Pub Date : 2025-07-23DOI: 10.1016/j.jmoldx.2025.07.001
Shiyi Xu , Xiaomei Luo , Bing Xiao , Huili Liu , Ting Xu , Linlin Chen , Tingting Yang , Na Xu , Yanjie Fan , Wenjuan Qiu , Ruifang Wang , Huiwen Zhang , Yanru Chen , Yongguo Yu , Yu Sun
Short tandem repeats (STRs) are associated with 70 genetic diseases. Because of the short read length of exome sequencing (ES), STR analysis is not routinely analyzed in clinical ES. So far, there has been limited systematic evaluation using large-scale clinical ES data to assess the diagnostic yield of pathogenic STR expansion. This study retrospectively analyzed 9580 exomes referred to our genetic laboratory between July 2019 and June 2024. The samples were divided into two groups: a genetically undiagnosed cohort (n = 4692) and a reference cohort with a low probability of carrying pathogenic STR expansions (n = 4888). An analysis pipeline was developed on the basis of the combination of multiple algorithms to analyze STRs detected in 30 known disease-related loci, achieving a precision of 54.9% and a sensitivity of 100%. STR verification by capillary electrophoresis analysis of STR confirmed 28 cases (0.6%) with pathogenic STR expansions in known disease-related loci. Fourteen of these cases (0.3%) could be explained by the STR findings, including seven neonates with DMPK expansions. The pipeline showed the potential to identity abnormal STR expansions at novel sites. In conclusion, this study demonstrates the clinical utility of ES-based STR analysis and advocates for its incorporation into the clinical ES workflow in genetic laboratories.
{"title":"Additional Diagnostic Yield through the Analysis of Short Tandem Repeats Based on Exome Sequencing Data","authors":"Shiyi Xu , Xiaomei Luo , Bing Xiao , Huili Liu , Ting Xu , Linlin Chen , Tingting Yang , Na Xu , Yanjie Fan , Wenjuan Qiu , Ruifang Wang , Huiwen Zhang , Yanru Chen , Yongguo Yu , Yu Sun","doi":"10.1016/j.jmoldx.2025.07.001","DOIUrl":"10.1016/j.jmoldx.2025.07.001","url":null,"abstract":"<div><div>Short tandem repeats (STRs) are associated with 70 genetic diseases. Because of the short read length of exome sequencing (ES), STR analysis is not routinely analyzed in clinical ES. So far, there has been limited systematic evaluation using large-scale clinical ES data to assess the diagnostic yield of pathogenic STR expansion. This study retrospectively analyzed 9580 exomes referred to our genetic laboratory between July 2019 and June 2024. The samples were divided into two groups: a genetically undiagnosed cohort (<em>n</em> = 4692) and a reference cohort with a low probability of carrying pathogenic STR expansions (<em>n</em> = 4888). An analysis pipeline was developed on the basis of the combination of multiple algorithms to analyze STRs detected in 30 known disease-related loci, achieving a precision of 54.9% and a sensitivity of 100%. STR verification by capillary electrophoresis analysis of STR confirmed 28 cases (0.6%) with pathogenic STR expansions in known disease-related loci. Fourteen of these cases (0.3%) could be explained by the STR findings, including seven neonates with <em>DMPK</em> expansions. The pipeline showed the potential to identity abnormal STR expansions at novel sites. In conclusion, this study demonstrates the clinical utility of ES-based STR analysis and advocates for its incorporation into the clinical ES workflow in genetic laboratories.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 10","pages":"Pages 1017-1025"},"PeriodicalIF":3.4,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719033","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 : 2025-07-23DOI: 10.1016/j.jmoldx.2025.06.006
Pia S. Henkel , Eline Aas , Hege G. Russnes , Ingrid Dyvik , G. Live Fagereng , Åslaug Helland , Hanna Røgenes , Tonje G. Lien , Kine Pedersen
Detailed cost analyses of genomic profiling for precision cancer medicine can inform strategic planning and cost-effectiveness analysis. A flexible costing framework was developed in this study to conduct microcosting of genomic profiling in precision cancer medicine using the broad gene panel TruSight Oncology 500 and accounting for its integration into the molecular tumor board within the national Infrastructure for Precision Diagnostics in Norway. The framework enables calculation of costs per sample, by workflow steps and cost categories. Site visits and discussions with staff at Oslo University Hospital informed the diagnostic workflow, validation of the framework, and resource use inputs. Sensitivity analysis addressed alternative resource use estimates, higher batch sizes, and investment costs for automation of the library preparation step. Total costs per sample were $2944 USD, ranging from $2366 to $4307 when considering uncertainties in estimates. Consumables and personnel were the most resource-intensive cost categories across analyses. Automating the resource-intensive library preparation step enabled a higher weekly batch size with slightly lower costs per sample ($2881) despite the additional equipment costs. The dynamic costing framework highlights how the choice of equipment and batch sizes affects sample costs and personnel needs for genomic profiling. Consumables and personnel offer the largest potential for costs savings, but potential personnel bottlenecks need to be considered when further upscaling capacity.
