Journal of Molecular Diagnostics最新文献_第10页

Validation and Implementation of a Somatic-Only Tumor Exome for Routine Clinical Application 用于常规临床应用的体细胞肿瘤外显子组的验证和实施。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-07-06 DOI: 10.1016/j.jmoldx.2024.05.013

引用次数: 0

Assessing the Risk Stratification of Breast Cancer Polygenic Risk Scores in a Brazilian Cohort 评估巴西队列中乳腺癌多基因风险评分的风险分层。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-07-06 DOI: 10.1016/j.jmoldx.2024.06.002

{"title":"Assessing the Risk Stratification of Breast Cancer Polygenic Risk Scores in a Brazilian Cohort","authors":"","doi":"10.1016/j.jmoldx.2024.06.002","DOIUrl":"10.1016/j.jmoldx.2024.06.002","url":null,"abstract":"<div><p>Polygenic risk scores (PRSs) for breast cancer have a clear clinical utility in risk prediction. PRS transferability across populations and ancestry groups is hampered by population-specific factors, ultimately leading to differences in variant effects, such as linkage disequilibrium and differences in variant frequency (allele frequency differences). Thus, locally sourced population-based phenotypic and genomic data sets are essential to assess the validity of PRSs derived from signals detected across populations. This study assesses the transferability of a breast cancer PRS composed of 313 risk variants (313-PRS) in a Brazilian trihybrid admixed ancestries (European, African, and Native American) whole-genome sequenced cohort, the Rare Genomes Project. 313-PRS was computed in the Rare Genomes Project (<em>n</em> = 853) using the UK Biobank (UKBB; <em>n</em> = 264,307) as reference. The Brazilian cohorts have a high European ancestry (EA) component, with allele frequency differences and to a lesser extent linkage disequilibrium patterns similar to those found in EA populations. The 313-PRS distribution was found to be inflated when compared with that of the UKBB, leading to potential overestimation of PRS-based risk if EA is taken as a standard. However, case controls lead to equivalent predictive power when compared with UKBB-EA samples with area under the receiver operating characteristic curve values of 0.66 to 0.62 compared with 0.63 for UKBB.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 9","pages":"Pages 825-831"},"PeriodicalIF":3.4,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555827","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 Utility of Real-Time PCR, Metagenomic Next-Generation Sequencing, and Culture in Bronchoalveolar Lavage Fluid for Diagnosis of Pulmonary Aspergillosis 实时 PCR、元基因组新一代测序和支气管肺泡灌洗液培养在诊断肺曲霉菌病中的实用性。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-07-06 DOI: 10.1016/j.jmoldx.2024.06.003

{"title":"The Utility of Real-Time PCR, Metagenomic Next-Generation Sequencing, and Culture in Bronchoalveolar Lavage Fluid for Diagnosis of Pulmonary Aspergillosis","authors":"","doi":"10.1016/j.jmoldx.2024.06.003","DOIUrl":"10.1016/j.jmoldx.2024.06.003","url":null,"abstract":"<div><p>Timely detection of <em>Aspergillus</em> infection is crucial given the high mortality rate of pulmonary aspergillosis (PA). Here, the diagnostic performances for PA of mycological culture, <em>Aspergillus</em> real-time PCR, and metagenomic next-generation sequencing (mNGS) assay from bronchoalveolar lavage fluid, were evaluated. In total, 139 patients with suspected fungal pneumonia were enrolled between December 2021 and July 2023, collecting 139 bronchoalveolar lavage fluid samples for real-time PCR and culture, with 87 undergoing mNGS assay. The sensitivity, specificity, positive predictive value, negative predictive value, and area under the curve with 95% CIs of these assays for PA were as follows: 35.3% (14.2%–61.7%), 100.0% (94.0%–100.0%), 100.0% (54.1%–100.0%), 84.5% (79.3%–88.6%), and 0.676 (0.560–0.779), respectively, for culture; 82.4% (56.6%–96.2%), 98.3% (91.1%–100.0%), 93.3% (66.4%–99.0%), 95.2% (87.6%–98.2%), and 0.903 (0.815–0.959), respectively, for same diagnostic performance of real-time PCR and mNGS; and 94.1% (71.3%–99.9%), 96.7% (88.5%–99.6%), 88.9% (67.1%–96.9%), 98.3% (89.6%–99.7%), and 0.954 (0.880–0.989), respectively, for real-time PCR combining mNGS; real-time PCR, mNGS, and their combination significantly improved in area under the curve values over culture (<em>P</em> < 0.001), but real-time PCR testing and mNGS had no significant difference with each other and their combination. Overall, the performance of culture was limited by low sensitivity; both real-time PCR and mNGS assays as single diagnostic tests are promising compared with culture and combined tests.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 9","pages":"Pages 832-842"},"PeriodicalIF":3.4,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555829","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

