Pub Date : 2025-07-21DOI: 10.1016/j.jmoldx.2025.05.011
Scott Spencer , Weicheng Ye , Siyang Peng , Denise Zou
Cancer treatment costs pose a significant global economic burden. By facilitating treatment plans tailored to the genomic profile of patients' cancer, genomic testing has the potential to reduce health care costs. Using real-world evidence, this study compared the cost-effectiveness of comprehensive genomic profiling (CGP) versus small panel (SP) testing in patients with advanced non–small-cell lung cancer in the United States and Germany. A partitioned survival model was developed to estimate the life years and drug acquisition costs associated with CGP and SP testing in patients receiving matched targeted therapy, matched immunotherapy, or no matched therapy/untreated. Key model parameters were informed by real-world data derived from the Syapse study. Scenario and sensitivity analyses were conducted. CGP improved the average overall survival by 0.10 years compared with SP. CGP was associated with higher health care costs because of a higher percentage of patients receiving targeted therapies. The estimated incremental cost-effectiveness ratio (ICER) of CGP versus SP was $174,782 and $63,158 per life-year gained in the United States and Germany, respectively. Increasing the number of patients receiving treatment decreased the ICERs ($86,826 in the United States and $29,235 in Germany), while switching from immunotherapy plus chemotherapy to chemotherapy alone increased the ICERs ($223,226 in the United States and $83,333 in Germany). Altogether, CGP has the potential to improve patient outcomes and is more cost-effective than SP.
{"title":"Cost-Effectiveness Analysis of Comprehensive Genomic Profiling in Patients with Advanced Non–Small-Cell Lung Cancer Using Real-World Data","authors":"Scott Spencer , Weicheng Ye , Siyang Peng , Denise Zou","doi":"10.1016/j.jmoldx.2025.05.011","DOIUrl":"10.1016/j.jmoldx.2025.05.011","url":null,"abstract":"<div><div>Cancer treatment costs pose a significant global economic burden. By facilitating treatment plans tailored to the genomic profile of patients' cancer, genomic testing has the potential to reduce health care costs. Using real-world evidence, this study compared the cost-effectiveness of comprehensive genomic profiling (CGP) versus small panel (SP) testing in patients with advanced non–small-cell lung cancer in the United States and Germany. A partitioned survival model was developed to estimate the life years and drug acquisition costs associated with CGP and SP testing in patients receiving matched targeted therapy, matched immunotherapy, or no matched therapy/untreated. Key model parameters were informed by real-world data derived from the Syapse study. Scenario and sensitivity analyses were conducted. CGP improved the average overall survival by 0.10 years compared with SP. CGP was associated with higher health care costs because of a higher percentage of patients receiving targeted therapies. The estimated incremental cost-effectiveness ratio (ICER) of CGP versus SP was $174,782 and $63,158 per life-year gained in the United States and Germany, respectively. Increasing the number of patients receiving treatment decreased the ICERs ($86,826 in the United States and $29,235 in Germany), while switching from immunotherapy plus chemotherapy to chemotherapy alone increased the ICERs ($223,226 in the United States and $83,333 in Germany). Altogether, CGP has the potential to improve patient outcomes and is more cost-effective than SP.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 850-858"},"PeriodicalIF":3.4,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144700229","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}
Pub Date : 2025-07-15DOI: 10.1016/j.jmoldx.2025.05.010
Min Young Park , Kang-Hee Lee , Yong-Jin Yang , Ji Young Seo , Jong Kwon Lee , Ja-Hyun Jang , Yong-Hak Sohn , Kyou-Sup Han , Duck Cho
Asian-type DEL (RHD, c.1227G>A) is relatively prevalent in East Asians and is essential to detect in serologic rhesus (Rh) D-negative individuals. Despite the recognized importance of identifying Asian-type DEL, traditional detection methods, such as adsorption-elution and Sanger sequencing, are complex and time-consuming. A reliable method is required for the rapid and precise detection of Asian-type DEL. A novel multiplex real-time PCR assay using allele-specific TaqMan hydrolysis probes was developed to target the Asian-type DEL variant. Analytical specificity and sensitivity were evaluated using RHD or RHCE synthetic DNAs with 1227G or 1227A. The assay was tested on 315 clinical samples, and the results were compared with Sanger sequencing to assess diagnostic performance. Analytical specificity evaluations confirmed that the assay selectively amplified RHD, 1227A, or 1227G without cross-reactivity to RHCE. Additionally, clinical sample tests showed the assay maintained high specificity and sensitivity even at high nucleic acid concentrations. The Asian-type DEL multiplex real-time PCR assay demonstrated 100% sensitivity and specificity, with complete concordance across all samples compared with reference methods. Compared with Sanger sequencing, the multiplex real-time PCR assay had a shorter analysis time. The assay developed in this study offers a fast, reliable, and accurate approach for detecting Asian-type DEL. This method significantly improves efficiency over conventional techniques and provides a valuable tool for managing transfusion safety and RhD alloimmunization risks in RhD-negative populations.
