Journal of Molecular Diagnostics最新文献

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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":"<p><p>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 ALK, BRAF, NRG1, NTRK3, ROS1, and RET. 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.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"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 ,&nbsp;Nachuan Cheng ,&nbsp;Yiqi Liu ,&nbsp;Dongyue Yue ,&nbsp;Mingshi Gao ,&nbsp;Chaoping Hu ,&nbsp;Kexin Jiao ,&nbsp;Ningning Wang ,&nbsp;Bochen Zhu ,&nbsp;Xuechun Chang ,&nbsp;Minghui Zeng ,&nbsp;Jie Song ,&nbsp;Chong Sun ,&nbsp;Chong Yan ,&nbsp;Jianying Xi ,&nbsp;Jie Lin ,&nbsp;Sushan Luo ,&nbsp;Zhiqiang Wang ,&nbsp;Jiahong Lu ,&nbsp;Peter L. Jones ,&nbsp;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 ,&nbsp;Ardashel Latsuzbaia ,&nbsp;Davy Vanden Broeck ,&nbsp;Philippe De Sutter ,&nbsp;Gilbert Donders ,&nbsp;Jean Doyen ,&nbsp;Wiebren A.A. Tjalma ,&nbsp;Steven Weyers ,&nbsp;Marc Arbyn ,&nbsp;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>&lt;</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>&lt;</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 ,&nbsp;Jishnu Raychaudhuri ,&nbsp;Lachlan Murphy ,&nbsp;Rebecca Barnard ,&nbsp;Taylor Firman ,&nbsp;Alisa A. Gaskell ,&nbsp;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
Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using High-Throughput Chromosome Conformation Capture 使用 Hi-C 检测 FFPE 实体瘤标本中的基因融合和重排。
IF 3.4 3区 医学
Journal of Molecular Diagnostics Pub Date : 2025-02-27 DOI: 10.1016/j.jmoldx.2025.01.007
Kristyn Galbraith , Jamin Wu , Kristin Sikkink , Hussein Mohamed , Derek Reid , Michelle Perez-Arreola , Jon-Matthew Belton , Sofia Nomikou , Shadi Melnyk , Yiying Yang , Benjamin L. Liechty , George Jour , Aristotelis Tsirigos , David J. Hermel , Alyssa Beck , Darren Sigal , Nathan A. Dahl , Rajeev Vibhakar , Anthony Schmitt , Matija Snuderl
{"title":"Detection of Gene Fusions and Rearrangements in Formalin-Fixed, Paraffin-Embedded Solid Tumor Specimens Using High-Throughput Chromosome Conformation Capture","authors":"Kristyn Galbraith ,&nbsp;Jamin Wu ,&nbsp;Kristin Sikkink ,&nbsp;Hussein Mohamed ,&nbsp;Derek Reid ,&nbsp;Michelle Perez-Arreola ,&nbsp;Jon-Matthew Belton ,&nbsp;Sofia Nomikou ,&nbsp;Shadi Melnyk ,&nbsp;Yiying Yang ,&nbsp;Benjamin L. Liechty ,&nbsp;George Jour ,&nbsp;Aristotelis Tsirigos ,&nbsp;David J. Hermel ,&nbsp;Alyssa Beck ,&nbsp;Darren Sigal ,&nbsp;Nathan A. Dahl ,&nbsp;Rajeev Vibhakar ,&nbsp;Anthony Schmitt ,&nbsp;Matija Snuderl","doi":"10.1016/j.jmoldx.2025.01.007","DOIUrl":"10.1016/j.jmoldx.2025.01.007","url":null,"abstract":"<div><div>Chromosomal structural variants (SVs) are major contributors to cancer development. Although multiple methods exist for detecting SVs, they are limited in throughput, such as fluorescent <em>in situ</em> hybridization and targeted panels, and use RNA, which degrades in formalin-fixed, paraffin-embedded (FFPE) blocks and is unable to detect SVs that do not produce a fusion transcript. High-throughput chromosome conformation capture (Hi-C) is a DNA-based next-generation sequencing (NGS) method that preserves the spatial conformation of the genome, capturing long-range genetic interactions and SVs. Herein, a retrospective study analyzing 71 FFPE specimens from 10 different solid tumors was performed. Results showed high concordance (98%) with clinical fluorescent <em>in situ</em> hybridization and RNA NGS in detecting known SVs. Furthermore, Hi-C provided insight into the mechanism