Journal of Molecular Diagnostics最新文献_第3页

Validation of the Clinical Performance and Reproducibility of the Savanna HSV 1+2/VZV Assay 热带草原HSV 1+2/VZV检测的临床性能和可重复性验证。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-23 DOI: 10.1016/j.jmoldx.2025.03.009

Matthew L. Faron , Jane M. Caldwell , Lavannya Sabharwal , Amorina Purpora , Jennifer Meece , Puspa Bhattarai , Julie O’Neill , Melody Christian , Neelam X. Dhiman , Jennifer Halliday , Jessica S. Hoff , Carrie V. Vause , Paul A. Granato

{"title":"Validation of the Clinical Performance and Reproducibility of the Savanna HSV 1+2/VZV Assay","authors":"Matthew L. Faron , Jane M. Caldwell , Lavannya Sabharwal , Amorina Purpora , Jennifer Meece , Puspa Bhattarai , Julie O’Neill , Melody Christian , Neelam X. Dhiman , Jennifer Halliday , Jessica S. Hoff , Carrie V. Vause , Paul A. Granato","doi":"10.1016/j.jmoldx.2025.03.009","DOIUrl":"10.1016/j.jmoldx.2025.03.009","url":null,"abstract":"<div><div>Herpes simplex virus 1 (HSV-1), HSV 2 (HSV-2), and varicella-zoster virus (VZV) cause nondescript cutaneous and mucocutaneous lesions requiring rapid, differential identification for appropriate diagnosis and patient counseling. Decentralized multiplex molecular assays may provide more rapid results than existing methodologies but require clinical validation. This multicenter study evaluated the clinical performance of the Savanna HSV 1+2/VZV Assay against the high-complexity Lyra Direct HSV 1+2/VZV real-time PCR nucleic acid test for the detection of HSV-1, HSV-2, and VZV from clinical specimens. The Savanna HSV 1+2/VZV Assay is an automated, moderate-complexity, real-time PCR assay recently cleared by the US Food and Drug Administration for the simultaneous detection and differentiation of HSV-1, HSV-2, and VZV DNA isolated from lesion swabs. In this study, 744 clinical specimens (531 female, 213 male) were evaluated by Savanna and compared with Lyra. Discrepant result analysis was conducted with the moderate-complexity Solana HSV 1+2/VZV isothermal nucleic acid test. For 744 clinical samples, Savanna exhibited overall, positive, and negative percent agreement of 99.5%, 100%, and 99.3% for HSV-1; 99.9%, 100%, and 99.8% for HSV-2; and 100%, 100%, and 100% for VZV. The Savanna HSV 1+2/VZV Assay exhibited excellent performance in a multicenter, clinical study. Savanna can provide laboratory-equivalent results outside of the central laboratory with the potential to deliver accurate results during the patient visit.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 7","pages":"Pages 605-614"},"PeriodicalIF":3.4,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144038495","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

Analytical Validation and Clinical Sensitivity of the Belay Summit Assay for the Detection of DNA Variants in Cerebrospinal Fluid of Primary and Metastatic Central Nervous System Cancer 原发性和转移性中枢神经系统癌脑脊液DNA变异检测的分析验证和临床敏感性

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-23 DOI: 10.1016/j.jmoldx.2025.03.010

Qian Nie, Kala F. Schilter, Kyle M. Hernandez, Jennifer N. Adams, Rakshitha Jagadish, Anthony Acevedo, Alexandra Larson, Brett A. Domagala, Samantha A. Vo, Sakshi Khurana, Kathleen Mitchell, Dean Ellis, Baymuhammet Muhammedov, Yuxuan Wang, Christopher Douville, Brian Coe, Chetan Bettegowda, Honey V. Reddi

