Journal of Molecular Diagnostics最新文献_第6页

A New Serotyping Method of Streptococcus pneumoniae Based on CRISPR/Cas9–Targeted Sequencing 基于 CRISPR/Cas9 靶向测序的肺炎链球菌血清分型新方法

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-25 DOI: 10.1016/j.jmoldx.2024.08.009

Yustinus Maladan , Endah Retnaningrum , Budi Setiadi Daryono , Rosantia Sarassari , Ratna Fathma Sari , Sarah Azhari Balqis , Ghina Athyah Wahid , Dodi Safari

{"title":"A New Serotyping Method of Streptococcus pneumoniae Based on CRISPR/Cas9–Targeted Sequencing","authors":"Yustinus Maladan , Endah Retnaningrum , Budi Setiadi Daryono , Rosantia Sarassari , Ratna Fathma Sari , Sarah Azhari Balqis , Ghina Athyah Wahid , Dodi Safari","doi":"10.1016/j.jmoldx.2024.08.009","DOIUrl":"10.1016/j.jmoldx.2024.08.009","url":null,"abstract":"<div><div>Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) application for targeted sequencing has made a breakthrough in the genomic research era. High diversity in the capsular polysaccharide (<em>cps</em>) locus of <em>Streptococcus pneumoniae</em> has hampered identification of the serotype. This study developed a new serotyping method for <em>S. pneumoniae</em> using CRISPR/Cas9–targeted sequencing with the Oxford Nanopore Technologies platform. A probe was designed at the position of the <em>cps</em> locus using an excision approach on two sides flanking genes between the <em>dexB</em> and <em>aliA</em> genes with approximately 20 kb. A native barcoding method was used for multiplexing. The probe will attach to a specific side followed by attachment of CRISPR/Cas9 to cut the recognition area. The study used <em>de novo</em> assembly to reconstruct sequence reads, which were analyzed using PneumoCRISPR, a new serotyping pipeline for Oxford Nanopore Technologies sequencing data output. Four CRISPR/Cas9 probes have been designed and recognize the <em>cps</em> locus of <em>S. pneumoniae</em>. Serotyping results align precisely with serotyping data from whole-genome sequencing. This serotyping method also allows researchers to use multiple samples in a single run. The new serotyping method based on CRISPR/Cas9–targeted sequencing holds immense promise for serotype identification of <em>S. pneumoniae</em>.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 12","pages":"Pages 1045-1054"},"PeriodicalIF":3.4,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721844","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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Changes and Challenges in Molecular Diagnostics 分子诊断的变化与挑战

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-25 DOI: 10.1016/j.jmoldx.2024.06.012

Karen L. Kaul , Timothy J. O'Leary , Barbara Zehnbauer

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Sensitivity and Specificity of Chimerism Tests in Predicting Leukemia Relapse Using Increasing Mixed Chimerism 利用不断增加的混合嵌合体预测白血病复发的嵌合体检验灵敏度和特异性

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-25 DOI: 10.1016/j.jmoldx.2024.09.003

Ruoheng Zhang , Yimeng Shang , Joseph Cioccio , Kevin Rakszawski , Myles Nickolich , Christopher Ehmann , Yoshitaka Inoue , Seema Naik , Witold Rybka , Hong Zheng , Joseph Mierski , Brooke Silar , Jason Liao , Robert Greiner , Valerie Brown , David Claxton , Jing Ning , Shouhao Zhou , Shin Mineishi , Kentaro Minagawa , Hiroko Shike

{"title":"Sensitivity and Specificity of Chimerism Tests in Predicting Leukemia Relapse Using Increasing Mixed Chimerism","authors":"Ruoheng Zhang , Yimeng Shang , Joseph Cioccio , Kevin Rakszawski , Myles Nickolich , Christopher Ehmann , Yoshitaka Inoue , Seema Naik , Witold Rybka , Hong Zheng , Joseph Mierski , Brooke Silar , Jason Liao , Robert Greiner , Valerie Brown , David Claxton , Jing Ning , Shouhao Zhou , Shin Mineishi , Kentaro Minagawa , Hiroko Shike","doi":"10.1016/j.jmoldx.2024.09.003","DOIUrl":"10.1016/j.jmoldx.2024.09.003","url":null,"abstract":"<div><div>Chimerism test was evaluated to predict leukemia relapse. Increasing mixed chimerism (IMC), defined as recipient increase ≥0.1% in peripheral blood total cell chimerism, was used as a surrogate of disease activity. Combination of quantitative PCR and short-tandem repeat method was applied to achieve high assay sensitivity. Total of 184 patients received stem cell transplant for acute myeloid leukemia (N = 110), acute lymphocytic leukemia (N = 41), myelodysplastic syndrome (N = 30), and 2389 chimerism tests (median follow-up, 1054 days). Sixty-six patients relapsed, and 118 patients did not. Cumulative incidence of relapse increased after 1 IMC or ≥2 consecutive IMCs (hazard ratios, 9.9 and 44.4, respectively). Predicted percentage relapse by day 30 after IMC was 0% (0 IMC), 10% (1 IMC), and 40% (≥2 IMCs). The last chimerism results before relapse detected IMC in 57 of 66 relapsed patients (sensitivity, 86.4%). Nine patients had no IMC before relapse (false negative) because of rapidly evolving relapse (N = 4) or extramural relapse (N = 5). In 118 patients without relapse, 158 of 1873 tests detected IMC (false positive, 8.4%; specificity, 91.6%). The false-positive rates increased with higher percentage recipient T-cell chimerism levels, indicating T-cell contamination as a cause. Chimerism monitoring predicts relapse. However, caution must be taken for false-positive or false-negative IMCs. T-cell removal can improve chimerism test specificity in patients with mixed T-cell chimerism.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 12","pages":"Pages 1159-1170"},"PeriodicalIF":3.4,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721941","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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Title page 扉页