Development, Validation, and Implementation of an Augmented Multiwell, Multitarget Quantitative PCR for the Analysis of Human Papillomavirus Genotyping through Software Automation, Data Science, and Artificial Intelligence 通过软件自动化、数据科学和人工智能，开发、验证和实施增强型多孔、多靶点定量 PCR-HPV 基因分型分析。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-07-05 DOI: 10.1016/j.jmoldx.2024.05.012

{"title":"Development, Validation, and Implementation of an Augmented Multiwell, Multitarget Quantitative PCR for the Analysis of Human Papillomavirus Genotyping through Software Automation, Data Science, and Artificial Intelligence","authors":"","doi":"10.1016/j.jmoldx.2024.05.012","DOIUrl":"10.1016/j.jmoldx.2024.05.012","url":null,"abstract":"<div><p>The value of human papillomavirus (HPV) testing for cervical cancer screening is well established; however, its use as a primary screening option or as a reflex test after atypical cytology results is now gaining wider acceptance. The importance of full genotyping and viral load determination has been demonstrated to enhance the clinical understanding of the viral infection progression during follow-up or after treatment, thereby providing clinicians with supplementary tools for optimized patient management. We developed a new analysis method for the RIATOL quantitative PCR assay, and validated and implemented it in the laboratory of clinical molecular pathology at Algemeen Medisch Laboratorium (AML), under national accreditation and following the International Organization for Standardization guidelines. This study presents the successful validation of a high-throughput, multitarget HPV analysis method, with enhanced accuracy on both qualitative and quantitative end results. This is achieved by software standardization and automation of PCR curve analysis and interpretation, using data science and artificial intelligence. Moreover, the user-centric functionality of the platform was demonstrated to enhance both staff training and routine analysis workflows, thereby saving time and laboratory personnel resources. Overall, the integration of the FastFinder plugin semi-automatic analysis algorithm with the RIATOL real-time quantitative PCR assay proved to be a remarkable advancement in high-throughput HPV quantification, with demonstrated capability to provide highly accurate clinical-grade results and to reduce manual variability and analysis time.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 9","pages":"Pages 781-791"},"PeriodicalIF":3.4,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824001491/pdfft?md5=2946f126a90ecf1d060162a13b5d0172&pid=1-s2.0-S1525157824001491-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141555828","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}

引用次数: 0

Plasma Protein Profiling to Discern Indolent from Advanced Systemic Mastocytosis 通过血浆蛋白图谱分析鉴别轻度和晚期系统性肥大细胞增多症。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-06-24 DOI: 10.1016/j.jmoldx.2024.05.010

{"title":"Plasma Protein Profiling to Discern Indolent from Advanced Systemic Mastocytosis","authors":"","doi":"10.1016/j.jmoldx.2024.05.010","DOIUrl":"10.1016/j.jmoldx.2024.05.010","url":null,"abstract":"<div><p>Mastocytosis is a heterogeneous disorder characterized by abnormal mast cell accumulation, in which the clinical severity may be explained by distinct molecular mechanisms. This study aimed to explore plasma protein biomarkers associated with systemic mastocytosis subtypes, as well as the cellular origin of the identified proteins. Plasma samples from patients with mastocytosis, including cutaneous mastocytosis (CM), indolent systemic mastocytosis (ISM), and advanced systemic mastocytosis (AdvSM), and a reference group of patients with polycythemia vera, were analyzed by Proximity Extension Assay technology targeting 275 proteins. Furthermore, potential cellular origin was explored using an available single-cell RNA-sequencing data set generated from patients with ISM. The study cohort included 16 patients with CM, 92 patients with systemic mastocytosis (ISM, <em>n</em> = 80; AdvSM, <em>n</em> = 12), and 60 patients with polycythemia vera. A principal component analysis based on 275 plasma proteins revealed one cluster of patients with CM and ISM that was separated from patients with AdvSM. Up to 29 proteins were associated with distinct severe activity in patients with systemic mastocytosis (ISM versus AdvSM), including IL-1 receptor type 1 (IL-1RT1) and tumor necrosis factor ligand superfamily member 13B (TNFSF13B) (q < 0.01). Furthermore, single-cell RNA-sequencing analysis from ISM-derived bone marrow cells revealed that the mRNA for the identified proteins was not exclusive of mast cells. Distinct plasma protein profiles show potential to refine ISM and AdvSM diagnoses, possibly reflecting differences in pathogenic mechanisms and diverse clinical manifestations.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 9","pages":"Pages 792-804"},"PeriodicalIF":3.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824001302/pdfft?md5=4cb224273eb6f37b9dc06a280845239e&pid=1-s2.0-S1525157824001302-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460482","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}