{"title":"Analytical Validation and Clinical Sensitivity of the Belay Summit Assay for the Detection of DNA Variants in Cerebrospinal Fluid of Primary and Metastatic Central Nervous System Cancer","authors":"Qian Nie, Kala F. Schilter, Kyle M. Hernandez, Jennifer N. Adams, Rakshitha Jagadish, Anthony Acevedo, Alexandra Larson, Brett A. Domagala, Samantha A. Vo, Sakshi Khurana, Kathleen Mitchell, Dean Ellis, Baymuhammet Muhammedov, Yuxuan Wang, Christopher Douville, Brian Coe, Chetan Bettegowda, Honey V. Reddi","doi":"10.1016/j.jmoldx.2025.03.010","DOIUrl":"10.1016/j.jmoldx.2025.03.010","url":null,"abstract":"<div><div>In contrast to most solid tumors, cancers of the central nervous system (CNS) pose a unique challenge for effective detection and tracking via plasma because of the blood-brain barrier. Informed diagnosis of primary and metastatic CNS tumors can be facilitated using a liquid biopsy assay that evaluates tumor-derived DNA from the cerebrospinal fluid (CSF), potentially increasing the efficacy of diagnosis and reducing the uncertainty and morbidities associated with the current standard of care that involves neurosurgical procedures. The Belay Summit assay involves tumor-derived DNA–based genomic profiling of CSF to inform diagnosis of CNS tumors. The analytical sensitivity of Summit for single-nucleotide/multinucleotide variants and insertions/deletions is 96% at a 95% limit of detection of 0.30% variant allele fraction. Analytical sensitivity for chromosomal arm-level aneuploidy is 91% at abs(log2r) of 0.09 limit of detection. Clinical sensitivity across a cohort of 124 specimens, including primary and metastatic CNS tumors, was demonstrated to be 90% with a specificity of 95%, supporting the potential for positive clinical utility. These results demonstrate that the Belay Summit assay can accurately and reproducibly be used to inform the diagnosis of primary and metastatic CNS tumors using CSF.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 7","pages":"Pages 615-629"},"PeriodicalIF":3.4,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042528","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

Fragile X Syndrome Carrier Screening Using a Nanopore Sequencing Assay 使用纳米孔测序法筛选脆性X综合征携带者。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-23 DOI: 10.1016/j.jmoldx.2025.03.008

Zhongmin Xia , Qiuxiao Deng , Ping Hu , Chunliu Gao , Yu Jiang , Yulin Zhou , Qiwei Guo

{"title":"Fragile X Syndrome Carrier Screening Using a Nanopore Sequencing Assay","authors":"Zhongmin Xia , Qiuxiao Deng , Ping Hu , Chunliu Gao , Yu Jiang , Yulin Zhou , Qiwei Guo","doi":"10.1016/j.jmoldx.2025.03.008","DOIUrl":"10.1016/j.jmoldx.2025.03.008","url":null,"abstract":"<div><div>Fragile X syndrome (FXS) is the leading cause of monogenic autism spectrum disorder and inherited intellectual disabilities. Although the value of population-based FXS carrier screening has been acknowledged, appropriate screening methods are urgently required to establish and implement screening programs. We developed a nanopore sequencing–based assay that includes data analysis software to identify FXS carriers. Reference and clinical samples were used to evaluate the performance of the nanopore sequencing assay. Triplet-primed PCR and PacBio sequencing assays were used for comparisons. Nanopore sequencing identified reference carrier samples with a full range of premutation alleles in single-, 10-, and 100-plex assays, and identified AGG interruptions in an allele-specific manner. Moreover, nanopore sequencing revealed no size preference for amplicons containing different-length CGG repeat regions. Finally, nanopore sequencing successfully identified three carriers among 10 clinical samples for preliminary clinical validation. The observed variation in CGG repeat region size resulted from the base calling process of nanopore sequencing. In conclusion, the nanopore sequencing assay is rapid, high-capacity, inexpensive, and easy to perform, thus providing a promising tool and paving the way for population-based FXS carrier screening.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 7","pages":"Pages 645-656"},"PeriodicalIF":3.4,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003650","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

Catching Up to Increased Complexity in Breast Cancer Molecular Testing 乳腺癌分子检测日益复杂。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-23 DOI: 10.1016/j.jmoldx.2025.03.007

Gregory R. Bean , Chieh-Yu Lin , Melissa Krystel-Whittemore , Lulu Sun

引用次数: 0

Clinical Bioinformatician Body of Knowledge—Molecular Diagnostics Core 临床生物信息学家知识体系-分子诊断核心：分子病理学协会报告。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-23 DOI: 10.1016/j.jmoldx.2025.03.006

Annette Leon , Eduardo Castro-Echeverry , Amber M. Fussell , Danielle Jordan , Nefize S. Kip , Angshumoy Roy , Carlos J. Suarez , Robyn L. Temple-Smolkin , Joshua Coleman

