Journal of Molecular Diagnostics最新文献

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Technical Advance Efficient and ultrasensitive identification of clinical somatic mutations by modified single duplex DNA sequencing. 技术进步利用改进的单双链DNA测序技术高效、超灵敏地鉴定临床体细胞突变。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-10-19 DOI: 10.1016/j.jmoldx.2026.09.004
Kelsi Peneweit, Adam Waalkes, Megan Nguyen, Scott R Kennedy, Eric Q Konnick, Stephen J Salipante
{"title":"Technical Advance Efficient and ultrasensitive identification of clinical somatic mutations by modified single duplex DNA sequencing.","authors":"Kelsi Peneweit, Adam Waalkes, Megan Nguyen, Scott R Kennedy, Eric Q Konnick, Stephen J Salipante","doi":"10.1016/j.jmoldx.2026.09.004","DOIUrl":"https://doi.org/10.1016/j.jmoldx.2026.09.004","url":null,"abstract":"<p><p>Conventional next-generation sequencing (NGS) implementations have poor sensitivity for low prevalence mutations due to their inherent error rate. Error suppression that reconciles individual strands of a DNA duplex can improve sensitivity. Concatenating Original Duplex for Error Correction (CODEC) is an emerging technology that physically links duplex strands to enable their comparison from a single read pair, circumventing high sequencing depths normally required to recover strands independently. However, use in clinical practice is constrained by technical shortcomings. We modified CODEC (mCODEC) to improve performance, workflow, scalability, and informatic analyses for clinical use. Redesigned adapters improve compatibility with hybridization capture procedures, increase multiplexing capacity and molecular identifier length per molecule, and enable enzymatic removal of uninformative ligation byproducts. We benchmarked mCODEC using bacteriophage reference material and clinical specimens. Relative to the original protocol, mCODEC improved on-target reads from a targeted gene enrichment panel by over an order of magnitude and reduced malformed ligation byproducts. mCODEC achieved equivalent error correction to CODEC (<5.4×10<sup>-5</sup> errors per nucleotide), making it two orders of magnitude more robust than conventional sequencing (∼3×10<sup>-3</sup> per nucleotide) while consuming only three-fold more reads. We explored clinical utility of mCODEC using targeted gene enrichment to examine patient neoplasms previously interrogated through a conventional NGS oncology assay, finding mCODEC able to identify low prevalence, clinically reportable mutations not detectable by standard-of-care testing.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149225355","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
Optimizing Pathogen Detection in Clinical Metagenomics: A Comprehensive Benchmarking of Bioinformatic Pipelines for Single-End Short Reads. 优化临床宏基因组学中的病原体检测:单端短Reads生物信息管道的综合基准测试。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-10-17 DOI: 10.1016/j.jmoldx.2026.09.003
Jun Ma, Ting Hao, Yahong Bai, Lei Xiao, Qianqian Yang, Penggao Dai, Huijuan Wang
{"title":"Optimizing Pathogen Detection in Clinical Metagenomics: A Comprehensive Benchmarking of Bioinformatic Pipelines for Single-End Short Reads.","authors":"Jun Ma, Ting Hao, Yahong Bai, Lei Xiao, Qianqian Yang, Penggao Dai, Huijuan Wang","doi":"10.1016/j.jmoldx.2026.09.003","DOIUrl":"https://doi.org/10.1016/j.jmoldx.2026.09.003","url":null,"abstract":"<p><p>Metagenomic next-generation sequencing for identifying pathogens has been increasingly utilized as a diagnostic tool. Prior research mostly emphasizes the selection of classification software based on reads above 100bp, neglecting the influence of sequencing data pre- and post-processing stages. Independently assessment was performed assessed the efficacy and effects of tools for each phase, encompassing quality control, host read elimination, taxonomic classification, and false positive removal, utilized in a metagenomics analysis pipeline employing single-end 50bp reads derived from sequencing 13 positive-control mock community samples. The efficacy of tool combinations