{"title":"Development of a Multiplex Real-Time PCR Assay for the Rapid Detection of the Asian-Type DEL","authors":"Min Young Park , Kang-Hee Lee , Yong-Jin Yang , Ji Young Seo , Jong Kwon Lee , Ja-Hyun Jang , Yong-Hak Sohn , Kyou-Sup Han , Duck Cho","doi":"10.1016/j.jmoldx.2025.05.010","DOIUrl":"10.1016/j.jmoldx.2025.05.010","url":null,"abstract":"<div><div>Asian-type DEL (<em>RHD</em>, c.1227G>A) is relatively prevalent in East Asians and is essential to detect in serologic rhesus (Rh) D-negative individuals. Despite the recognized importance of identifying Asian-type DEL, traditional detection methods, such as adsorption-elution and Sanger sequencing, are complex and time-consuming. A reliable method is required for the rapid and precise detection of Asian-type DEL. A novel multiplex real-time PCR assay using allele-specific TaqMan hydrolysis probes was developed to target the Asian-type DEL variant. Analytical specificity and sensitivity were evaluated using <em>RHD</em> or <em>RHCE</em> synthetic DNAs with 1227G or 1227A. The assay was tested on 315 clinical samples, and the results were compared with Sanger sequencing to assess diagnostic performance. Analytical specificity evaluations confirmed that the assay selectively amplified <em>RHD</em>, 1227A, or 1227G without cross-reactivity to <em>RHCE.</em> Additionally, clinical sample tests showed the assay maintained high specificity and sensitivity even at high nucleic acid concentrations. The Asian-type DEL multiplex real-time PCR assay demonstrated 100% sensitivity and specificity, with complete concordance across all samples compared with reference methods. Compared with Sanger sequencing, the multiplex real-time PCR assay had a shorter analysis time. The assay developed in this study offers a fast, reliable, and accurate approach for detecting Asian-type DEL. This method significantly improves efficiency over conventional techniques and provides a valuable tool for managing transfusion safety and RhD alloimmunization risks in RhD-negative populations.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 841-849"},"PeriodicalIF":3.4,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144660930","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}
Pub Date : 2025-06-26DOI: 10.1016/j.jmoldx.2025.05.009
Kaisha Gonzalez, Giulia Amicarelli
Molecular syndromic assays have improved respiratory diagnostics by enabling the simultaneous detection of multiple pathogens from a single sample. However, fixed-panel designs may not align with age-specific prevalence patterns or evolving epidemiologic trends, limiting clinical utility and reimbursement viability. In this study, 1520 positive nasopharyngeal swabs from symptomatic individuals collected during the 2022 to 2023 respiratory season were analyzed by using the LIAISON PLEX Respiratory Flex Assay to evaluate the benefits of customizable, tiered testing strategies. Diagnostic yields from a standard-of-care panel were compared with tiered (core-plus-reflex) frameworks across pediatric (age ≤21 years), adult (age 22 to 64 years), and elderly (age ≥65 years) cohorts. Weighted analyses revealed that 99.8% of cases were viral, while bacterial pathogens accounted for <1%. The most commonly detected viruses included severe acute respiratory syndrome coronavirus 2 (28.2%), human enterovirus/rhinovirus (17.1%), influenza A (11.9%), and human coronavirus (7.4%). Age-related differences were observed, with human enterovirus/rhinovirus and adenovirus more common in pediatric patients, whereas severe acute respiratory syndrome coronavirus 2 and influenza A predominated in adults and the elderly. Standard-of-care panels captured only 58% of infections overall and 33% in pediatric patients; the tiered testing approach identified ≥99% of infections using flexible core-plus-reflex panels. Moreover, core panel targets alone accounted for >76% of all detections. These findings underscore the diagnostic, clinical, operational, and cost management value of age-informed, customizable testing frameworks to improve detection, reduce unnecessary testing, and support stewardship.