{"title":"Clinical Bioinformatician Body of Knowledge—Molecular Diagnostics Core","authors":"Annette Leon , Eduardo Castro-Echeverry , Amber M. Fussell , Danielle Jordan , Nefize S. Kip , Angshumoy Roy , Carlos J. Suarez , Robyn L. Temple-Smolkin , Joshua Coleman","doi":"10.1016/j.jmoldx.2025.03.006","DOIUrl":"10.1016/j.jmoldx.2025.03.006","url":null,"abstract":"<div><div>Clinical bioinformaticians play a critical role in clinical molecular diagnostics laboratories as developers of data analysis pipelines, tools, and databases. They also contribute to a variety of other tasks, such as genomic data interpretation, database administration, hardware engineering, informatics, information technology, infrastructure support, and software engineering. To effectively perform these functions, the clinical bioinformaticians must possess a strong foundational knowledge of molecular biology, genetics, genomics, computational biology, and the relevant federal, state, and/or regional regulations, laboratory accreditation requirements, and other standards and best practices. This first article in the Association for Molecular Pathology's Clinical Bioinformatician Body of Knowledge series provides a comprehensive core knowledge base on molecular biology, genetics, genomics, clinical laboratory practices, sequencing technologies, databases, and clinical applications. This resource serves not only to equip clinical bioinformaticians for their professional roles but also as a valuable reference for laboratorians.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 7","pages":"Pages 546-565"},"PeriodicalIF":3.4,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036942","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

High-Throughput Multiplex Detection of Antibiotic-Resistant Genes and Virulence Factors in Escherichia coli Using Digital Multiplex Ligation Assay 利用数字多重连接法高通量多重检测大肠杆菌耐药基因和毒力因子。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-14 DOI: 10.1016/j.jmoldx.2025.03.003

Sheena Conforti , Pablo Rossi Orts , Manu Tamminen , Timothy R. Julian

{"title":"High-Throughput Multiplex Detection of Antibiotic-Resistant Genes and Virulence Factors in Escherichia coli Using Digital Multiplex Ligation Assay","authors":"Sheena Conforti , Pablo Rossi Orts , Manu Tamminen , Timothy R. Julian","doi":"10.1016/j.jmoldx.2025.03.003","DOIUrl":"10.1016/j.jmoldx.2025.03.003","url":null,"abstract":"<div><div><em>Escherichia coli</em> causes >400,000 annual deaths in children aged <5 years worldwide, with morbidity and mortality exacerbated by antimicrobial-resistant strains. A high-throughput multiplexing assay called digital multiplex ligation assay (dMLA) was developed to detect simultaneously 43 priority genes in <em>E. coli</em> related to the following: antibiotic resistance (<em>n</em> = 19), virulence factors (<em>n</em> = 16), and phylogroup markers (<em>n</em> = 6) with controls (<em>uidA</em>, <em>gapdh</em>). Genes are detected via PCR amplification of adjacent probe pairs that ligate in the presence of target gene-specific DNA, followed by sequencing of amplicons on short-read sequencers. The assay was tested in technical replicates on 63 synthetic DNA controls, and applied to 58 <em>E. coli</em>, 2 <em>Staphylococcus aureus</em>, 2 <em>Klebsiella pneumoniae</em>, 1 <em>Klebsiella oxytoca</em>, 1 <em>Vibrio cholera</em>, 1 <em>Pseudomonas lurida</em>, and 1 <em>Salmonella enterica</em> isolates in duplicate. Whole-genome sequencing was used to assess specificity and sensitivity. dMLA showed 100% sensitivity and >99.9% specificity and balanced accuracy on synthetic DNA. Balanced accuracy, calculated as the average of sensitivity and specificity, accounts for imbalanced data sets where negative outcomes are significantly more prevalent than positive ones. dMLA achieved a balanced accuracy of 90% for bacterial isolates. The results underline dMLA's effectiveness in high-throughput characterization of <em>E. coli</em> libraries for antimicrobial resistance genes and virulence factors, leveraging sequencing for massively parallel multiplexing of gene regions on multiple samples simultaneously, and are extendable to targets beyond <em>E. coli.</em></div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 511-524"},"PeriodicalIF":3.4,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144056840","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 Screening and Monitoring of UBA1 Mutations in VEXAS Syndrome VEXAS综合征中UBA1突变的快速筛选和监测。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-14 DOI: 10.1016/j.jmoldx.2025.03.004

Iván Martín Castillo , Elvira Mora , Rafael Hernani , Jose V. Cervera , María J. Fernandez , Blanca Ferrer-Lores , Esperanza Such , Marisa Calabuig , Rosario Abellán , Marina Díaz-Beyá , Juan C. Hernández-Boluda , Carlos Solano , Eva Villamón , Mar Tormo