引用次数: 0

Improved Genetic Characterization of Congenital Adrenal Hyperplasia by Long-Read Sequencing Compared with Multiplex Ligation-Dependent Probe Amplification Plus Sanger Sequencing 与多重连接依赖性探针扩增加桑格测序法相比，长线程测序法改进了先天性肾上腺增生症的遗传特征描述。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-06-24 DOI: 10.1016/j.jmoldx.2024.05.009

{"title":"Improved Genetic Characterization of Congenital Adrenal Hyperplasia by Long-Read Sequencing Compared with Multiplex Ligation-Dependent Probe Amplification Plus Sanger Sequencing","authors":"","doi":"10.1016/j.jmoldx.2024.05.009","DOIUrl":"10.1016/j.jmoldx.2024.05.009","url":null,"abstract":"<div><p>Genetic analysis of congenital adrenal hyperplasia (CAH) has been challenging because of high homology between <em>CYP21A2</em> and its pseudogene <em>CYP21A1P</em>. This study aimed to evaluate the clinical utility of long-read sequencing (LRS) in diagnosis of CAH attributable to 21-hydroxylase deficiency by comparing with multiplex ligation-dependent probe amplification plus Sanger sequencing. In this retrospective study, 69 samples, including 49 probands from 47 families with high-risk of CAH, were enrolled and blindly subjected to detection of CAH by LRS. The genotype results were compared with control methods, and discordant samples were validated by additional Sanger sequencing. LRS successfully identified biallelic variants of <em>CYP21A2</em> in the 39 probands diagnosed as having CAH. The remaining 10 probands were not patients with CAH. Additionally, LRS directly identified two pathogenic single-nucleotide variations (SNVs; c.293-13C/A>G and c.955C>T) in the presence of interference caused by nearby insertions/deletions (indels). The <em>cis</em>-<em>trans</em> configuration of two or more SNVs and indels identified in 18 samples was directly determined by LRS without family analysis. Eight <em>CYP21A1P/A2</em> or <em>TNXA/B</em> deletion chimeras, composed of five subtypes, were identified; and the junction sites were precisely determined. Moreover, LRS determined the exact genotype in two probands who had three heterozygous SNVs/indels and duplication, which could not be clarified by control methods. These findings highlight that LRS could assist in more accurate genotype imputation and more precise CAH diagnosis.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 9","pages":"Pages 770-780"},"PeriodicalIF":3.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824001296/pdfft?md5=97afdb5a234db4132211f866324c16d0&pid=1-s2.0-S1525157824001296-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460480","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}

引用次数: 0

Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing–Based Diagnosis of Bloodstream Infection 基于快速测序诊断血流感染的宿主清除和病原体富集方法的进展。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-06-24 DOI: 10.1016/j.jmoldx.2024.05.008

{"title":"Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing–Based Diagnosis of Bloodstream Infection","authors":"","doi":"10.1016/j.jmoldx.2024.05.008","DOIUrl":"10.1016/j.jmoldx.2024.05.008","url":null,"abstract":"<div><p>Bloodstream infection is a major cause of morbidity and death worldwide. Timely and appropriate treatment can reduce mortality among critically ill patients. Current diagnostic methods are too slow to inform precise antibiotic choice, leading to the prescription of empirical antibiotics, which may fail to cover the resistance profile of the pathogen, risking poor patient outcomes. Additionally, overuse of broad-spectrum antibiotics may lead to more resistant organisms, putting further pressure on the dwindling pipeline of antibiotics, and risk transmission of these resistant organisms in the health care environment. Therefore, rapid diagnostics are urgently required to better inform antibiotic choice early in the course of treatment. Sequencing offers great promise in reducing time to microbiological diagnosis; however, the amount of host DNA compared with the pathogen in patient samples presents a significant obstacle. Various host-depletion and bacterial-enrichment strategies have been used in samples, such as saliva, urine, or tissue. However, these methods have yet to be collectively integrated and/or extensively explored for rapid bloodstream infection diagnosis. Although most of these workflows possess individual strengths, their lack of analytical/clinical sensitivity and/or comprehensiveness demands additional improvements or synergistic application. This review provides a distinctive classification system for various methods based on their working principles to guide future research, and discusses their strengths and limitations and explores potential avenues for improvement to assist the reader in workflow selection.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 9","pages":"Pages 741-753"},"PeriodicalIF":3.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824001284/pdfft?md5=4af83dd2c14e1a8cc057a07be9d99feb&pid=1-s2.0-S1525157824001284-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460464","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}