{"title":"Age-Stratified Epidemiology of Respiratory Pathogens and the Value of Customizable Syndromic Testing Using the LIAISON PLEX Respiratory Flex Assay","authors":"Kaisha Gonzalez, Giulia Amicarelli","doi":"10.1016/j.jmoldx.2025.05.009","DOIUrl":"10.1016/j.jmoldx.2025.05.009","url":null,"abstract":"<div><div>Molecular syndromic assays have improved respiratory diagnostics by enabling the simultaneous detection of multiple pathogens from a single sample. However, fixed-panel designs may not align with age-specific prevalence patterns or evolving epidemiologic trends, limiting clinical utility and reimbursement viability. In this study, 1520 positive nasopharyngeal swabs from symptomatic individuals collected during the 2022 to 2023 respiratory season were analyzed by using the LIAISON PLEX Respiratory <em>Flex</em> Assay to evaluate the benefits of customizable, tiered testing strategies. Diagnostic yields from a standard-of-care panel were compared with tiered (core-plus-reflex) frameworks across pediatric (age ≤21 years), adult (age 22 to 64 years), and elderly (age ≥65 years) cohorts. Weighted analyses revealed that 99.8% of cases were viral, while bacterial pathogens accounted for <1%. The most commonly detected viruses included severe acute respiratory syndrome coronavirus 2 (28.2%), human enterovirus/rhinovirus (17.1%), influenza A (11.9%), and human coronavirus (7.4%). Age-related differences were observed, with human enterovirus/rhinovirus and adenovirus more common in pediatric patients, whereas severe acute respiratory syndrome coronavirus 2 and influenza A predominated in adults and the elderly. Standard-of-care panels captured only 58% of infections overall and 33% in pediatric patients; the tiered testing approach identified ≥99% of infections using flexible core-plus-reflex panels. Moreover, core panel targets alone accounted for >76% of all detections. These findings underscore the diagnostic, clinical, operational, and cost management value of age-informed, customizable testing frameworks to improve detection, reduce unnecessary testing, and support stewardship.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 809-818"},"PeriodicalIF":3.4,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144530805","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}
Pub Date : 2025-06-25DOI: 10.1016/j.jmoldx.2025.05.008
Cheryl L. Sesler , Guzel I. Shaginurova , Lukasz S. Wylezinski , Elena V. Grigorenko , Franklin R. Cockerill III , Charles F. Spurlock III
Next-generation RNA sequencing (RNA-seq) enables comprehensive transcriptomic profiling for disease characterization, biomarker discovery, and precision medicine. Despite its potential, RNA-seq has not yet been widely adopted for clinical applications, and a key barrier to its adoption is the variability introduced during processing and analysis. Quality controls (QCs) must be considered through all stages of biomarker discovery. This study describes a comprehensive QC framework for effective RNA-seq biomarker discovery. Multilayered quality metrics were established across preanalytical, analytical, and postanalytical processes. Total RNA-seq was performed by using RNA isolated from whole blood (PAXgene Blood RNA tubes). Bulk RNA controls were incorporated to monitor sequencing batches. This framework was applied to a catalog of prospectively collected or biobanked clinical specimens spanning multiple disease indications. Among all QCs, preanalytical metrics (specimen collection, RNA integrity, and genomic DNA contamination) exhibited the highest failure rates and resulted in the addition of a secondary DNase treatment, which reduced genomic DNA levels. The additional DNase treatment significantly lowered intergenic read alignment and provided sufficient RNA for downstream sequencing and analysis. This end-to-end QC framework for RNA-seq biomarker discovery was developed and implemented to enhance the confidence and reliability of results. To advance the clinical adoption of RNA-seq, developing and implementing standards will improve reliability, accelerate biomarker discovery, and facilitate its translation into clinically actionable diagnostics and therapeutics.
