Journal of Molecular Diagnostics最新文献_第3页

A Comprehensive Guide to Achieving New York State Clinical Laboratory Evaluation Program Approval for Next-Generation Sequencing Assays 实现纽约州临床实验室评估计划批准下一代测序测定的综合指南。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-28 DOI: 10.1016/j.jmoldx.2025.02.009

Phillip M. Galbo Jr. , Robert F. Klees , Blake Burgher , Kiersten M. Miles , Carl M. Morrison , Sean T. Glenn

{"title":"A Comprehensive Guide to Achieving New York State Clinical Laboratory Evaluation Program Approval for Next-Generation Sequencing Assays","authors":"Phillip M. Galbo Jr. , Robert F. Klees , Blake Burgher , Kiersten M. Miles , Carl M. Morrison , Sean T. Glenn","doi":"10.1016/j.jmoldx.2025.02.009","DOIUrl":"10.1016/j.jmoldx.2025.02.009","url":null,"abstract":"<div><div>The US Food and Drug Administration's recent move to regulate laboratory-developed tests as <em>in vitro</em> diagnostics has raised significant interest and concerns regarding its implementation. The New York State Department of Health's Clinical Laboratory Evaluation Program (CLEP) provides a useful framework for understanding laboratory-developed test oversight, particularly through its guidelines for next-generation sequencing assays. These CLEP requirements for analytical validation are widely recognized as a national standard, yet there is limited peer-reviewed literature detailing the studies needed for CLEP approval. This study presents the validation of the Rapid Pan-Heme (RPPH) assay, a genomic profiling tool for hematopoietic neoplasms, developed in compliance with CLEP standards. The RPPH assay features a comprehensive next-generation sequencing panel targeting >400 genes with clinically relevant variants, including single-nucleotide variants, insertions and deletions, and fusions critical for classifying hematopoietic malignancies. CLEP approval mandates detailed documentation, quality control metrics, validation studies (accuracy, precision, and reproducibility), and compliant clinical reporting. It is demonstrated that RPPH achieves CLEP's stringent analytical sensitivity and reproducibility criteria. Variants were orthogonally validated, and proper controls were implemented. Additionally, it is outlined how RPPH's clinical reports align with CLEP requirements. Overall, this study establishes RPPH as a robust molecular diagnostic tool and provides actionable insights for researchers navigating regulatory compliance and assay validation in clinical settings.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 485-501"},"PeriodicalIF":3.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755541","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}

引用次数: 0

Performance Evaluation of a Next-Generation Sequencing–Based T-Cell Receptor Gene Rearrangement Assay 基于测序的下一代t细胞受体基因重排测定的性能评价。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-28 DOI: 10.1016/j.jmoldx.2025.02.010

Danica Wiredja , Diane Libert , Diwash Jangam , Chandler Ho , Jack Tung , Bing Melody Zhang

{"title":"Performance Evaluation of a Next-Generation Sequencing–Based T-Cell Receptor Gene Rearrangement Assay","authors":"Danica Wiredja , Diane Libert , Diwash Jangam , Chandler Ho , Jack Tung , Bing Melody Zhang","doi":"10.1016/j.jmoldx.2025.02.010","DOIUrl":"10.1016/j.jmoldx.2025.02.010","url":null,"abstract":"<div><div>T-cell receptor (TCR) gene rearrangement clonality studies help resolve atypical T-cell proliferations in the context of suspected malignancy. However, the interpretation criteria for this assay using a next-generation sequencing (NGS) platform have not been extensively explored and standardized. Thus, this project assessed the current performance of the Stanford Health Care in-house NGS-based TCR clonality diagnostic testing with the goal of optimizing the interpretation criteria and identifying recurrent analytical challenges. The current assay identifies a predominant clonotype when its sequence comprises at least 2.5% of the total reads with at least 5× fold change from the background. Using concurrent pathology reports as the clinical truth, this project analyzed 619 cases and determined that the current assay performs at 74% sensitivity and 85% specificity. Receiver operating characteristic analysis identified an optimized interpretation criterion that only improved the diagnostic yield marginally compared with the preexisting algorithm. Further clinicopathologic evaluation of discordant cases revealed that discrepancies mostly arose from technical limitations or the underlying nuanced biology of the diagnosis. Overall, this study provides an objective approach in establishing the interpretation criteria of the current NGS-based TCR clonality test and offers a roadmap for other laboratories considering implementing a similar assay.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 465-474"},"PeriodicalIF":3.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755589","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}

