analysis of TRBV-TRBD-TRBJ, TRBD-TRBJ, and TRGV-TRGJ rearrangements was performed using the two-step PCR protocols developed by EuroClonality. The nucleotide sequences were analyzed for abundance, clonotype, and functionality. Both the NGS-based and the conventional clonality assays resulted in a high detection of clonality (97% and 94%, respectively), including both monoclonal and biclonal cases. There was an overrepresentation of TRBV20-1 and TRBV19 gene use that was in line with the frequent use of these genes in T cells of reactive lymph nodes and tonsils. The NGS-based approach detected two or more clonal targets in all clonal samples, whereas the conventional assay detected a single (isolated) dominant rearrangement in three cases. Hence, NGS enables more reliable detection of even small clones, as is frequent in nTFHL. NGS-based TR rearrangement analysis provides the abundance, the sequences, clonotypes, and productivity of the clonal rearrangements and thus stresses the need for novel guidelines for interpretation.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1154-1165"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151698","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":"Performance Evaluation of the Aptima hrHPV Nucleic Acid Amplification and Papanicolaou Co-Testing in Cervical Cancer Screening","authors":"Sagee Tal ,&nbsp;Jordan A. Vowels ,&nbsp;Daniel González ,&nbsp;Efstathia Polychronopoulou ,&nbsp;Ranjana S. Nawgiri ,&nbsp;Ping Ren","doi":"10.1016/j.jmoldx.2025.08.006","DOIUrl":"10.1016/j.jmoldx.2025.08.006","url":null,"abstract":"<div><div>Cervical cancer screening is evolving, with guidelines increasingly favoring high-risk human papillomavirus (hrHPV) nucleic acid amplification tests (NAATs) as a primary method. Although hrHPV NAATs offer high sensitivity for HPV-driven cervical cancers, Papanicolaou (Pap) cytology can detect additional gynecologic malignancies, including HPV-independent ones. This study evaluated the Hologic Aptima hrHPV NAAT and Pap co-testing using 61,089 samples from patients aged ≥21 years screened between 2018 and 2023. The cohort was predominantly White (78.4%), with 16.5% Black, 4.1% Asian, and 38.9% Hispanic subjects. Overall percentage agreement (PA) between hrHPV NAAT and Pap was 87.9%, with high negative PA (93.6%) and lower positive PA (52.3%). Excluding atypical squamous/glandular cell abnormalities improved overall and positive PA to 93.0% and 78.3%, respectively. The Aptima hrHPV NAAT showed high sensitivity for high-grade squamous intraepithelial lesions (98.3%) and squamous cell carcinoma (90.0%) but lower sensitivity for low-grade lesions (73.3%), adenocarcinoma (13.3%), and other malignancies (28.6%). Notably, 29 high-grade lesions or malignant cases had abnormal Pap but were hrHPV negative; 24 (82.8%) were histologically confirmed, including endometrial, cervical, ovarian, and fallopian tube carcinomas (mostly non–HPV-related). These findings emphasize cytology's role in detecting malignancies potentially missed by hrHPV testing alone and support co-testing in diverse populations. The Aptima hrHPV NAAT is not approved by the US Food and Drug Administration for primary HPV screening, reinforcing this need.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1166-1173"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151663","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":"TAG-CLL, a Novel Tagmentation-Based Approach to Somatic Hypermutation Testing of IGHV Reveals the Weak Points of Both Sanger and Next-Generation Sequencing Methods","authors":"Marzena Wojtaszewska ,&nbsp;Monika Szelest ,&nbsp;Marta Szarawarska ,&nbsp;Jarosław Grzyb ,&nbsp;Beata Blajer-Olszewska ,&nbsp;Michał Gniot ,&nbsp;Emilia Jaskuła ,&nbsp;Jarosław Dybko ,&nbsp;Michał Soin ,&nbsp;Katarzyna Wasilewska ,&nbsp;Sylwia Czekalska ,&nbsp;Magdalena Zawada ,&nbsp;Magdalena