{"title":"Development of an End-to-End Total RNA Sequencing Quality Control Framework for Blood-Based Biomarker Discovery","authors":"Cheryl L. Sesler , Guzel I. Shaginurova , Lukasz S. Wylezinski , Elena V. Grigorenko , Franklin R. Cockerill III , Charles F. Spurlock III","doi":"10.1016/j.jmoldx.2025.05.008","DOIUrl":"10.1016/j.jmoldx.2025.05.008","url":null,"abstract":"<div><div>Next-generation RNA sequencing (RNA-seq) enables comprehensive transcriptomic profiling for disease characterization, biomarker discovery, and precision medicine. Despite its potential, RNA-seq has not yet been widely adopted for clinical applications, and a key barrier to its adoption is the variability introduced during processing and analysis. Quality controls (QCs) must be considered through all stages of biomarker discovery. This study describes a comprehensive QC framework for effective RNA-seq biomarker discovery. Multilayered quality metrics were established across preanalytical, analytical, and postanalytical processes. Total RNA-seq was performed by using RNA isolated from whole blood (PAXgene Blood RNA tubes). Bulk RNA controls were incorporated to monitor sequencing batches. This framework was applied to a catalog of prospectively collected or biobanked clinical specimens spanning multiple disease indications. Among all QCs, preanalytical metrics (specimen collection, RNA integrity, and genomic DNA contamination) exhibited the highest failure rates and resulted in the addition of a secondary DNase treatment, which reduced genomic DNA levels. The additional DNase treatment significantly lowered intergenic read alignment and provided sufficient RNA for downstream sequencing and analysis. This end-to-end QC framework for RNA-seq biomarker discovery was developed and implemented to enhance the confidence and reliability of results. To advance the clinical adoption of RNA-seq, developing and implementing standards will improve reliability, accelerate biomarker discovery, and facilitate its translation into clinically actionable diagnostics and therapeutics.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 869-881"},"PeriodicalIF":3.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512714","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}
Pub Date : 2025-06-25DOI: 10.1016/j.jmoldx.2025.05.007
William A. LaFramboise , Patti Petrosko , Phillip H. Gallo , Louis Gil , Tuong L. Lam , Robin M. Barr , Philip E. Schumacher , Harmeet K. Kharoud , Katherine M. Taylor , Emily Dalton , Bella Bapat , Sefali Patel , John Nakayama , Christie J. Hilton , Lisa B. Ercolano , Ali H. Zaidi , Casey J. Allen , Thomas Rachman , Oana Carja , Russell Schwartz , David L. Bartlett
Blood collection, plasma processing, and cell-free DNA (cfDNA) purification were optimized to capture circulating tumor DNA without blood cell background DNA among 874 patients with cancer. cfDNA comprised predominantly mononucleosomal fragments [n = 874; mean () ± SD = 166 ± 5 bp] that generated comparably sized sequencing reads ( ± SD = 162 ± 25 bp). Despite a vast range of cfDNA concentrations (0.50 to 1132.9 ng/mL) across 21 tumor types, matched tumor and blood specimens (n = 430 patients) revealed high concordance for coding (median = 97%) and clinical oncogenic mutations (median = 88% concordance). Therapeutically actionable mutations were identified in 233 patients by both assays, whereas 126 patients had oncogenic mutations without an established pharmacotherapeutic agent. An additional 48 patients (11%) had actionable mutations detected only in cfDNA assays, whereas 23 patients (5%) had mutations in tumor only. Concordance was high in both prevalent (lung, breast, and colon) and rare tumors (appendiceal, sarcoma). Cell-free DNA levels from diagnostic blood specimens were a strong indicator of patient survival duration independent of age, sex, tumor type, and stage, demonstrative of a potentially important role as a prognostic biomarker. Mutations in established oncogenes and tumor suppressors were readily detectable across all tumor types in circulating tumor DNA, indicating a diagnostic role for cfDNA from blood extending beyond the identification of companion therapeutics to patient screening and monitoring.
{"title":"Cell-Free DNA, Tumor Molecular Concordance, and Clinical Correlates of Patients with Cancer Treated in a Large Community Health Care Network","authors":"William A. LaFramboise , Patti Petrosko , Phillip H. Gallo , Louis Gil , Tuong L. Lam , Robin M. Barr , Philip E. Schumacher , Harmeet K. Kharoud , Katherine M. Taylor , Emily Dalton , Bella Bapat , Sefali Patel , John Nakayama , Christie J. Hilton , Lisa B. Ercolano , Ali H. Zaidi , Casey J. Allen , Thomas Rachman , Oana Carja , Russell Schwartz , David L. Bartlett","doi":"10.1016/j.jmoldx.2025.05.007","DOIUrl":"10.1016/j.jmoldx.2025.05.007","url":null,"abstract":"<div><div>Blood collection, plasma processing, and cell-free DNA (cfDNA) purification were optimized to capture circulating tumor DNA without blood cell background DNA among 874 patients with cancer. cfDNA comprised predominantly mononucleosomal fragments [<em>n</em> = 874; mean (<span><math><mrow><mover><mtext>x</mtext><mo>¯</mo></mover></mrow></math></span>) ± SD = 166 ± 5 bp] that generated comparably sized sequencing reads (<span><math><mrow><mover><mtext>x</mtext><mo>¯</mo></mover></mrow></math></span> ± SD = 162 ± 25 bp). Despite a vast range of cfDNA concentrations (0.50 to 1132.9 ng/mL) across 21 tumor types, matched tumor and blood specimens (<em>n</em> = 430 patients) revealed high