引用次数: 0

Deciphering Genomic Complexity of Multiple Myeloma Using Optimized Optical Genome Mapping 利用优化的光学基因组图谱破译多发性骨髓瘤的基因组复杂性

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-25 DOI: 10.1016/j.jmoldx.2025.01.003

Hélène Guermouche , Pauline Roynard , Francesca Servoli , Valentin Lestringant , Benoît Quilichini , Christine Terré , Sabine Defasque , Catherine Roche-Lestienne , Dominique Penther , Agnès Daudignon

{"title":"Deciphering Genomic Complexity of Multiple Myeloma Using Optimized Optical Genome Mapping","authors":"Hélène Guermouche , Pauline Roynard , Francesca Servoli , Valentin Lestringant , Benoît Quilichini , Christine Terré , Sabine Defasque , Catherine Roche-Lestienne , Dominique Penther , Agnès Daudignon","doi":"10.1016/j.jmoldx.2025.01.003","DOIUrl":"10.1016/j.jmoldx.2025.01.003","url":null,"abstract":"<div><div>The genomic evaluation of multiple myeloma in routine diagnostics involves isolating plasma cells expressing CD138, usually followed by fluorescence <em>in situ</em> hybridization analyses. However, cell sorting often yields a limited number of cells, restricting the number of probes that can be used and limiting the analysis to a few markers required for minimal prognostic classification. Optical genome mapping is a high-resolution technology capable of identifying structural variants and copy number variations across the entire genome; however, it currently requires 1 million cells. To overcome this constraint, an innovative strategy was implemented in this work based on mixing CD138-positive and CD138-negative fractions from the same patient, optimizing the use of available CD138-positive cells for genome-wide analysis. First, dilution experiments demonstrated that a 50% CD138-positive mix was sufficient to achieve complete detection of clonal structural and copy number variants, while establishing a detection threshold of 24% for copy number variants. Using this optimized protocol, 13 additional samples from 13 patients were analyzed. Optical genome mapping achieved 93% (13/15) concordance with fluorescence <em>in situ</em> hybridization for clonal anomalies and revealed >22 additional genomic variations not detected by fluorescence <em>in situ</em> hybridization. This strategy consolidated multiple analyses into a single test, minimized material requirements, and addressed critical prognostic and increasingly described anomalies, providing refined stratification for patients with multiple myeloma.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 4","pages":"Pages 306-322"},"PeriodicalIF":3.4,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143696861","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}

引用次数: 0

Careers Can Turn on Tiny Events—Be Prepared for Them 职业生涯可能会因为小事而改变——为此做好准备

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-25 DOI: 10.1016/j.jmoldx.2024.10.006

Daniel H. Farkas

引用次数: 0

Platelets, Chromogranin A, and C-Reactive Protein Predict Therapy Failure of Metastatic Hormone-Sensitive Prostate Cancer while miR-375 Outperforms Prostate-Specific Antigen in Stratifying Castration-Resistant Prostate Cancer 血小板、嗜铬粒蛋白A和c反应蛋白预测转移性激素敏感性前列腺癌治疗失败，而miR-375在去势抵抗性前列腺癌分层方面优于PSA。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-24 DOI: 10.1016/j.jmoldx.2025.02.006