was assessed using single-end 50 bp data from identical mock samples processed using different wet-lab methodologies. The findings indicate that the selection of quality control and host-removal techniques is essential, significantly influencing the extraction of microbial reads from clinical metagenomic sequencing data and resulting in elevated alpha diversity. While false-positive filtering enhances precision for trimming tool-based combinations without impacting recall, its effect is limited for combinations utilizing the bt2 aligner. The tool combination pipelines integrated with various false positive methodologies for four microbial categories: no filtering for bacteria, bracken for fungi, relative abundance (>0.1%) for DNA viruses, and z-score (z > 3) for RNA virus identification, as implemented in the prior R Shiny application for forthcoming benchmarking. This study highlights the critical role of preprocessing and classifier selection in accurate metagenomic pathogen identification.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149217351","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
Presubmission Pathologic Quality Control for FoundationOne CDx Comprehensive Genomic Profiling. FoundationOne CDx综合基因组图谱的提交前病理质量控制。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-10-14 DOI: 10.1016/j.jmoldx.2026.09.002
Yume Natori, Yosuke Hirotsu, Masahiro Shibusawa, Kaito Nakamura, Shunsuke Watanabe, Saki Amemiya, Yuki Nagakubo, Ryosuke Tajiri, Toshio Oyama, Hitoshi Mochizuki, Masao Omata
{"title":"Presubmission Pathologic Quality Control for FoundationOne CDx Comprehensive Genomic Profiling.","authors":"Yume Natori, Yosuke Hirotsu, Masahiro Shibusawa, Kaito Nakamura, Shunsuke Watanabe, Saki Amemiya, Yuki Nagakubo, Ryosuke Tajiri, Toshio Oyama, Hitoshi Mochizuki, Masao Omata","doi":"10.1016/j.jmoldx.2026.09.002","DOIUrl":"10.1016/j.jmoldx.2026.09.002","url":null,"abstract":"<p><p>Comprehensive genomic profiling using FoundationOne CDx (F1CDx) requires formalin-fixed, paraffin-embedded specimens with sufficient tumor area and DNA yield. Presubmission pathologic assessment is critical but has not been systematically evaluated in real-world practice. This study analyzed 371 consecutive F1CDx requests at a cancer genomic medicine designated hospital in Japan. Presubmission quality checks assessed tumor surface area and estimated section numbers and residual specimen volume. Assay outcomes were classified as presubmission cancellation, temporary suspension (insufficient DNA, suspected contamination, or technical issues), qualified, or pass. Of 371 requests, 52 (14.0%) were cancelled before submission, mainly because of insufficient specimen volume or clinical decision. Among 319 submitted cases, 22 (6.9%) were temporarily suspended. Among 297 cases with returned results, 256 (86.2%) achieved pass quality and 41 (13.8%) were qualified. Tumor content-related parameters, including institutional tumor content, laboratory-assessed tumor content, and sequencing-estimated tumor content, were all significantly lower in qualified than in pass cases. In qualified cases, evaluation of tumor mutational burden and microsatellite instability was successful in only 31.7% and 19.5%, respectively. In multivariable analysis, lower tumor content was the only independent predictor of quality control failure. These findings indicate most F1CDx assay failures are attributable to insufficient tumor content or specimen volume. Strengthened presubmission quality control and coordinated workflows can meaningfully improve comprehensive genomic profiling success. Limitations include the retrospective single-institution design and lack of external validation.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149185696","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
Protecting Access to Medicare Act, What Molecular Professionals and Laboratories Need to Know. 保护获得医疗法案,分子专业人员和实验室需要知道的。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-10-09 DOI: 10.1016/j.jmoldx.2026.08.006
Victoria M Pratt, Eric Q Konnick, Samantha K Pettersen, Jay L Patel