of SV formation, including chromothripsis and extrachromosomal DNA, and detected rearrangements between genes and regulatory regions, all of which are undetectable by RNA NGS. Lastly, SVs were detected in 71% of cases in which previous clinical methods failed to identify a driver. Of these, 14% were clinically actionable based on current medical guidelines, and an additional 14% were not in medical guidelines but involve targetable biomarkers. Current data suggest that Hi-C is a robust and accurate method for genome-wide SV analyses from FFPE tissue and can be incorporated into current clinical NGS workflows.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 5","pages":"Pages 346-359"},"PeriodicalIF":3.4,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537013","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
A Novel and Comprehensive Whole-Genome Sequencing–Based Preimplantation Genetic Testing Approach for Different Genetic Conditions 一种针对不同遗传条件的基于全基因组测序的植入前基因检测方法。
IF 3.4 3区 医学
Journal of Molecular Diagnostics Pub Date : 2025-02-27 DOI: 10.1016/j.jmoldx.2025.02.002
Shuyuan Li , Chunxin Chang , Haiyan Bai , Weiping Qian , Yangyun Zou , Dandan Wu , Wenjing Hu , Yulin Chen , Tuan Li , Sijia Lu , Wen Li , Juanzi Shi , Zhiwei Liu
{"title":"A Novel and Comprehensive Whole-Genome Sequencing–Based Preimplantation Genetic Testing Approach for Different Genetic Conditions","authors":"Shuyuan Li ,&nbsp;Chunxin Chang ,&nbsp;Haiyan Bai ,&nbsp;Weiping Qian ,&nbsp;Yangyun Zou ,&nbsp;Dandan Wu ,&nbsp;Wenjing Hu ,&nbsp;Yulin Chen ,&nbsp;Tuan Li ,&nbsp;Sijia Lu ,&nbsp;Wen Li ,&nbsp;Juanzi Shi ,&nbsp;Zhiwei Liu","doi":"10.1016/j.jmoldx.2025.02.002","DOIUrl":"10.1016/j.jmoldx.2025.02.002","url":null,"abstract":"<div><div>Preimplantation genetic testing (PGT) is an essential tool for selecting embryos free of genetic abnormalities. However, current PGT methods often require separate platforms for aneuploidy (PGT-A), monogenic disorders (PGT-M), and structural rearrangements (PGT-SR), leading to increased costs and operational complexity when multiple PGT tests are needed for a single embryo. Here, we present KaryoSeq, a low-pass whole-genome sequencing–based comprehensive PGT approach that integrates PGT-A, PGT-M, and PGT-SR into a single platform. An assistant decision-making system was constructed to pre-evaluate the required sequencing depth for specific genes or regions. Clinical validation of KaryoSeq was performed on 166 blastocyst samples from 31 families previously diagnosed by using conventional PGT methods. KaryoSeq achieved 100% concordance with traditional platforms using the Infinium Asian Screening Array in combination with low-coverage whole-genome sequencing (approximately 0.1×); it also offered improved whole-genome coverage, reduced variability, and efficient simultaneous analysis of PGT-A, PGT-M, and PGT-SR at a whole-genome sequencing depth of approximately 2× for most genes. In addition, KaryoSeq identified triploidy, uniparental disomy, parental origin of copy number variations, and maternal cell contamination, further enhancing its clinical utility and efficiency in PGT applications.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 5","pages":"Pages 395-404"},"PeriodicalIF":3.4,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143536739","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
Impact and Reproducibility of In-House Targeted Next-Generation Sequencing Biomarker Testing in Non–Small-Cell Lung Cancer 非小细胞肺癌内部靶向下一代测序生物标志物检测的影响和可重复性:意大利多机构经验。
IF 3.4 3区 医学