{"title":"Microcosting Study of Genomic Profiling for Precision Cancer Medicine","authors":"Pia S. Henkel , Eline Aas , Hege G. Russnes , Ingrid Dyvik , G. Live Fagereng , Åslaug Helland , Hanna Røgenes , Tonje G. Lien , Kine Pedersen","doi":"10.1016/j.jmoldx.2025.06.006","DOIUrl":"10.1016/j.jmoldx.2025.06.006","url":null,"abstract":"<div><div>Detailed cost analyses of genomic profiling for precision cancer medicine can inform strategic planning and cost-effectiveness analysis. A flexible costing framework was developed in this study to conduct microcosting of genomic profiling in precision cancer medicine using the broad gene panel TruSight Oncology 500 and accounting for its integration into the molecular tumor board within the national Infrastructure for Precision Diagnostics in Norway. The framework enables calculation of costs per sample, by workflow steps and cost categories. Site visits and discussions with staff at Oslo University Hospital informed the diagnostic workflow, validation of the framework, and resource use inputs. Sensitivity analysis addressed alternative resource use estimates, higher batch sizes, and investment costs for automation of the library preparation step. Total costs per sample were $2944 USD, ranging from $2366 to $4307 when considering uncertainties in estimates. Consumables and personnel were the most resource-intensive cost categories across analyses. Automating the resource-intensive library preparation step enabled a higher weekly batch size with slightly lower costs per sample ($2881) despite the additional equipment costs. The dynamic costing framework highlights how the choice of equipment and batch sizes affects sample costs and personnel needs for genomic profiling. Consumables and personnel offer the largest potential for costs savings, but potential personnel bottlenecks need to be considered when further upscaling capacity.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 10","pages":"Pages 945-953"},"PeriodicalIF":3.4,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144719036","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 : 2025-07-22DOI: 10.1016/j.jmoldx.2025.06.005
Danielle K. Manning , Guruprasad Ananda , Cheryl Eifert , Vanesa Rojas-Rudilla , William Swanton , Shawn Keefe , Elizabeth P. Garcia , Michael D'Eletto , Erica Holdmore , Satyakam Mishra , Kirill Borziak , Pieter Lukasse , Phani Davineni , Monica D. Manam , Priyanka Shivdasani , Arezou A. Ghazani , Ai Ling Wang , Murat Bastepe , Himisha Beltran , Katherine A. Janeway , Laura E. MacConaill
Genomic profiling of cancers informs diagnostic and prognostic classification and aids in selection of targeted therapeutics. Targeted, next-generation sequencing of cancer-specific genes is clinically feasible and enables comprehensive somatic reporting; without a matched germline specimen, germline alterations can confound analyses of the somatic profile and generate uncertainty in interpretation. This work reports the validation and implementation of optional matched tumor/germline sequencing in a precision cancer medicine program. DNA from 63 patient samples was analyzed using OncoPanel, a hybrid capture-based sequencing assay of 461 genes. Three analytical pipelines were implemented: tumor only, matched tumor/germline, and germline only. For matched tumor/germline, germline alterations in 19 genes with actionable/therapeutic implications were rescued. Retrospective analysis of the first 1600 matched cases was done to determine the potential clinical utility of this approach. Limit of detection for point mutations/insertions and deletions was 3% allele fraction; reproducibility was >98%. Matched tumor/germline concordance across 938 somatic calls was 100%. The average tumor mutational burden (TMB) was approximately 4 mutations/Mb lower than tumor-only sequencing. TMB-high patients were accurately reclassified as TMB-low in 14% of cases. Twenty-five percent of validation cases (14% after launch) had a pathogenic or likely pathogenic germline variant conferring cancer susceptibility; 14% of validation cases (7% after launch) harbored a germline variant of therapeutic significance. Matched tumor/germline sequencing is more accurate than tumor-only sequencing, while still encompassing all genomic findings that inform targeted therapy selection.