Eva Chrenková , Radka Spurná , Kateřina Holá , Jana Vrbková , Jana Knillová , Monika Levková , Hana Študentová , Jan Bouchal

{"title":"Platelets, Chromogranin A, and C-Reactive Protein Predict Therapy Failure of Metastatic Hormone-Sensitive Prostate Cancer while miR-375 Outperforms Prostate-Specific Antigen in Stratifying Castration-Resistant Prostate Cancer","authors":"Eva Chrenková , Radka Spurná , Kateřina Holá , Jana Vrbková , Jana Knillová , Monika Levková , Hana Študentová , Jan Bouchal","doi":"10.1016/j.jmoldx.2025.02.006","DOIUrl":"10.1016/j.jmoldx.2025.02.006","url":null,"abstract":"<div><div>Androgen deprivation therapy has long been the first-line treatment for hormone-sensitive prostate cancer (HSPC). After progression to castration-resistant prostate cancer (CRPC), androgen receptor pathway inhibitors (ARPIs) are commonly used. Recently, combined therapy with androgen deprivation and an ARPI has been recommended for metastatic HSPC patients. Novel markers are urgently needed for monitoring this disease and for making therapeutic decisions. Plasma samples were collected from 140 patients with either metastatic HSPC (<em>n</em> = 72) or CRPC (<em>n</em> = 68) before the start of ARPI therapy. Digital PCR was used to assess <em>AR</em> gene amplification, while the expression levels of miR-375 were measured by quantitative PCR. Sixteen other clinical markers were also evaluated, including prostate-specific antigen (PSA), chromogranin A (CGA), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), C-reactive protein (CRP), lymphocyte-to-monocyte ratio, and platelet count. A multivariate analysis, adjusted for age and metastatic dissemination, identified miR-375 expression and lymphocyte-to-monocyte ratio to be the independent negative predictors of ARPI therapy failure in CRPC patients. Regarding the HSPC patients, this article reports the primary finding of the independent negative predictive value of platelet count, CRP, and CGA for the failure of combined androgen deprivation therapy and ARPI.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 446-456"},"PeriodicalIF":3.4,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143732845","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}

引用次数: 0

New Resources to Identify Characterized DNA Reference Materials for Pharmacogenetic (PGx) and Human Leukocyte Antigen (HLA) Testing 基因检测参考物质（GeT-RM）程序PGx搜索工具和GeT-RM整合PGx和HLA表：鉴定鉴定PGx和HLA检测特征DNA参考物质的新资源

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-21 DOI: 10.1016/j.jmoldx.2025.02.008

Laura Scheinfeldt , Dara Kusic , Andrea Gaedigk , Amy J. Turner , Ann M. Moyer , Victoria M. Pratt , Lisa V. Kalman

{"title":"New Resources to Identify Characterized DNA Reference Materials for Pharmacogenetic (PGx) and Human Leukocyte Antigen (HLA) Testing","authors":"Laura Scheinfeldt , Dara Kusic , Andrea Gaedigk , Amy J. Turner , Ann M. Moyer , Victoria M. Pratt , Lisa V. Kalman","doi":"10.1016/j.jmoldx.2025.02.008","DOIUrl":"10.1016/j.jmoldx.2025.02.008","url":null,"abstract":"<div><div>Regulations, accreditation standards, and professional guidance require laboratories to use reference materials for assay development, validation, quality control, and proficiency testing of clinical genetic tests. There are, however, few publicly available reference materials for most genetic tests. To address this issue, the CDC's Genetic Testing Reference Material Program (GeT-RM), the Coriell Institute for Medical Research, and the genetic testing community have conducted 19 studies, including nine for pharmacogenetic (PGx) and human leukocyte antigen (HLA) testing, to generate characterized, renewable, and publicly available DNA samples for use as reference materials. Because new PGx alleles are frequently identified, and allele designations change over time, many samples were reanalyzed for the same gene(s) in subsequent GeT-RM studies. These studies used more comprehensive and sensitive methods and panels that examined additional single-nucleotide variants and/or star alleles to expand and update the consensus genotypes. Up-to-date information is available in two newly established resources: the GeT-RM Consolidated PGx and HLA Table and the GeT-RM PGx Search Tool. These resources contain all available PGx and HLA genotypes for 363 publicly available samples characterized during nine GeT-RM PGx or HLA studies for 34 genes/loci in a consolidated and searchable format.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 457-464"},"PeriodicalIF":3.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694290","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}