{"title":"Rapid Screening and Monitoring of UBA1 Mutations in VEXAS Syndrome","authors":"Iván Martín Castillo , Elvira Mora , Rafael Hernani , Jose V. Cervera , María J. Fernandez , Blanca Ferrer-Lores , Esperanza Such , Marisa Calabuig , Rosario Abellán , Marina Díaz-Beyá , Juan C. Hernández-Boluda , Carlos Solano , Eva Villamón , Mar Tormo","doi":"10.1016/j.jmoldx.2025.03.004","DOIUrl":"10.1016/j.jmoldx.2025.03.004","url":null,"abstract":"<div><div>VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) is a severe adult-onset autoinflammatory disease associated with hematologic conditions, such as myelodysplastic syndrome. VEXAS is mostly due to an acquired mutation affecting methionine 41 (p.M41) of the <em>UBA1</em> gene, which is present in >90% of patients and usually at a high burden. Treatment strategies are diverse, but many aim to suppress the <em>UBA1</em> mutant clone with hypomethylating agents or by allogeneic hematopoietic cell transplantation. In the present study, we have developed a high-resolution melting tool for rapid detection of <em>UBA1</em> p.M41 mutations, useful in diagnostic discrimination, and three sensitive real-time allele-specific oligonucleotide PCRs to determine the variant allele frequency of p.M41T/V/L mutations, applicable in the molecular monitoring of the disease.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 431-437"},"PeriodicalIF":3.4,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030496","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

Robust Assessment of Homologous Recombination Deficiency Genomic Instability by OncoScan Microarrays OncoScan微阵列对HRD基因组不稳定性的可靠评估。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-04-04 DOI: 10.1016/j.jmoldx.2025.02.011

Ariadna Lara Gutierrez , Iris Halbwedl , Stefan Sauer , Peter Regitnig , Edgar Petru , Rita Seeböck , Susanne Schubert , Cornelia Peternell , Koppány Bodó , Kurt Prein , Karl Kashofer

{"title":"Robust Assessment of Homologous Recombination Deficiency Genomic Instability by OncoScan Microarrays","authors":"Ariadna Lara Gutierrez , Iris Halbwedl , Stefan Sauer , Peter Regitnig , Edgar Petru , Rita Seeböck , Susanne Schubert , Cornelia Peternell , Koppány Bodó , Kurt Prein , Karl Kashofer","doi":"10.1016/j.jmoldx.2025.02.011","DOIUrl":"10.1016/j.jmoldx.2025.02.011","url":null,"abstract":"<div><div>Genomic instability scars are markers for detecting homologous recombination deficiency (HRD) status in patients with ovarian cancer and predicting the response to poly (ADP-ribose) polymerase inhibitor treatment. Currently, only a few reliable and validated assays are available, with the Myriad myChoice CDx being the most commonly used commercial assay for genomic instability scar score determination. Given the need for a more straightforward, accessible, and reliable method for detecting genomic instability scars methods, in this work, we describe the feasibility of using the microarray OncoScan copy number variant assay and open-source software packages to quantify genomic instability scores, and the development of an open-access online platform for genomic instability score calculation. The laboratory-developed test accurately classified homologous recombination–proficient and recombination–deficient samples based on genomic instability scores derived from the OncoScan copy number variant assay. Internally evaluated genomic instability scores demonstrated a 92% overall agreement and a higher sample success rate compared with externally analyzed genomic instability scar scores. The availability of HRD determination has doubled the number of patients eligible for poly (ADP-ribose) polymerase therapy. The assay can be conveniently performed on individual samples, and the open-access online platform facilitates HRD determination without the need for specialized bioinformatics support.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 475-484"},"PeriodicalIF":3.4,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143796973","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 of a Clinically Applicable High-Resolution Assay for Sperm Mosaicism 一种临床适用的高分辨率精子嵌合检测方法的开发。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-28 DOI: 10.1016/j.jmoldx.2025.03.002

Shan Wei , Miriam Temmeh Lattin , Stephanie Morgan , Leah DiBianco , Jocelyn Chen , Stephanie Galloway , Sinem Karipcin , Ronald Wapner , Chaim Landau , Eric J. Forman , Wendy K. Chung , Zev Williams