{"title":"Protecting Access to Medicare Act, What Molecular Professionals and Laboratories Need to Know.","authors":"Victoria M Pratt, Eric Q Konnick, Samantha K Pettersen, Jay L Patel","doi":"10.1016/j.jmoldx.2026.08.006","DOIUrl":"10.1016/j.jmoldx.2026.08.006","url":null,"abstract":"","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149148718","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
Clonal Relatedness Index: Practical and Reliable Tool for Establishing Clonal Relatedness in Gastrointestinal, Hepatopancreaticobiliary, and Peritoneal Carcinomas. 克隆相关性指数-建立胃肠道、肝、胰、胆管和腹膜癌克隆相关性的实用可靠工具。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-09-25 DOI: 10.1016/j.jmoldx.2026.09.001
Gertruda Evaristo, Mina Saber Farag, Pankhuri Wanjari, Aniela Mitchell, Joseph Guter, Ardaman Shergill, Chih-Yi Liao, Blase Polite, Peng Wang, Melissa Yuwono Tjota, Jeremy Segal, Namrata Setia
{"title":"Clonal Relatedness Index: Practical and Reliable Tool for Establishing Clonal Relatedness in Gastrointestinal, Hepatopancreaticobiliary, and Peritoneal Carcinomas.","authors":"Gertruda Evaristo, Mina Saber Farag, Pankhuri Wanjari, Aniela Mitchell, Joseph Guter, Ardaman Shergill, Chih-Yi Liao, Blase Polite, Peng Wang, Melissa Yuwono Tjota, Jeremy Segal, Namrata Setia","doi":"10.1016/j.jmoldx.2026.09.001","DOIUrl":"10.1016/j.jmoldx.2026.09.001","url":null,"abstract":"<p><p>Although accepted as gold standard, conventional morphology and immunohistochemistry-based methods of determining clonal relatedness between two neoplasms are inconclusive in a subset of patients. Next-generation sequencing data can be used for this purpose; however, this approach has not been widely clinically validated for gastrointestinal (GI)/hepatopancreaticobiliary (HPB)/peritoneal carcinomas. This study evaluated tumor-specific alterations in 120 paired GI/HPB/peritoneal tumors from 60 patients, previously established as clonal (n = 52) or non-clonal (n = 8) based on their clinicopathologic characteristics. A clonal relatedness index (CRI) was calculated as proportion of shared over the average of total alterations and was compared versus phenotype-based clonality prediction. Based on 1508 assessed alterations, the median CRI was 0.85 (interquartile range, 0.69 to 0.95) for clonal cohorts and 0.24 (interquartile range, 0.06 to 0.43) for non-clonal cohorts. CRI receiver-operating characteristic analysis yielded area under the curve of 0.986 (95% CI, 0.962-1.0; P < 0.01), with optimal sensitivity (Sn) and specificity (Sp) at CRI = 0.53. In the overall cohort, phenotype predicted clonality with Sn = 71.2%, Sp = 62.5%, and positive predictive value (PPV) of 92.5% (P = 1), versus CRI with 96.2%, 100%, and 100% (P < 0.001), respectively. In tumors associated with hypermutability, Sn of phenotype dropped to 42.9%, Sp = 33.3%, and PPV = 60.0% (P = 1), whereas CRI maintained Sn = 85.7%, Sp = 100%, and PPV = 100% (P = 0.03). CRI performance remained robust in a validation cohort and with the addition of alternative genomic alterations. CRI is a practical, clinically accessible, and highly relevant tool that outperforms the phenotype-based method and is essential in reliably establishing clonal relatedness in GI/HPB/peritoneal carcinomas.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149065647","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
The 10-Year Evolution of Sherloc, a Points-Based Framework for Genetic Variant Classification. 基于点的遗传变异分类框架Sherloc的十年进化。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-09-22 DOI: 10.1016/j.jmoldx.2026.08.005
Yuya Kobayashi, Marjorie Jody Westbrook, Christopher A Tan, Carla Marquez Luna, Alexander Wahl, Daniel Swartzlander, Karen Ouyang, Robert D Daber