concordance for coding (median = 97%) and clinical oncogenic mutations (median = 88% concordance). Therapeutically actionable mutations were identified in 233 patients by both assays, whereas 126 patients had oncogenic mutations without an established pharmacotherapeutic agent. An additional 48 patients (11%) had actionable mutations detected only in cfDNA assays, whereas 23 patients (5%) had mutations in tumor only. Concordance was high in both prevalent (lung, breast, and colon) and rare tumors (appendiceal, sarcoma). Cell-free DNA levels from diagnostic blood specimens were a strong indicator of patient survival duration independent of age, sex, tumor type, and stage, demonstrative of a potentially important role as a prognostic biomarker. Mutations in established oncogenes and tumor suppressors were readily detectable across all tumor types in circulating tumor DNA, indicating a diagnostic role for cfDNA from blood extending beyond the identification of companion therapeutics to patient screening and monitoring.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 882-898"},"PeriodicalIF":3.4,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144512713","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}
Pub Date : 2025-06-24DOI: 10.1016/j.jmoldx.2025.03.011
Carolin K. Scriba , Fathimath Faiz , Michael Black , Rebecca Gooding , Padma Sivadorai , Daniel Trajanoski , Adriana Botero , Cheryl Wise , Gianina Ravenscroft , Mark R. Davis , Nigel G. Laing
Neurogenetic disorders are a large group of genetic and phenotypically heterogeneous diseases, making diagnosis challenging. Sequencing hundreds of disease genes concurrently using massively parallel sequencing is, therefore, invaluable for diagnosis of these disorders. The PathWest neuromuscular disease gene panels include all known genes associated with neurologic and muscle disorders. Initially implemented in 2013, covering 336 genes, the gene panel has undergone various updates in chemistries and seen the addition of many newly described neurogenic disease genes. The results from versions 3 and 5 of the panel are reported, which included 644 and 830 genes, respectively. In total, 3961 patients were tested across 20 phenotypic subpanels: 2740 on version 3 and 1221 on version 5. Overall diagnostic success was 23.0%, with 8.4% of diagnoses attributed to newly added genes. Diagnostic success varied greatly between phenotypic subpanels, from 63.4% for the congenital muscular dystrophy subpanel to 2.6% for the Alzheimer disease/frontotemporal dementia subpanel. The five most frequently reported genes, DMD, RYR1, SPG7, PMP22, and NOTCH3, accounted for 22% of all diagnoses. Changing chemistries improved coverage of regions that were previously not well resolved. This enabled improved copy number variant calling, with 10.5% of diagnoses from version 5 attributed to copy number variants. The data generated have enabled identification of factors broadly affecting diagnosis of neuromuscular disorders and potential limitations hampering diagnostic success.
{"title":"Diagnosis of Australasian Patients with Neuromuscular Disease","authors":"Carolin K. Scriba , Fathimath Faiz , Michael Black , Rebecca Gooding , Padma Sivadorai , Daniel Trajanoski , Adriana Botero , Cheryl Wise , Gianina Ravenscroft , Mark R. Davis , Nigel G. Laing","doi":"10.1016/j.jmoldx.2025.03.011","DOIUrl":"10.1016/j.jmoldx.2025.03.011","url":null,"abstract":"<div><div>Neurogenetic disorders are a large group of genetic and phenotypically heterogeneous diseases, making diagnosis challenging. Sequencing hundreds of disease genes concurrently using massively parallel sequencing is, therefore, invaluable for diagnosis of these disorders. The PathWest neuromuscular disease gene panels include all known genes associated with neurologic and muscle disorders. Initially implemented in 2013, covering 336 genes, the gene panel has undergone various updates in chemistries and seen the addition of many newly described neurogenic disease genes. The results from versions 3 and 5 of the panel are reported, which included 644 and 830 genes, respectively. In total, 3961 patients were tested across 20 phenotypic subpanels: 2740 on version 3 and 1221 on version 5. Overall diagnostic success was 23.0%, with 8.4% of diagnoses attributed to newly added genes. Diagnostic success varied greatly between phenotypic subpanels, from 63.4% for the congenital muscular dystrophy subpanel to 2.6% for the Alzheimer disease/frontotemporal dementia subpanel. The five most frequently reported genes, <em>DMD</em>, <em>RYR1</em>, <em>SPG7</em>, <em>PMP22</em>, and <em>NOTCH3</em>, accounted for 22% of all diagnoses. Changing chemistries improved coverage of regions that were previously not well resolved. This enabled improved copy number variant calling, with 10.5% of diagnoses from version 5 attributed to copy number variants. The data generated have enabled identification of factors broadly affecting diagnosis of neuromuscular disorders and potential limitations hampering diagnostic success.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 7","pages":"Pages 630-644"},"PeriodicalIF":3.4,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144366246","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}
Pub Date : 2025-06-19DOI: 10.1016/j.jmoldx.2025.05.005
B. Ethan Nunley , Amelia Weixler , Hyeong Geon Kim , Hong Xie , Jaydee Sereewit , Pooneh Hajian , Sean Ellis , Margaret G. Mills , Ailyn C. Pérez-Osorio , Stephanie Goya , Jolene Gov , Rebecca Dewar , Goncalo Fernandes , Kate E. Templeton , Daniel M. Maloney , Alexander L. Greninger , Pavitra Roychoudhury