引用次数: 0

Comparison of Targeted RNA-Sequencing Platforms for Oncogenic Fusion Detection in Non–Small-Cell Lung Cancer 非小细胞肺癌致癌融合检测靶向RNA测序平台的比较。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-21 DOI: 10.1016/j.jmoldx.2025.02.007

Alicia Dillard , Kemin Xu , Yichao Sun , Han-Hsuan Lin , Cong Shen , Eric Song , Ashish Saxena , Erika Hissong , Anna Yemelyanova , Neal I. Lindeman , Priya D. Velu , James P. Solomon

{"title":"Comparison of Targeted RNA-Sequencing Platforms for Oncogenic Fusion Detection in Non–Small-Cell Lung Cancer","authors":"Alicia Dillard , Kemin Xu , Yichao Sun , Han-Hsuan Lin , Cong Shen , Eric Song , Ashish Saxena , Erika Hissong , Anna Yemelyanova , Neal I. Lindeman , Priya D. Velu , James P. Solomon","doi":"10.1016/j.jmoldx.2025.02.007","DOIUrl":"10.1016/j.jmoldx.2025.02.007","url":null,"abstract":"<div><div>Oncogenic fusion detection is an essential part of clinical diagnosis and management of non–small-cell lung carcinoma. Numerous methods are available for detection of oncogenic fusions in the clinical laboratory, although RNA sequencing has rapidly gained prominence. Accordingly, however, multiple different RNA-sequencing assays exist, with diverse methods and varying performance characteristics. Here, a single-institutional clinical experience with a testing algorithm for non–small-cell lung carcinoma that uses amplicon-based DNA/RNA sequencing, followed by reflex hybridization-capture–based RNA sequencing if the initial testing is negative for oncogenic drivers, is reported. A total of 1211 non–small-cell lung carcinoma specimens were received for molecular testing, and 120 (approximately 10%) were reflexed for hybridization-capture–based RNA sequencing. Of the 120 cases tested, oncogenic fusions were identified in 9 and included clinically actionable fusions involving <em>ALK</em>, <em>BRAF</em>, <em>NRG1</em>, <em>NTRK3</em>, <em>ROS1</em>, and <em>RET</em>. None of these fusions was detected by the amplicon-based assay. Review of the 20,900 non–small-cell lung cancer cases in the American Association for Cancer Research Project Genie version 15.1 publicly available database (registration required) revealed that of the 1081 cases harboring fusions, 893 (82.6%) could theoretically be detected by the amplicon-based assay. Overall, this study shows that the addition of reflex hybridization-capture–based RNA sequencing could improve detection of rare and novel oncogenic fusions, maximizing patient eligibility for appropriate targeted therapies or clinical trials.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 438-445"},"PeriodicalIF":3.4,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694289","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}

引用次数: 0

4qA D4Z4 Methylation Test as a Valuable Complement for Differential Diagnosis in Patients with a Facioscapulohumeral Muscular Dystrophy–Like Phenotype 4qA D4Z4甲基化检测作为fshd样表型患者鉴别诊断的有价值补充。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-18 DOI: 10.1016/j.jmoldx.2025.02.003

Xingyu Xia , Nachuan Cheng , Yiqi Liu , Dongyue Yue , Mingshi Gao , Chaoping Hu , Kexin Jiao , Ningning Wang , Bochen Zhu , Xuechun Chang , Minghui Zeng , Jie Song , Chong Sun , Chong Yan , Jianying Xi , Jie Lin , Sushan Luo , Zhiqiang Wang , Jiahong Lu , Peter L. Jones , Wenhua Zhu