{"title":"Clinical Implementation of Matched Tumor/Germline Sequencing Improves Accuracy of Tumor Genomic Profiling and Therapeutic Recommendations","authors":"Danielle K. Manning , Guruprasad Ananda , Cheryl Eifert , Vanesa Rojas-Rudilla , William Swanton , Shawn Keefe , Elizabeth P. Garcia , Michael D'Eletto , Erica Holdmore , Satyakam Mishra , Kirill Borziak , Pieter Lukasse , Phani Davineni , Monica D. Manam , Priyanka Shivdasani , Arezou A. Ghazani , Ai Ling Wang , Murat Bastepe , Himisha Beltran , Katherine A. Janeway , Laura E. MacConaill","doi":"10.1016/j.jmoldx.2025.06.005","DOIUrl":"10.1016/j.jmoldx.2025.06.005","url":null,"abstract":"<div><div>Genomic profiling of cancers informs diagnostic and prognostic classification and aids in selection of targeted therapeutics. Targeted, next-generation sequencing of cancer-specific genes is clinically feasible and enables comprehensive somatic reporting; without a matched germline specimen, germline alterations can confound analyses of the somatic profile and generate uncertainty in interpretation. This work reports the validation and implementation of optional matched tumor/germline sequencing in a precision cancer medicine program. DNA from 63 patient samples was analyzed using OncoPanel, a hybrid capture-based sequencing assay of 461 genes. Three analytical pipelines were implemented: tumor only, matched tumor/germline, and germline only. For matched tumor/germline, germline alterations in 19 genes with actionable/therapeutic implications were rescued. Retrospective analysis of the first 1600 matched cases was done to determine the potential clinical utility of this approach. Limit of detection for point mutations/insertions and deletions was 3% allele fraction; reproducibility was >98%. Matched tumor/germline concordance across 938 somatic calls was 100%. The average tumor mutational burden (TMB) was approximately 4 mutations/Mb lower than tumor-only sequencing. TMB-high patients were accurately reclassified as TMB-low in 14% of cases. Twenty-five percent of validation cases (14% after launch) had a pathogenic or likely pathogenic germline variant conferring cancer susceptibility; 14% of validation cases (7% after launch) harbored a germline variant of therapeutic significance. Matched tumor/germline sequencing is more accurate than tumor-only sequencing, while still encompassing all genomic findings that inform targeted therapy selection.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 10","pages":"Pages 969-988"},"PeriodicalIF":3.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709677","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 : 2025-07-22DOI: 10.1016/j.jmoldx.2025.06.004
Alexa Dickson , Kelsey R. Cone , Barbara K. Fortini , Jennifer Goldstein , Michelle L. Thompson , Matheus V.M.B. Wilke , Anna C.E. Hurst , Molly C. Schroeder , Katarzyna Polonis , Kevin M. Bowling
Genomic testing has proven utility in disease diagnostics, guiding clinical management and improving outcomes. Use of high-throughput sequencing by clinical laboratories has generated opportunities and challenges in data analysis, resulting in the emergence of a laboratory role termed variant scientist. The aim of this study was to characterize this laboratory role. A 30-item survey was developed to collect information describing the current demographic landscape, salary ranges, work environments, training options, and professional development of variant scientists. The survey was disseminated to individuals conducting variant analysis in the United States from November 6, 2023, to March 15, 2024. Survey responders (n = 87) were predominantly female (78%), aged ≤40 years (64%), hold advanced degrees (38% master's, 47% doctoral), and report ≥4 years of experience (75%). Responders report involvement in a diverse set of laboratory tasks and received relevant training on the job (78%). This workforce is satisfied with their career path (70%) and reports adequate support from employers, but perceives that resources and recognition from professional organizations are currently lacking. Characterization of this workforce will be of interest to individuals working as variant scientists, individuals interested in careers in variant science, and laboratory directors seeking assistance for effectively maintaining and efficiently growing clinical laboratory operations.