{"title":"Development of a Clinically Applicable High-Resolution Assay for Sperm Mosaicism","authors":"Shan Wei , Miriam Temmeh Lattin , Stephanie Morgan , Leah DiBianco , Jocelyn Chen , Stephanie Galloway , Sinem Karipcin , Ronald Wapner , Chaim Landau , Eric J. Forman , Wendy K. Chung , Zev Williams","doi":"10.1016/j.jmoldx.2025.03.002","DOIUrl":"10.1016/j.jmoldx.2025.03.002","url":null,"abstract":"<div><div>Sperm mosaicism, the presence of a pathogenic variant in a subset of sperm, is an important cause of heritable genetic disease. However, clinical testing for sperm mosaicism outside research has been limited by the lack of Clinical Laboratory Improvement Amendments (CLIA)–validated results deliverable to patients. We developed the Sensitive Assay for Mosaicism (SAM), a two-phase method for sperm mosaicism detection. In phase 1, sperm DNA undergoes deep sequencing using next-generation sequencing or nanopore-based sequencing with unique molecular identifiers (UMIs) to improve accuracy. In phase 2, PCR primers specific to UMI sequences generate amplicons for CLIA-validated Sanger sequencing, providing patient-ready results. SAM's performance was characterized and tested on semen samples from 14 participants, each with a prior offspring with a <em>de novo</em> pathogenic variant. SAM demonstrated a detection limit of approximately 0.005%. The UMI strategy improved sequencing accuracy on next-generation sequencing and nanopore platforms from 99.9% to >99.999%, and from 93% to >99.99%, respectively. Sperm mosaicism was identified in two tested cases: <em>FAM111A</em> (5.51%) and <em>FGFR3</em> (0.0129%), with <em>FGFR3</em> exhibiting selfish mutation validated in unrelated individuals showing varying mosaicism levels. SAM provides sensitive detection of low-level sperm mosaicism with CLIA-validated results for patients, enabling recurrence risk assessment and guiding risk mitigation strategies such as <em>in vitro</em> fertilization with preimplantation genetic testing for monogenic disease, sperm donation, and prenatal diagnosis.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 525-537"},"PeriodicalIF":3.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755543","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 Dual-Mode Targeted Nanopore Sequencing Assay for Comprehensive SMN1 and SMN2 Variant Analysis 一种用于SMN1和SMN2变异综合分析的双模式靶向纳米孔测序方法。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-03-28 DOI: 10.1016/j.jmoldx.2025.03.001

Bradley Hall , Sawsan Alyafei , Sathishkumar Ramaswamy , Shruti Sinha , Maha El Naofal , Fatima Rabea , Bryan J. Killinger , Gary J. Latham , Ahmad Abou Tayoun

{"title":"A Dual-Mode Targeted Nanopore Sequencing Assay for Comprehensive SMN1 and SMN2 Variant Analysis","authors":"Bradley Hall , Sawsan Alyafei , Sathishkumar Ramaswamy , Shruti Sinha , Maha El Naofal , Fatima Rabea , Bryan J. Killinger , Gary J. Latham , Ahmad Abou Tayoun","doi":"10.1016/j.jmoldx.2025.03.001","DOIUrl":"10.1016/j.jmoldx.2025.03.001","url":null,"abstract":"<div><div>Spinal muscular atrophy (SMA) is one of the most common recessive disorders, for which several life-saving treatment options are available. It is therefore essential to establish universal SMA screening and diagnostic programs using scalable, cost-effective, and accessible platforms to accurately identify all variation types. This task is complicated by high sequence homology between the <em>SMN1</em> and <em>SMN2</em> genes. Toward this goal, a dual-mode PCR-based target-enrichment method was developed, optimized, and evaluated in an external laboratory as a proof-of-concept for scalable and deployable any-length nanopore sequencing. The assay generates 2.7- to 11.2-kb amplicons spanning exons 3 to 8 of the <em>SMN1</em> and <em>SMN2</em> genes, which are then analyzed using a variant calling model that reports sequence and copy number variants specific to each gene from paralog-specific sequences and read-depth data. Overall, the assay detected single-nucleotide variants, insertions/deletions, and copy number variants with >98% genotype agreement across >750 samples, including cell lines, residual presumed-normal whole-blood donors, and patients with known <em>SMN1</em> and <em>SMN2</em> genotypes. The assay also demonstrated a dynamic sample throughput, 9-hour turnaround time, and 4-hour hands-on time. Together with the modest capital investment and consumable costs per sample, this assay can help to increase access to SMA testing in low- and middle-income settings. As a result, this PCR/Nanopore sequencing assay and analysis pipeline has the potential for universal implementation in SMA carrier screening and diagnostic programs.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 6","pages":"Pages 502-510"},"PeriodicalIF":3.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143755542","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