{"title":"4qA D4Z4 Methylation Test as a Valuable Complement for Differential Diagnosis in Patients with a Facioscapulohumeral Muscular Dystrophy–Like Phenotype","authors":"Xingyu Xia , Nachuan Cheng , Yiqi Liu , Dongyue Yue , Mingshi Gao , Chaoping Hu , Kexin Jiao , Ningning Wang , Bochen Zhu , Xuechun Chang , Minghui Zeng , Jie Song , Chong Sun , Chong Yan , Jianying Xi , Jie Lin , Sushan Luo , Zhiqiang Wang , Jiahong Lu , Peter L. Jones , Wenhua Zhu","doi":"10.1016/j.jmoldx.2025.02.003","DOIUrl":"10.1016/j.jmoldx.2025.02.003","url":null,"abstract":"<div><div>Facioscapulohumeral muscular dystrophy (FSHD) is caused by pleiotropic contractions of the D4Z4 repeat array on chromosome 4q35 (FSHD1) or by mutations in repressive chromatin regulators of the D4Z4 loci (FSHD2), both resulting in epigenetic dysregulation at the D4Z4 array. DNA methylation of the D4Z4 repeat array has been proposed for diagnosis and prognosis of FSHD disease severity; however, further validation in larger populations is needed. Two hundred forty-seven clinically suspected FSHD cases were retrospectively analyzed with D4Z4 analysis by optical genome mapping or molecular combing and tested the DNA methylation levels for 75 patients and 49 healthy controls. A D4Z4 repeat length–dependent nonlinear increase was observed in both distal and global D4Z4 methylation levels. Distal D4Z4 methylation levels identified patients with FSHD1 with a sensitivity of 100% and a specificity of 97.96% at a cutoff value of 39.66% compared with controls. Distal FSHD1-like hypomethylation was also observed in one subject carrying a special D4Z4 rearrangement, resulting in a proximal contracted array. Clinically, distal methylation levels demonstrated a strong correlation with the age-corrected clinical severity score and onset age. Mediation analysis revealed that the influence of distal methylation on age-corrected clinical severity score was partially mediated by onset age. This study further confirms the distal 4qA D4Z4 methylation analysis as a valuable complement for differential diagnosis in patients with suspected FSHD, including those with complex structural variants.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 5","pages":"Pages 405-418"},"PeriodicalIF":3.4,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671415","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}

引用次数: 0

Equivalent Clinical Accuracy of Human Papillomavirus DNA Testing Using Cobas 4800 and 6800 Human Papillomavirus Systems in Paired Urine and Cervical Samples 在配对尿液和宫颈样本中使用cobas 4800和6800 HPV系统进行HPV DNA检测的同等临床准确性

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-18 DOI: 10.1016/j.jmoldx.2025.02.004

Severien Van Keer , Ardashel Latsuzbaia , Davy Vanden Broeck , Philippe De Sutter , Gilbert Donders , Jean Doyen , Wiebren A.A. Tjalma , Steven Weyers , Marc Arbyn , Alex Vorsters