Accurate genomic characterization of respiratory syncytial virus (RSV) is crucial for studies of epidemiology and viral evolution, including monitoring potential escape from newly authorized vaccines and prophylactic monoclonal antibodies. A viral genome tiling amplicon panel (UW-ARTIC) was adapted to develop a custom bioinformatic pipeline for high-throughput, cost-effective sequencing of both RSV-A and RSV-B subgroups. Genome acceptability criteria were established and the performance characteristics of the panel were determined, including assay sensitivity, specificity, breadth of genome recovery, accuracy, and precision, using contrived and remnant clinical specimens. High-quality genomes (>95% genome completeness; >500× and >1000× average depth for whole genome and fusion gene, respectively) were recovered from samples with cycle threshold ≤ 30 (approximately 594 and 2004 copies per reaction for RSV-A and RSV-B, respectively). Minor variants were accurately identified at >5% allele frequency. The assay showed high accuracy when compared with Sanger, shotgun metagenomic, and hybridization capture-based sequencing, as well as high repeatability and reproducibility. The UW-ARTIC RSV panel has utility for cost-effective RSV genome recovery in public health, clinical, and research applications. It has been used to generate US Food and Drug Administration–reportable data for clinical trials of RSV antiviral products, with robust performance in global samples from as recently as the 2023/2024 season. Continued genomic surveillance and future updates to primers will be essential for continued recovery of genomes as RSV continues to evolve.
{"title":"Clinical Performance Evaluation of a Tiling Amplicon Panel for Whole-Genome Sequencing of Respiratory Syncytial Virus","authors":"B. Ethan Nunley , Amelia Weixler , Hyeong Geon Kim , Hong Xie , Jaydee Sereewit , Pooneh Hajian , Sean Ellis , Margaret G. Mills , Ailyn C. Pérez-Osorio , Stephanie Goya , Jolene Gov , Rebecca Dewar , Goncalo Fernandes , Kate E. Templeton , Daniel M. Maloney , Alexander L. Greninger , Pavitra Roychoudhury","doi":"10.1016/j.jmoldx.2025.05.005","DOIUrl":"10.1016/j.jmoldx.2025.05.005","url":null,"abstract":"<div><div>Accurate genomic characterization of respiratory syncytial virus (RSV) is crucial for studies of epidemiology and viral evolution, including monitoring potential escape from newly authorized vaccines and prophylactic monoclonal antibodies. A viral genome tiling amplicon panel (UW-ARTIC) was adapted to develop a custom bioinformatic pipeline for high-throughput, cost-effective sequencing of both RSV-A and RSV-B subgroups. Genome acceptability criteria were established and the performance characteristics of the panel were determined, including assay sensitivity, specificity, breadth of genome recovery, accuracy, and precision, using contrived and remnant clinical specimens. High-quality genomes (>95% genome completeness; >500× and >1000× average depth for whole genome and fusion gene, respectively) were recovered from samples with cycle threshold ≤ 30 (approximately 594 and 2004 copies per reaction for RSV-A and RSV-B, respectively). Minor variants were accurately identified at >5% allele frequency. The assay showed high accuracy when compared with Sanger, shotgun metagenomic, and hybridization capture-based sequencing, as well as high repeatability and reproducibility. The UW-ARTIC RSV panel has utility for cost-effective RSV genome recovery in public health, clinical, and research applications. It has been used to generate US Food and Drug Administration–reportable data for clinical trials of RSV antiviral products, with robust performance in global samples from as recently as the 2023/2024 season. Continued genomic surveillance and future updates to primers will be essential for continued recovery of genomes as RSV continues to evolve.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 819-831"},"PeriodicalIF":3.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340561","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}
Pub Date : 2025-06-19DOI: 10.1016/j.jmoldx.2025.05.004
Ziyan Li , Zhenyi Huang , Mengxi Li , Yunshan Cao , Yating Li , Jinlv Liu , Suping Zhong , Lijuan Lin , Yanping Fang , Zhaoying Su , Yongxin Huang , Wanjun Zhou , Lingxiao Jiang
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common inherited disorder worldwide and is particularly prevalent in historically malaria-endemic countries. This study established a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) assay for G6PD mutation detection. This MALDI-TOF-MS assay with single-base extension was developed to efficiently and accurately test 19 common G6PD variants in the Chinese population. The MALDI-TOF-MS assay was used to analyze a total of 2205 peripheral blood samples, including 1111 normal individuals and 1094 G6PD gene mutation carriers. All 2205 sample results were validated by Sanger sequencing in a blinded study. The MALDI-TOF-MS assay developed in this study was applied to detect G6PD mutations in 300 uncharacterized blood donor samples, of which 17 (5.67%) were found to carry G6PD gene mutations. The baseline and follow-up characteristics of the 17 blood donors were summarized. In this study, a MALDI-TOF-MS assay was applied to detect common G6PD mutations in samples from blood donors in Guangdong, China, which provided a new concept for establishing the information regarding the blood bank database of G6PD-deficient donors.