Wojtas ,&nbsp;Iwona Solarska ,&nbsp;Agnieszka Kwak ,&nbsp;Piotr Wójcik ,&nbsp;Ewelina Nowak-Ozimek ,&nbsp;Artur Kowalik ,&nbsp;Tomasz Stokłosa ,&nbsp;Agnieszka Chudy ,&nbsp;Mirosław Markiewicz","doi":"10.1016/j.jmoldx.2025.08.005","DOIUrl":"10.1016/j.jmoldx.2025.08.005","url":null,"abstract":"<div><div>Somatic hypermutation (SHM) status of <em>IGHV</em> gene, despite being a mature diagnostic biomarker in chronic lymphocytic leukemia (CLL), poses serious methodological problems for molecular laboratories. They may choose between inefficient Sanger sequencing protocols and expensive, recently developed next-generation sequencing–based methods. The performance of both types of methods seemed incomparable, and concerted validation of different protocols between laboratories was inconsiderable. Here, a new tagmentation-based approach to sequencing of <em>IGHV</em> locus is presented, which is agnostic to the amplification protocol used and enables direct comparison of the amplicons and libraries dedicated to different platforms (Sanger, IonTorrent, and Illumina). To demonstrate its potential, the 12 associated molecular diagnostics laboratories were asked to amplify an artificially prepared oligoclonal DNA sample containing a near-equimolar mixture of <em>IGHV</em> clonotypes from six different classes. The PCR products collected from laboratories were then tagmented and sequenced according to the common TAG-CLL workflow. The productivity, degree of germline identity, and SHM status concordance between laboratories have been analyzed. Moreover, systematic biases toward uneven amplification of different clonotypes and the prevalence of accidental artifacts <em>in vitro</em> and <em>in silico</em> have been evaluated, providing a framework for future validation of <em>IGHV</em> SHM methods and next-generation sequencing immunoinformatic pipeline benchmarking.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1137-1153"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151680","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":"Comparative Performance of a Targeted Next-Generation Sequencing Assay Against Multiplexed Digital PCR Assays in Detecting ERBB2, ESR1, and PIK3CA Mutations in Plasma Circulating Cell-Free DNA from Liquid Biopsies","authors":"Julien Corné ,&nbsp;Florence Godey ,&nbsp;Angelina Legros ,&nbsp;Laurent Castéra ,&nbsp;Sophie Krieger ,&nbsp;Mathilde Chérel ,&nbsp;Agathe Cochet ,&nbsp;Fanny Le Du ,&nbsp;Héloïse Bourien ,&nbsp;Antoine Deleuze ,&nbsp;Laurence Crouzet ,&nbsp;Christophe Perrin ,&nbsp;Claudia Lefeuvre-Plesse ,&nbsp;Véronique Diéras ,&nbsp;Thibault De la Motte Rouge","doi":"10.1016/j.jmoldx.2025.08.012","DOIUrl":"10.1016/j.jmoldx.2025.08.012","url":null,"abstract":"<div><div>Analyzing somatic mutations in liquid biopsies poses a real challenge in treating patients with breast cancer. Because of the high sensitivity required to detect circulating tumor DNA, which may be present at low levels, digital PCR analysis seems highly appropriate. However, new targeted next-generation sequencing solutions are now available, enabling highly sensitive multigene analysis that could benefit patients. This study compared the analytical performance of multiplex digital PCR and targeted next-generation sequencing in detecting somatic erb-b2 receptor tyrosine kinase 2 (<em>ERBB2</em>), estrogen receptor 1 (<em>ESR1</em>), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (<em>PIK3CA</em>) mutations in a series of 32 plasma samples from patients with metastatic breast cancer. Forty-four mutations were detected, with an overall concordance of 95% (90/95) and a high degree of correlation (<em>R</em>² = 0.9786). Interestingly, two <em>ESR1</em> mutations detected in multiplex drop-off digital PCR were also detected by targeted next-generation sequencing with comparable mutant allele frequencies, enabling the identification of these specific variants (p.D538N and p.536LYD&gt;P). Moreover, an additional <em>PIK3CA</em> mutation (p.P539R) was first detected using targeted next-generation sequencing and later confirmed with a newly designed digital PCR assay. Although more expensive than multiplex digital PCR, these new types of small targeted next-generation sequencing gene panels could provide a rapid answer to a specific clinical question with a ready-to-use solution, which could benefit patients.