{"title":"The 10-Year Evolution of Sherloc, a Points-Based Framework for Genetic Variant Classification.","authors":"Yuya Kobayashi, Marjorie Jody Westbrook, Christopher A Tan, Carla Marquez Luna, Alexander Wahl, Daniel Swartzlander, Karen Ouyang, Robert D Daber","doi":"10.1016/j.jmoldx.2026.08.005","DOIUrl":"10.1016/j.jmoldx.2026.08.005","url":null,"abstract":"<p><p>Variant classification underpins the clinical utility of genetic testing. Sherloc is a refinement of the 2015 American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines that implements a structured, points-based scoring framework. It has been applied to 2.6 million variants through 19 versions [version 4.2 (v4.2) to version 7.1] for 5.5 million individuals referred for genetic testing. Here, iterative updates to Sherloc over 10 years were evaluated for their effect on variant classification. Refinements to the scoring framework were expected to progressively reduce the rate of variants of uncertain significance (VUSs). Furthermore, it was hypothesized that points-based scores would serve as quantitative predictors of VUS reclassification outcomes. Tracking 32,241 variants initially classified with v4.2, 3834 VUSs had been reclassified by the study end; 2801 (73%) of these relied on evidence criteria introduced after v4.2. Separately, in a simulated removal of post-v4.2 evidence criteria from 615,341 recent classifications, removing artificial intelligence-related criteria altered classifications for 129,459 (21.0%) variants. The Sherloc score was strongly correlated with the log ratio of upgrades to downgrades (adjusted r<sup>2</sup> = 0.95) and moderately correlated with the overall reclassification rate (adjusted r<sup>2</sup> = 0.49). High-scoring VUSs were disproportionately reclassified by cascade family testing or RNA analysis, although most variants reclassified by these approaches had low scores. These findings demonstrate that adaptive, points-based classification systems materially reduce VUS rates and support quantitative, score-based variant evaluation.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149026670","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
Parallel Analysis of Repeat Expansions: An Updated Clinical Nanopore Cas9-Targeted Sequencing Workflow for Nanopore R10 Flow Cells. 重复扩增的平行分析:纳米孔R10流细胞的更新clint - cats工作流程。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-09-15 DOI: 10.1016/j.jmoldx.2026.04.007
Veronika Scholz, Veronika Schönrock, Hannes Erdmann, Vitus Prokosch, Maria Schoedel, Manuela Almus, Mayra Sauer, Veronika Mayer, Eva Breithausen, Inga van Buren, Christine Dineiger, Madeline Golibrzuch, Minerva Montero-Hernández, Annette Lischka, Katja Eggermann, Caroline Heintz, Ariane Hallermayr, Teresa Neuhann, Elke Holinski-Feder, Angela Abicht, Anna Benet-Pagès, Morghan C Lucas
{"title":"Parallel Analysis of Repeat Expansions: An Updated Clinical Nanopore Cas9-Targeted Sequencing Workflow for Nanopore R10 Flow Cells.","authors":"Veronika Scholz, Veronika Schönrock, Hannes Erdmann, Vitus Prokosch, Maria Schoedel, Manuela Almus, Mayra Sauer, Veronika Mayer, Eva Breithausen, Inga van Buren, Christine Dineiger, Madeline Golibrzuch, Minerva Montero-Hernández, Annette Lischka, Katja Eggermann, Caroline Heintz, Ariane Hallermayr, Teresa Neuhann, Elke Holinski-Feder, Angela Abicht, Anna Benet-Pagès, Morghan C Lucas","doi":"10.1016/j.jmoldx.2026.04.007","DOIUrl":"10.1016/j.jmoldx.2026.04.007","url":null,"abstract":"<p><p>Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. An updated Clinical Nanopore Cas9-Targeted Sequencing workflow is presented for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the Oxford Nanopore Technologies wf-human-variation Epi2Me workflow, including the Straglr tool to analyze base-called reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 and introduces new gene panels for ataxia, myopathy, neurodegeneration, and amyotrophic lateral sclerosis/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches. In this work, the use of multiplexing, Flongle flow cells, and single-gene targeting were explored as alternatives to panel-based approaches in the Clinical Nanopore Cas9-Targeted Sequencing workflow, finding that only single-gene targeting provides compatibility and reliable performance.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148978551","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