{"title":"Screening G6PD Mutations in Blood Donors by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry with High-Throughput and Multiple Targets","authors":"Ziyan Li , Zhenyi Huang , Mengxi Li , Yunshan Cao , Yating Li , Jinlv Liu , Suping Zhong , Lijuan Lin , Yanping Fang , Zhaoying Su , Yongxin Huang , Wanjun Zhou , Lingxiao Jiang","doi":"10.1016/j.jmoldx.2025.05.004","DOIUrl":"10.1016/j.jmoldx.2025.05.004","url":null,"abstract":"<div><div>Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a common inherited disorder worldwide and is particularly prevalent in historically malaria-endemic countries. This study established a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) assay for <em>G6PD</em> mutation detection. This MALDI-TOF-MS assay with single-base extension was developed to efficiently and accurately test 19 common <em>G6PD</em> variants in the Chinese population. The MALDI-TOF-MS assay was used to analyze a total of 2205 peripheral blood samples, including 1111 normal individuals and 1094 <em>G6PD</em> gene mutation carriers. All 2205 sample results were validated by Sanger sequencing in a blinded study. The MALDI-TOF-MS assay developed in this study was applied to detect <em>G6PD</em> mutations in 300 uncharacterized blood donor samples, of which 17 (5.67%) were found to carry <em>G6PD</em> gene mutations. The baseline and follow-up characteristics of the 17 blood donors were summarized. In this study, a MALDI-TOF-MS assay was applied to detect common <em>G6PD</em> mutations in samples from blood donors in Guangdong, China, which provided a new concept for establishing the information regarding the blood bank database of G6PD-deficient donors.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 832-840"},"PeriodicalIF":3.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340562","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}
Pub Date : 2025-06-19DOI: 10.1016/j.jmoldx.2025.05.006
Mònica Coll , Mireia Alcalde , Anna Fernández-Falgueras , Anna Iglesias , Laia Nogué-Navarro , Coloma Tiron , Oscar Campuzano , Marisa Ortega , Santiago Crespo , Eneko Barberia , Ramon Brugada
Genetic testing, as part of the medicolegal autopsy in cases of suspected sudden cardiac death, has been recommended for several years; however, it is rarely performed. The aim was to assess the value of postmortem genetic testing in unexplained sudden death in the young. This is a prospective study including all cases with unexplained natural sudden death cases in individuals aged ≤50 years undergoing a legal autopsy. Postmortem genetic testing was routinely performed in cases aged ≤35 years and aged >35 years only when no cause of death was identified or there was suspicion of a possible inherited cardiac phenotype after a complete autopsy. In cases aged ≤35 years, genetic testing showed a positivity rate of 7.6%. The most striking finding has been the positivity rate of thoracic aorta aneurysms and myocarditis cases at 33%. In cases between the ages of 36 and 50 years, the positivity rate was 4.9%. If this group was approached with direct genetic analysis, as was done with the younger cohort, the yield of positive genetic testing would decrease to 2.5%. This is the largest study of postmortem genetic testing in the young to date, and the first to address its value in consecutive cases, free of selection bias.