Journal of Molecular Diagnostics Pub Date : 2025-02-27 DOI: 10.1016/j.jmoldx.2025.02.001
Ida Rapa , Francesca Bertola , Gaia Roversi , Davide Seminati , Federica Panebianco , Cecília Durães , Enzo Gallo , Biagio E. Leone , Aldo Palange , Luisella Righi , Paolo Visca , Marco Volante , Simonetta Buglioni
{"title":"Impact and Reproducibility of In-House Targeted Next-Generation Sequencing Biomarker Testing in Non–Small-Cell Lung Cancer","authors":"Ida Rapa ,&nbsp;Francesca Bertola ,&nbsp;Gaia Roversi ,&nbsp;Davide Seminati ,&nbsp;Federica Panebianco ,&nbsp;Cecília Durães ,&nbsp;Enzo Gallo ,&nbsp;Biagio E. Leone ,&nbsp;Aldo Palange ,&nbsp;Luisella Righi ,&nbsp;Paolo Visca ,&nbsp;Marco Volante ,&nbsp;Simonetta Buglioni","doi":"10.1016/j.jmoldx.2025.02.001","DOIUrl":"10.1016/j.jmoldx.2025.02.001","url":null,"abstract":"<div><div>Next-generation sequencing (NGS) allows the detection of multiple genetic targets in different tumor types. This study aimed to confirm the benefits of implementing in-house NGS testing for non–small-cell lung cancer (NSCLC) samples in molecular pathology laboratories. A multi-institutional study was conducted to evaluate the analytical performance, turnaround time, and feasibility of in-house NGS testing of 50 genes from 283 NSCLC samples. The first phase was a retrospective study with interlaboratory testing (21 samples), and the second phase was a prospective study with intralaboratory testing (262 samples). The retrospective study showed a 100% sequencing success rate for DNA and RNA, high interlaboratory concordance (95.2%), and a strong correlation (<em>R</em><sup>2</sup> = 0.94) between observed and expected single-nucleotide variant/insertion and/or deletion variant allele fraction. The prospective study showed a sequencing success rate of 99.2% for DNA and 98% for RNA. NGS identified 285 relevant variants (81.1% single-nucleotide variants/insertion and/or deletion variants, 9.8% copy number variants, and 9.1% gene fusions). Co-mutations with potential clinical relevance were detected in 20.5% of samples positive for the main oncogenic drivers in NSCLC. Additionally, 11% of samples wild type for the main oncogenic drivers carried alterations in other relevant genes. The in-house NGS testing had a median turnaround time from sample processing to molecular report of 4 days. This study demonstrates the advantages of implementing in-house NGS testing in molecular pathology laboratories.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 5","pages":"Pages 371-382"},"PeriodicalIF":3.4,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537514","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
Reviewer Acknowledgment 评论家承认
IF 3.4 3区 医学
Journal of Molecular Diagnostics Pub Date : 2025-02-24 DOI: 10.1016/j.jmoldx.2025.01.001
{"title":"Reviewer Acknowledgment","authors":"","doi":"10.1016/j.jmoldx.2025.01.001","DOIUrl":"10.1016/j.jmoldx.2025.01.001","url":null,"abstract":"","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 3","pages":"Pages 233-234"},"PeriodicalIF":3.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143474168","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
Retaining Clinical Genomics Technologists in the Post–COVID-19 Era 后covid -19时代保留临床基因组学技术人员
IF 3.4 3区 医学
Journal of Molecular Diagnostics Pub Date : 2025-02-24 DOI: 10.1016/j.jmoldx.2024.10.005
Marco L. Leung , Barbara Anderson