引用次数: 0

Mono- and Biallelic Replication–Coupled Gene Editing Discriminates Dominant-Negative and Loss-of-Function Variants of DNA Mismatch Repair Genes 单复制和双复制耦合基因编辑可区分 DNA 错配修复基因的显性阴性变体和功能缺失变体。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-06-24 DOI: 10.1016/j.jmoldx.2024.05.011

{"title":"Mono- and Biallelic Replication–Coupled Gene Editing Discriminates Dominant-Negative and Loss-of-Function Variants of DNA Mismatch Repair Genes","authors":"","doi":"10.1016/j.jmoldx.2024.05.011","DOIUrl":"10.1016/j.jmoldx.2024.05.011","url":null,"abstract":"<div><p>Replication-coupled gene editing using locked nucleic acid–modified single-stranded DNA oligonucleotides (LMOs) can genetically engineer mammalian cells with high precision at single nucleotide resolution. Based on this method, oligonucleotide-directed mutation screening (ODMS) was developed to determine whether variants of uncertain clinical significance of DNA mismatch repair (MMR) genes can cause Lynch syndrome. In ODMS, the appearance of 6-thioguanine–resistant colonies upon introduction of the variant is indicative for defective MMR and hence pathogenicity. Whereas mouse embryonic stem cells (mESCs) hemizygous for MMR genes were used previously, we now show that ODMS can also be applied in wild-type mESCs carrying two functional alleles of each MMR gene. 6-Thioguanine resistance can result from two possible events: first, the mutation is present in only one allele, which is indicative for dominant-negative activity of the variant; and second, both alleles contain the planned modification, which is indicative for a regular loss-of-function variant. Thus, ODMS in wild-type mESCs can discriminate fully disruptive and dominant-negative MMR variants. The feasibility of biallelic targeting suggests that the efficiency of LMO-mediated gene targeting at a nonselectable locus may be enriched in cells that had undergone a simultaneous selectable LMO targeting event. This turned out to be the case and provided a protocol to improve recovery of LMO-mediated gene modification events.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 9","pages":"Pages 805-814"},"PeriodicalIF":3.4,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1525157824001314/pdfft?md5=de613d64d15dd3a73d9da0ccec8d4271&pid=1-s2.0-S1525157824001314-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141460481","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}

引用次数: 0

Variant Detection in 3′ Exons of PMS2 Using Exome Sequencing Data 利用外显子组测序数据检测 PMS2 3' 外显子中的变异。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-06-24 DOI: 10.1016/j.jmoldx.2024.06.001

引用次数: 0

CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza 基于 CRISPR 的检测方法用于流感的即时检测和亚型鉴定

IF 4.1 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-06-18 DOI: 10.1016/j.jmoldx.2024.04.004

Yibin B. Zhang , Jon Arizti-Sanz , A'Doriann Bradley , Yujia Huang , Tinna-Solveig F. Kosoko-Thoroddsen , Pardis C. Sabeti , Cameron Myhrvold

{"title":"CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza","authors":"Yibin B. Zhang , Jon Arizti-Sanz , A'Doriann Bradley , Yujia Huang , Tinna-Solveig F. Kosoko-Thoroddsen , Pardis C. Sabeti , Cameron Myhrvold","doi":"10.1016/j.jmoldx.2024.04.004","DOIUrl":"https://doi.org/10.1016/j.jmoldx.2024.04.004","url":null,"abstract":"<div><p>The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.</p></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 7","pages":"Pages 599-612"},"PeriodicalIF":4.1,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141423632","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