The Effect of Unique Molecular Identifier Family Size Using Tumor-Informed Circulating Tumor DNA Analysis in Childhood Cancers. 使用肿瘤信息循环肿瘤dna分析的独特分子标识符家族大小对儿童癌症的影响。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-09-11 DOI: 10.1016/j.jmoldx.2026.08.002
Tobias Österlund, Daniel Andersson, Raghda R Ibrahim, Elisabeth Mellström, Jenny Lundmark, Junrui Li, Stefan Filges, Peter Micallef, Manuel Luna Santamaría, Mandy Escobar, Pia Mouhanna, Firaol T Kebede, Christoffer Vannas, Ida Rahmqvist, Fani Pujol-Calderón, Agnes Dahlstrand Rudin, Wilma Franssila, Åsa Torinsson Naluai, Serik Sagitov, Joakim Håkansson, Henrik Fagman, Martin Dalin, Anders Ståhlberg
{"title":"The Effect of Unique Molecular Identifier Family Size Using Tumor-Informed Circulating Tumor DNA Analysis in Childhood Cancers.","authors":"Tobias Österlund, Daniel Andersson, Raghda R Ibrahim, Elisabeth Mellström, Jenny Lundmark, Junrui Li, Stefan Filges, Peter Micallef, Manuel Luna Santamaría, Mandy Escobar, Pia Mouhanna, Firaol T Kebede, Christoffer Vannas, Ida Rahmqvist, Fani Pujol-Calderón, Agnes Dahlstrand Rudin, Wilma Franssila, Åsa Torinsson Naluai, Serik Sagitov, Joakim Håkansson, Henrik Fagman, Martin Dalin, Anders Ståhlberg","doi":"10.1016/j.jmoldx.2026.08.002","DOIUrl":"10.1016/j.jmoldx.2026.08.002","url":null,"abstract":"<p><p>Analysis of circulating tumor DNA (ctDNA) provides a molecular assessment that can complement routine imaging in childhood cancer management. Detailed monitoring of ctDNA levels may provide information on treatment efficacy and resistance and minimal residual disease and allows for early detection of relapse. Here, tumor-informed ctDNA analysis was applied to 90 blood plasma samples collected from eight children with malignant tumors. A total of 4 to 10 tumor-specific mutations per patient were assessed using SiMSen-Seq, a digital sequencing approach using unique molecular identifiers (UMIs). The effects of individual SiMSen-Seq assays and plasma samples were evaluated in relation to their impact on background error rate, number of detected target molecules, and mutant calling using different UMI family size cutoff settings. The use of at least two sequencing reads per UMI provided the best overall performance by generating the highest number of detected target molecules and hence the optimal chance to detect low-frequency mutations. Data were consistent between SiMSen-Seq assays and plasma samples, providing robust ctDNA profiling over time for all patients. In conclusion, the results show that optimal use of UMIs in tumor-informed ctDNA analysis enables sensitive molecular readout that can assist in management of childhood cancers.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946091","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
Long-Read Sequencing Resolves Complex CYP21A2 Variants and Identifies 2+0 Carriers in 21-Hydroxylase Deficiency. 长读测序解决了复杂的CYP21A2变异,并鉴定了21-羟化酶缺乏的2+0携带者。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-09-11 DOI: 10.1016/j.jmoldx.2026.08.004
Yanjie Xia, Di Cui, Danhua Li, Libao Chen, Xiaohang Chen, Shitong Wu, Aiping Mao, Xiangdong Kong
{"title":"Long-Read Sequencing Resolves Complex CYP21A2 Variants and Identifies 2+0 Carriers in 21-Hydroxylase Deficiency.","authors":"Yanjie Xia, Di Cui, Danhua Li, Libao Chen, Xiaohang Chen, Shitong Wu, Aiping Mao, Xiangdong Kong","doi":"10.1016/j.jmoldx.2026.08.004","DOIUrl":"10.1016/j.jmoldx.2026.08.004","url":null,"abstract":"<p><p>The complex CYP21A2 variants arising from high homology with its pseudogene CYP21A1P challenge the diagnosis of 21-hydroxylase deficiency (21-OHD). This study systematically evaluated long-read sequencing (LRS) for identifying complex structural variants of the CYP21A2 gene in 21-OHD in comparison with conventional molecular diagnostic methods, including multiplex ligation-dependent probe amplification, CNVplex, and SNaPshot. Twenty patients with suspected 21-OHD and defined CYP21A2 structural variants identified via initial multiplex ligation-dependent probe amplification