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-01 DOI: 10.1016/S1525-1578(24)00230-7

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Disclosure Statement 披露声明

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-01 DOI: 10.1016/S1525-1578(24)00231-9

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Navigating the Flood 在洪水中航行：2019年冠状病毒疾病爆发期间的高效稿件处理。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-10-24 DOI: 10.1016/j.jmoldx.2024.03.011

Yi-Wei Tang , Barbara A. Zehnbauer

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25 Years of Publishing The Journal of Molecular Diagnostics 分子诊断学杂志》出版 25 周年。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-10-24 DOI: 10.1016/j.jmoldx.2024.08.003

Emily H. Essex

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The Era of Molecular Hematopathology 分子血液病理学时代：回到未来。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-10-24 DOI: 10.1016/j.jmoldx.2024.06.011

Pawel Mroz , Mark D. Ewalt , Susan E. Harley , Patricia C. Tsang , Rena R. Xian , Craig R. Soderquist

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Detection and Interpretation of Clonal Hematopoiesis Variants during Routine Solid Tumor Next-Generation Sequencing 常规实体瘤新一代测序过程中克隆造血变异的检测与解读：单个机构的经验。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-10-02 DOI: 10.1016/j.jmoldx.2024.09.004

Adil Menon, Madina Sukhanova, Kevin L. Nocito, Juehua Gao, Lawrence J. Jennings, Erica R. Vormittag-Nocito

{"title":"Detection and Interpretation of Clonal Hematopoiesis Variants during Routine Solid Tumor Next-Generation Sequencing","authors":"Adil Menon, Madina Sukhanova, Kevin L. Nocito, Juehua Gao, Lawrence J. Jennings, Erica R. Vormittag-Nocito","doi":"10.1016/j.jmoldx.2024.09.004","DOIUrl":"10.1016/j.jmoldx.2024.09.004","url":null,"abstract":"<div><div>Clonal hematopoiesis (CH) and clonal cytopenia of undetermined significance (CCUS) are recently recognized diagnostic entities that serve as independent risk factors for cardiovascular disease and myeloid malignancy. CH is an incidental finding, and evaluation of the incidence of CH/CCUS-associated mutations in solid tumor next-generation sequencing samples was undertaken to better understand the prevalence of mutations in this population. A retrospective review of clinical sequencing data for solid tumor malignancies diagnosed between February 2022 and April 2023 on next-generation sequencing data was performed. Cases were reviewed for variants in genes associated with CH/CCUS. Variant allele frequencies and other factors of the sequencing data were assessed for determining risk of CH/CCUS. A total of 2479 cases were evaluated during the study period. Of these, 29 cases demonstrated potential CH/CCUS-associated mutations, with a total of 33 variants identified. These were identified in a variety of tumor types, with gliomas being the most common. Significant cardiac histories were found in over half of cases identified, and few cases had abnormal blood counts. Detailed criteria for flagging variants as suspicious for CH and recommendations for these criteria as future guidelines for reporting are described. These variants are incidental findings that require more extensive follow-up or change in therapy management using a single institutional cohort.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 12","pages":"Pages 1149-1158"},"PeriodicalIF":3.4,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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A Single Multiplex PCR and Single-Nucleotide Extension Assay for the Detection of Common Thanatophoric Dysplasia I and II Mutations 用于检测常见甲状腺发育不良 I 型和 II 型突变的单一多重 PCR 和单核苷酸延伸测定。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-09-30 DOI: 10.1016/j.jmoldx.2024.08.008

Mohamed A. Jama , N. Scott Reading , Eric Fredrickson , Sherin Shaaban , Yuan Ji

{"title":"A Single Multiplex PCR and Single-Nucleotide Extension Assay for the Detection of Common Thanatophoric Dysplasia I and II Mutations","authors":"Mohamed A. Jama , N. Scott Reading , Eric Fredrickson , Sherin Shaaban , Yuan Ji","doi":"10.1016/j.jmoldx.2024.08.008","DOIUrl":"10.1016/j.jmoldx.2024.08.008","url":null,"abstract":"<div><div>Mutation analysis provides confirmation of a clinical and radiological diagnosis of thanatophoric dysplasia types I and II (TD I and II). We developed a single multiplexed PCR and a single-nucleotide extension (SNE) assay to identify 14 common mutations causing 99% of TD I and TD II, including the challenging three adjacent mutations in the stop codon of exon 18 of the <em>FGFR3</em> gene. The assay design also provides a solution for resolving SNE PCR product sizing using performance optimized polymer-7. The assay was validated using 37 previously characterized, de-identified patient samples representing the nine wild-types and 10 of 14 mutant genotypes. Four artificial templates were synthesized to mimic four TD I mutations not represented in the available patient samples. Fragment size and fluorophore channel for each SNE product from 10 samples and the four artificial templates were used to define bins and panels for analysis with GeneMarker version 3.0 and GeneMapper version 6.0 software. Allele calls (bin placement within the panels) were verified using the remaining 27 previously characterized samples. This TD I and II PCR and SNE assay is a robust multiplexed assay, streamlined, to identify 14 mutations in one single reaction. This assay has a shorter turnaround time in comparison to traditional Sanger or next-generation sequencing.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 12","pages":"Pages 1102-1108"},"PeriodicalIF":3.4,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367258","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