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1202-1212"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145276489","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":"Analysis of the Fragmentation and Integrity of Urine Cell-Free DNA as a Diagnostic and Staging Biomarker for Bladder Cancer","authors":"Raquel Herranz ,&nbsp;Julia Oto ,&nbsp;Emma Plana ,&nbsp;Javier Pérez-Ardavín ,&nbsp;Patricia Verger ,&nbsp;Manuel Martínez-Sarmiento ,&nbsp;César D. Vera-Donoso ,&nbsp;Pilar Medina","doi":"10.1016/j.jmoldx.2025.08.010","DOIUrl":"10.1016/j.jmoldx.2025.08.010","url":null,"abstract":"<div><div>Bladder cancer (BC) is a lethal urological malignancy, with current diagnostic and follow-up methods being invasive and costly. Cell-free DNA (cfDNA) in liquid biopsies has shown promise in cancer diagnostics, but its fragmentation and integrity in urine remain underexplored in BC, becoming the aim of this study. cfDNA was isolated from the urine of 156 patients with BC of most stages and 79 matched controls without renal or bladder conditions. The amount of a large (&gt;250-bp) and a nested small (&lt;125-bp) fragment of <em>ACTB</em>, <em>AR</em>, <em>MYC</em>, <em>BCAS1</em>, and <em>STOX1</em> was quantified by quantitative real-time PCR. Fragmentation and integrity (ratio of large/small) were analyzed with ordinal logistic regression. The increase in the ratio of large/small ACTB fragments and the small fragments of <em>AR</em> and <em>MYC</em> may represent a valuable tool to diagnose and stage BC when classified as both non–muscle-invasive and muscle-invasive BC or considering grades and stages separately. The small fragment of <em>MYC</em>, leading the effect observed, displayed a valuable diagnostic capacity [area under the receiver operating characteristic (ROC) curve = 0.7221; 95% CI, 0.6527–0.7915; <em>P</em> &lt; 0.0001; sensitivity = 50%; specificity = 95%], particularly for muscle-invasive BC (area under the ROC curve = 0.8098; 95% CI, 0.6674–0.9523; <em>P</em> &lt; 0.0001; sensitivity = 70%; specificity = 97%). Herein, the analysis of urine cfDNA fragmentation and integrity of these surrogate markers is proposed as noninvasive biomarkers to diagnose and stage BC. Once validated, the proposed biomarkers could improve patient management by reinforcing or substituting current invasive and expensive techniques.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1189-1201"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187330","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":"Analytical Validation of a Pan-Cancer Next-Generation Sequencing Assay for In-House Liquid Biopsy Testing","authors":"Gaëlle Lescuyer ,&nbsp;Alexandre Harlé ,&nbsp;Hari Shankar Kumar ,&nbsp;Pantelis Constantoulakis ,&nbsp;Nicole Pfarr ,&nbsp;Ellen Heitzer ,&nbsp;Clémence Michon ,&nbsp;Gianluca Russo ,&nbsp;Ernst-Jan M. Speel ,&nbsp;Marie Piecyk ,&nbsp;Marie Husson ,&nbsp;Georgia Christopoulou ,&nbsp;Eva-Maria Mayr ,&nbsp;Mai-Lan Koppermann ,&nbsp;Christophe Passot ,&nbsp;Ricarda Graf ,&nbsp;Anes Hadjadj Aoul ,&nbsp;Violaine Bourdon ,&nbsp;Hendrikus J. Dubbink ,&nbsp;Ronald van Marion ,&nbsp;Léa Payen","doi":"10.1016/j.jmoldx.2025.08.008","DOIUrl":"10.1016/j.jmoldx.2025.08.008","url":null,"abstract":"<div><div>Liquid biopsy assays are transforming precision oncology by providing a less invasive alternative to tissue