{"title":"Retaining Clinical Genomics Technologists in the Post–COVID-19 Era","authors":"Marco L. Leung ,&nbsp;Barbara Anderson","doi":"10.1016/j.jmoldx.2024.10.005","DOIUrl":"10.1016/j.jmoldx.2024.10.005","url":null,"abstract":"","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 3","pages":"Pages 163-165"},"PeriodicalIF":3.4,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143474288","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
Repurposing the Whole Expression Transcriptome Assay for the Genetic Diagnosis of T-Cell Acute Lymphoblastic Leukemia and Lymphoma 全表达转录组测定在t细胞急性淋巴细胞白血病和淋巴瘤的遗传诊断中的应用。
IF 3.4 3区 医学
Journal of Molecular Diagnostics Pub Date : 2025-02-19 DOI: 10.1016/j.jmoldx.2025.01.006
Valentina Bardelli , Silvia Arniani , Valentina Pierini , Carlotta Nardelli , Caterina Matteucci , Anair Graciela Lema Fernandez , Maria Crocioni , Marco Cerrano , Prassede Salutari , Cristina Papayanidis , Silvia Trappolini , Fabio Giglio , Sara Mastaglio , Patrizia Zappasodi , Crescenza Pasciolla , Marzia Defina , Matteo Piccini , Giuseppe Lanzarone , Danika Di Giacomo , Simona Sica , Roberta La Starza
{"title":"Repurposing the Whole Expression Transcriptome Assay for the Genetic Diagnosis of T-Cell Acute Lymphoblastic Leukemia and Lymphoma","authors":"Valentina Bardelli ,&nbsp;Silvia Arniani ,&nbsp;Valentina Pierini ,&nbsp;Carlotta Nardelli ,&nbsp;Caterina Matteucci ,&nbsp;Anair Graciela Lema Fernandez ,&nbsp;Maria Crocioni ,&nbsp;Marco Cerrano ,&nbsp;Prassede Salutari ,&nbsp;Cristina Papayanidis ,&nbsp;Silvia Trappolini ,&nbsp;Fabio Giglio ,&nbsp;Sara Mastaglio ,&nbsp;Patrizia Zappasodi ,&nbsp;Crescenza Pasciolla ,&nbsp;Marzia Defina ,&nbsp;Matteo Piccini ,&nbsp;Giuseppe Lanzarone ,&nbsp;Danika Di Giacomo ,&nbsp;Simona Sica ,&nbsp;Roberta La Starza","doi":"10.1016/j.jmoldx.2025.01.006","DOIUrl":"10.1016/j.jmoldx.2025.01.006","url":null,"abstract":"<div><div>Unlike other cases of acute leukemia, the diagnosis of T-cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL) is uniquely based on morphology and flow cytometry. Although the genomic background has been broadly uncovered, the large spectrum of genes involved and the variability of the molecular mechanisms underlying gene deregulation have delayed the introduction of molecular cytogenetics into diagnostic flowcharts. To overcome these limitations and implement a genetic diagnosis of T-ALL/LBLs, a whole transcriptome expression assay (WTEa) was repurposed as a “priority test” to classify T-ALL/LBLs into the major genetic subtypes. A WTEa classifier based on a set of 312 probes on 215 T-ALL/LBLs was set up and applied, which properly assigned &gt;95% of cases with subtype-defining alterations to the corresponding subgroups (ie, <em>TAL/LMO, HOXA, TLX1, TLX3</em>, <em>BCL11B</em>). It pinpointed cases that harbored cryptic alterations, such as noncoding mutations that generate new enhancer at <em>TAL1</em> and <em>LMO2</em> loci (8% of <em>TAL/LMO</em>), and duplications of noncoding element downstream <em>BCL11B</em> (BETA) (18% of <em>BCL11B</em>). It was also suitable to classify lymphoma cases for which only formalin-fixed embedded tissues were available, as confirmed in cases harboring <em>TLX1</em> or <em>TLX3</em> rearrangements, and distinguished new putative subtypes. WTEa offers a unifying tool to provide a genetic classification of T-ALL/LBLs. If introduced in multicenter prospective studies, it will facilitate evaluation of the clinical impact of genetic classification.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 5","pages":"Pages 360-370"},"PeriodicalIF":3.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472983","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}
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