{"title":"Value of Molecular Autopsy in Suspected Sudden Cardiac Death in the Young","authors":"Mònica Coll , Mireia Alcalde , Anna Fernández-Falgueras , Anna Iglesias , Laia Nogué-Navarro , Coloma Tiron , Oscar Campuzano , Marisa Ortega , Santiago Crespo , Eneko Barberia , Ramon Brugada","doi":"10.1016/j.jmoldx.2025.05.006","DOIUrl":"10.1016/j.jmoldx.2025.05.006","url":null,"abstract":"<div><div>Genetic testing, as part of the medicolegal autopsy in cases of suspected sudden cardiac death, has been recommended for several years; however, it is rarely performed. The aim was to assess the value of postmortem genetic testing in unexplained sudden death in the young. This is a prospective study including all cases with unexplained natural sudden death cases in individuals aged ≤50 years undergoing a legal autopsy. Postmortem genetic testing was routinely performed in cases aged ≤35 years and aged >35 years only when no cause of death was identified or there was suspicion of a possible inherited cardiac phenotype after a complete autopsy. In cases aged ≤35 years, genetic testing showed a positivity rate of 7.6%. The most striking finding has been the positivity rate of thoracic aorta aneurysms and myocarditis cases at 33%. In cases between the ages of 36 and 50 years, the positivity rate was 4.9%. If this group was approached with direct genetic analysis, as was done with the younger cohort, the yield of positive genetic testing would decrease to 2.5%. This is the largest study of postmortem genetic testing in the young to date, and the first to address its value in consecutive cases, free of selection bias.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 9","pages":"Pages 859-868"},"PeriodicalIF":3.4,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340563","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}
Pub Date : 2025-06-13DOI: 10.1016/j.jmoldx.2025.05.003
Susan J. Hsiao , Destin Black , Kelly A. Devereaux , Ian S. Hagemann , Lawrence J. Jennings , Diana Mandelker , Vera A. Paulson , Michelle Shiller , Tracy L. Stockley , Eric Vail , Praveen Vikas , Anna Yemelyanova
Homologous recombination deficiency (HRD) is a genomic feature present in some malignant neoplasms and is attributed to the failure of the homologous recombination repair pathway. Tumors with an HRD-positive status may have a distinct prognosis and/or response to therapies, including poly (ADP-ribose) polymerase inhibitors. The Association for Molecular Pathology assembled an expert panel to examine current practice and perform a scoping review of the medical literature pertaining to the molecular detection of HRD in the clinical setting. The expert panel examined the following topics: components of existing and proposed HRD and genomic instability biomarkers (including mutational signatures, loss of heterozygosity, mutations in homologous recombination repair–associated genes, and epigenetic silencing of RAD51C, BRCA1, or BRCA2); technical considerations for identifying genomic scars from tumor and germline next-generation sequencing results; guidelines on interpretation and caveats when reporting assessments of genomic instability and HRD scores; and the clinical significance of HRD. The panel formulated a set of expert consensus opinion recommendations regarding HRD assay design and validation to guide laboratories in developing HRD tests to ensure high-quality and reproducible results.
{"title":"Recommendations for Clinical Molecular Laboratories for Detection of Homologous Recombination Deficiency in Cancer","authors":"Susan J. Hsiao , Destin Black , Kelly A. Devereaux , Ian S. Hagemann , Lawrence J. Jennings , Diana Mandelker , Vera A. Paulson , Michelle Shiller , Tracy L. Stockley , Eric Vail , Praveen Vikas , Anna Yemelyanova","doi":"10.1016/j.jmoldx.2025.05.003","DOIUrl":"10.1016/j.jmoldx.2025.05.003","url":null,"abstract":"<div><div>Homologous recombination deficiency (HRD) is a genomic feature present in some malignant neoplasms and is attributed to the failure of the homologous recombination repair pathway. Tumors with an HRD-positive status may have a distinct prognosis and/or response to therapies, including poly (ADP-ribose) polymerase inhibitors. The Association for Molecular Pathology assembled an expert panel to examine current practice and perform a scoping review of the medical literature pertaining to the molecular detection of HRD in the clinical setting. The expert panel examined the following topics: components of existing and proposed HRD and genomic instability biomarkers (including mutational signatures, loss of heterozygosity, mutations in homologous recombination repair–associated genes, and epigenetic silencing of <em>RAD51C</em>, <em>BRCA1</em>, or <em>BRCA2</em>); technical considerations for identifying genomic scars from tumor and germline next-generation sequencing results; guidelines on interpretation and caveats when reporting assessments of genomic instability and HRD scores; and the clinical significance of HRD. The panel formulated a set of expert consensus opinion recommendations regarding HRD assay design and validation to guide laboratories in developing HRD tests to ensure high-quality and reproducible results.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 685-704"},"PeriodicalIF":3.4,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303456","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}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号