{"title":"Equivalent Clinical Accuracy of Human Papillomavirus DNA Testing Using Cobas 4800 and 6800 Human Papillomavirus Systems in Paired Urine and Cervical Samples","authors":"Severien Van Keer , Ardashel Latsuzbaia , Davy Vanden Broeck , Philippe De Sutter , Gilbert Donders , Jean Doyen , Wiebren A.A. Tjalma , Steven Weyers , Marc Arbyn , Alex Vorsters","doi":"10.1016/j.jmoldx.2025.02.004","DOIUrl":"10.1016/j.jmoldx.2025.02.004","url":null,"abstract":"<div><div>The use of urine for cervical cancer screening is gaining international attention, although more data on the relative clinical accuracy of validated human papillomavirus (HPV) DNA tests on urine versus cervical samples are needed. This study primarily seeks to evaluate the clinical performance of Roche cobas 4800 and 6800 HPV Systems in first-void urine, collected at home, compared with clinician-collected cervical samples. Paired first-void urine (index test) and cervical samples (comparator test) from 499 females enrolled at five Belgian colposcopy clinics were analyzed with cobas HPV Systems. Colposcopy and histology of biopsies were used as reference test (trial registration number: NCT03064087). Sample processing protocols and clinical thresholds proposed by the manufacturer for cervical samples were also applied for first-void urine. In the total study population, HPV testing on first-void urine was similarly sensitive [ratio<sub>CIN2+</sub>, 0.98; 95% CI, 0.93–1.02] and specific for cobas 4800 HPV (ratio<sub><</sub><sub>CIN2</sub>, 1.00; 95% CI, 0.91–1.10) and cobas HPV for use on the cobas 6800 System (ratio<sub>CIN2+</sub>, 0.96; 95% CI, 0.91–1.02; ratio<sub><</sub><sub>CIN2</sub>, 1.01; 95% CI, 0.93–1.09) compared with cervical samples (<em>P</em> ≥ 0.05). Good to excellent HPV test agreements between paired samples were observed (κ = 0.68 to 0.87). In summary, HPV testing using cobas 4800 and 6800 HPV Systems was as accurate on first-void urine as on cervical samples collected by a clinician.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 5","pages":"Pages 419-429"},"PeriodicalIF":3.4,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143671419","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}

引用次数: 0

Rapid, Reliable, and Interpretable Copy Number Variant Curation Visualizations for Diagnostic Settings with SeeNV 快速，可靠，可解释的CNV策展可视化与SeeNV诊断设置。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-03 DOI: 10.1016/j.jmoldx.2025.01.008

Michael S. Bradshaw , Jishnu Raychaudhuri , Lachlan Murphy , Rebecca Barnard , Taylor Firman , Alisa A. Gaskell , Ryan M. Layer

{"title":"Rapid, Reliable, and Interpretable Copy Number Variant Curation Visualizations for Diagnostic Settings with SeeNV","authors":"Michael S. Bradshaw , Jishnu Raychaudhuri , Lachlan Murphy , Rebecca Barnard , Taylor Firman , Alisa A. Gaskell , Ryan M. Layer","doi":"10.1016/j.jmoldx.2025.01.008","DOIUrl":"10.1016/j.jmoldx.2025.01.008","url":null,"abstract":"<div><div>Copy number variants (CNVs), structural alterations in the genome involving duplication or deletion of DNA segments, are implicated in various health conditions. Despite their clinical significance, accurate identification and interpretation of CNVs remain challenging, especially in the context of whole-exome sequencing (WES), which is commonly used in clinical diagnostic laboratories. Although WES offers economic advantages over whole-genome sequencing, it struggles with CNV detection because of technical noise introduced by laboratory and analytic processes. Manual curation of CNV calls generated by these tools is labor intensive and error prone. To address this, SeeNV, a command-line tool, is introduced to aid manual curation of CNVs at scale. SeeNV is one solution to these issues, developed in collaboration with and used by the Precision Diagnostics Laboratory at Children's Hospital Colorado. SeeNV generates static infographics for each CNV, incorporating sample and cohort sequencing coverage statistics, CNV population frequency, and, more, facilitating rapid and precise assessment. Using CNV calls identified in publicly available WES and whole-genome sequencing samples, users can rapidly and reliably curate CNV calls, needing only 4.3 seconds to curate a call, achieving 0.95 recall (analytical sensitivity) and 0.74 precision (positive predictive value). SeeNV is freely available for download on GitHub.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 5","pages":"Pages 336-345"},"PeriodicalIF":3.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568766","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}

引用次数: 0