biopsies. These assays screen for tumor genetic alterations in circulating free DNA, which typically requires detecting variants at low allele frequencies and, therefore, a high sensitivity and specificity. This international, multicenter analytical performance study evaluated the Hedera Profiling 2 circulating tumor DNA test panel (HP2), a hybrid capture–based next-generation sequencing assay for the detection of somatic alterations in circulating free DNA. Covering 32 genes, HP2 enables the detection of single-nucleotide variants (SNVs), insertions and deletions (Indels), fusions, copy number variations, and microsatellite instability status from a single DNA-only workflow. The analytical performance was assessed using reference standards and a diverse cohort of 137 clinical samples precharacterized by orthogonal methods. In reference standards with variants spiked in at 0.5% allele frequency, sensitivity and specificity were 96.92% and 99.67%, respectively, for SNVs/Indels and 100% for fusions. In clinical samples, SNV/Indel detection showed high concordance (94% for European Society for Medical Oncology Scale of Clinical Actionability for Molecular Targets level I variants) with orthogonal methods. Evidence for solid sensitivity was also found for copy number variation detection and microsatellite instability status determination. Overall, the HP2 assay showed significant potential as a sensitive and efficient pan-cancer test for liquid biopsy testing in a decentralized molecular pathology laboratory setting.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1174-1188"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182383","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":"Yield of an Active Candida auris Molecular Surveillance Program at a Tertiary Care Cancer Center","authors":"Krupa Jani ,&nbsp;Tracy McMillen ,&nbsp;Cindy Lee ,&nbsp;Edwin Miranda ,&nbsp;Stephanie Rizzo ,&nbsp;Anoshe Aslam ,&nbsp;Tania Bubb ,&nbsp;Mini Kamboj ,&nbsp;N. Esther Babady","doi":"10.1016/j.jmoldx.2025.09.009","DOIUrl":"10.1016/j.jmoldx.2025.09.009","url":null,"abstract":"<div><div><em>Candida auris</em> is a high-priority multidrug-resistant yeast. In New York, <em>C. auris</em> is reportable, and surveillance screening is recommended for high-risk patients. This study provides a retrospective review of the yield and characteristics of <em>C. auris</em> cases detected through active surveillance testing at a tertiary cancer care center. Testing for <em>C. auris</em> was performed using a laboratory-developed real-time PCR test on patients admitted to the intensive care unit. Sample sources included axilla, groin, and nares swabs. <em>Candida auris–</em>positive PCR samples were further tested by culture with recovered isolates identified and further characterized by whole-genome sequencing and antifungal susceptibility testing. From 2019 to 2023, 27,299 samples were tested, with 139 positive samples (0.5%) on 16 unique patients. Positive swabs included 40 of 139 (28.7%) axilla, 44 of 139 (31.7%) nares, and 55 of 139 (39.5%) groin. A total of 134 of 139 (96.4%) samples were cultured, and 76 of 134 (56.7%) were positive in culture. An increase in positive swabs was noted. Four patients developed disseminated infections following a positive surveillance swab. Whole-genome sequencing classified all isolates as clade I, except for one isolate identified as clade III. Resistance to fluconazole was detected in 80% of isolates. Although the positivity rate remained low in this patient population, the recent increase in cases of <em>C. auris</em> nationwide underlies the need for active surveillance to prevent spread of this multidrug-resistant organism.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1224-1231"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356661","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}