{"title":"Survey of Demographics, Training, Duties, and Professional Development for Variant Scientists in Genomic Medicine","authors":"Alexa Dickson , Kelsey R. Cone , Barbara K. Fortini , Jennifer Goldstein , Michelle L. Thompson , Matheus V.M.B. Wilke , Anna C.E. Hurst , Molly C. Schroeder , Katarzyna Polonis , Kevin M. Bowling","doi":"10.1016/j.jmoldx.2025.06.004","DOIUrl":"10.1016/j.jmoldx.2025.06.004","url":null,"abstract":"<div><div>Genomic testing has proven utility in disease diagnostics, guiding clinical management and improving outcomes. Use of high-throughput sequencing by clinical laboratories has generated opportunities and challenges in data analysis, resulting in the emergence of a laboratory role termed variant scientist. The aim of this study was to characterize this laboratory role. A 30-item survey was developed to collect information describing the current demographic landscape, salary ranges, work environments, training options, and professional development of variant scientists. The survey was disseminated to individuals conducting variant analysis in the United States from November 6, 2023, to March 15, 2024. Survey responders (<em>n</em> = 87) were predominantly female (78%), aged ≤40 years (64%), hold advanced degrees (38% master's, 47% doctoral), and report ≥4 years of experience (75%). Responders report involvement in a diverse set of laboratory tasks and received relevant training on the job (78%). This workforce is satisfied with their career path (70%) and reports adequate support from employers, but perceives that resources and recognition from professional organizations are currently lacking. Characterization of this workforce will be of interest to individuals working as variant scientists, individuals interested in careers in variant science, and laboratory directors seeking assistance for effectively maintaining and efficiently growing clinical laboratory operations.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 10","pages":"Pages 936-944"},"PeriodicalIF":3.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709678","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 : 2025-07-22DOI: 10.1016/j.jmoldx.2025.06.007
Lauren M. Petersen , Rachana Sainger , Paulina Sanchez , Jillian Burke , Joshua D. Wemmer , Bradley Patay , Jeffrey E. Miller
KMT2A fusions are a critical oncogenic driver in 5% to 10% of patients with acute myeloid leukemia (AML) and are associated with poor prognosis. Currently, there are no published somatic guidelines for fusions in AML, and developing methods to accurately classify fusions, especially those involving KMT2A, is essential for patient care. Therefore, the Laboratory for Personalized Molecular Medicine (LabPMM) KMT2A Fusions Workflow was developed utilizing the framework of the somatic guidelines by Horak et al, where classification of oncogenicity is based on points awarded for varying types of evidence. Fusions previously detected by LabPMM's CAP/CLIA–certified MyAML and MyMRD gene panels were used to test this workflow. A total of 100 KMT2A fusions were reassessed, and 97 of these had a breakpoint in the major breakpoint cluster region. There were 20 distinct partner genes for KMT2A, and the most common partners were MLLT3, ELL, AFDN, MLLT10, and AFF1. Five KMT2A fusions had a novel partner (MYB, RC3H1, SNAPC3, STPG1, and HPSE2). Breakpoints in the partner genes were assessed to better understand their potential role in driving leukemogenesis. Of the 100 fusions reassessed, 9 had a classification change. This LabPMM KMT2A Fusions Workflow provides a points-based system for curation that allows for standardization and clarity both within and among genetic diagnostic laboratories reporting on KMT2A fusions in AML.
{"title":"A Systematic, Evidence-Based Workflow for Classifying KMT2A Fusions in Acute Myeloid Leukemia","authors":"Lauren M. Petersen , Rachana Sainger , Paulina Sanchez , Jillian Burke , Joshua D. Wemmer , Bradley Patay , Jeffrey E. Miller","doi":"10.1016/j.jmoldx.2025.06.007","DOIUrl":"10.1016/j.jmoldx.2025.06.007","url":null,"abstract":"<div><div><em>KMT2A</em> fusions are a critical oncogenic driver in 5% to 10% of patients with acute myeloid leukemia (AML) and are associated with poor prognosis. Currently, there are no published somatic guidelines for fusions in AML, and developing methods to accurately classify fusions, especially those involving <em>KMT2A</em>, is essential for patient care. Therefore, the Laboratory for Personalized Molecular Medicine (LabPMM) <em>KMT2A</em> Fusions Workflow was developed utilizing the framework of the somatic guidelines by Horak et al, where classification of oncogenicity is based on points awarded for varying types of evidence. Fusions previously detected by LabPMM's CAP/CLIA–certified MyAML and MyMRD gene panels were used to test this workflow. A total of 100 <em>KMT2A</em> fusions were reassessed, and 97 of these had a breakpoint in the major breakpoint cluster region. There were 20 distinct partner genes for <em>KMT2A</em>, and the most common partners were <em>MLLT3</em>, <em>ELL</em>, <em>AFDN, MLLT10</em>, and <em>AFF1</em>. Five <em>KMT2A</em> fusions had a novel partner (<em>MYB</em>, <em>RC3H1</em>, <em>SNAPC3</em>, <em>STPG1</em>, and <em>HPSE2</em>). Breakpoints in the partner genes were assessed to better understand their potential role in driving leukemogenesis. Of the 100 fusions reassessed, 9 had a classification change. This LabPMM <em>KMT2A</em> Fusions Workflow provides a points-based system for curation that allows for standardization and clarity both within and among genetic diagnostic laboratories reporting on <em>KMT2A</em> fusions in AML.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 10","pages":"Pages 989-1002"},"PeriodicalIF":3.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144709676","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 : 2025-07-21DOI: 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}
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