screening were enrolled. Variants were further analyzed using CNVplex and SNaPshot, then all samples underwent LRS for comprehensive variant detection, breakpoint mapping, and haplotype resolution. LRS overcame key limitations of conventional methods. It reliably identified a novel large-fragment deletion and defined its boundaries. Notably, LRS identified 2+0 carriers, where deletions masked by duplications cause false negatives with standard techniques. Moreover, LRS accurately distinguished CYP21A1P/CYP21A2_CH-4 and CH-9 chimera subtypes, which were indistinguishable by the combined conventional assays. Furthermore, LRS enabled the precise identification and characterization of TNXA/TNXB chimeric deletions. These are frequently misclassified as CYP21A1P/CYP21A2 chimeras by conventional methods but are critical for diagnosing associated conditions such as congenital adrenal hyperplasia-X syndrome. LRS provides a superior, integrated solution for the molecular diagnosis of 21-OHD, offering precise structural variant characterization, accurate carrier detection, and reliable breakpoint mapping. Its application enhances diagnostic accuracy, supports advanced genetic counseling, and paves the way for genotype-informed clinical management.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946105","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
Toward a Robust Cell-free DNA Isolation Protocol for Next-Generation Sequencing Applications in a Clinical Molecular Diagnostics Setting. 迈向一个强大的无细胞DNA分离协议NGS应用于临床分子诊断设置。
IF 3.9 3区 医学
Journal of Molecular Diagnostics Pub Date : 2026-09-11 DOI: 10.1016/j.jmoldx.2026.08.003
Melina Apweiler, Julian Broche, Marion Loitz, Luise Hackenbruch, Stephan Ossowski, Christopher Schroeder, Kristopher J Schmit
{"title":"Toward a Robust Cell-free DNA Isolation Protocol for Next-Generation Sequencing Applications in a Clinical Molecular Diagnostics Setting.","authors":"Melina Apweiler, Julian Broche, Marion Loitz, Luise Hackenbruch, Stephan Ossowski, Christopher Schroeder, Kristopher J Schmit","doi":"10.1016/j.jmoldx.2026.08.003","DOIUrl":"10.1016/j.jmoldx.2026.08.003","url":null,"abstract":"<p><p>Cell-free (cf) DNA, released from apoptotic and necrotic cells into bodily fluids, is a noninvasive source of genetic information for disease prediction, diagnosis, and monitoring. However, its low abundance makes cfDNA highly susceptible to various preanalytical influences, potentially increasing high-molecular-weight or genomic DNA, compromising downstream cfDNA analysis. This study evaluated the impact of different cfDNA-stabilizing blood collection tubes (Cell-Free DNA BCT, Streck; S-Monovette cfDNA Exact, Sarstedt) stored at room temperature for 1, 5, or 10 days prior to plasma isolation using different isolation methods (magnetic bead based or silica column based) on cfDNA stability and yield. DNA quantity and quality were assessed by fluorometric quantification, automated fragment analysis, and gene-specific real-time quantitative PCR. Streck-based workflows maintained stable cfDNA yields and characteristic mononucleosomal fragmentation profiles across all storage times. In contrast, Sarstedt tubes showed reduced cfDNA concentrations after 5 days and a pronounced increase at 10 days, accompanied by high-molecular-weight DNA patterns consistent with white blood cell lysis. These trends were largely independent of the extraction method. Overall, the results demonstrate that blood collection tube chemistry critically influences cfDNA integrity during delayed processing. The Streck tubes, particularly when combined with the silica column-based isolation method, provided the most robust and reproducible workflow for routine molecular diagnostics, whereas the Sarstedt tubes produced physiologically implausible results after extended storage.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.9,"publicationDate":"2026-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946080","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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