Pub Date : 2025-12-01Epub Date: 2025-10-21DOI: 10.1016/j.jmoldx.2025.09.009
Krupa Jani , Tracy McMillen , Cindy Lee , Edwin Miranda , Stephanie Rizzo , Anoshe Aslam , Tania Bubb , Mini Kamboj , N. Esther Babady
Candida auris is a high-priority multidrug-resistant yeast. In New York, C. auris is reportable, and surveillance screening is recommended for high-risk patients. This study provides a retrospective review of the yield and characteristics of C. auris cases detected through active surveillance testing at a tertiary cancer care center. Testing for C. auris was performed using a laboratory-developed real-time PCR test on patients admitted to the intensive care unit. Sample sources included axilla, groin, and nares swabs. Candida auris–positive PCR samples were further tested by culture with recovered isolates identified and further characterized by whole-genome sequencing and antifungal susceptibility testing. From 2019 to 2023, 27,299 samples were tested, with 139 positive samples (0.5%) on 16 unique patients. Positive swabs included 40 of 139 (28.7%) axilla, 44 of 139 (31.7%) nares, and 55 of 139 (39.5%) groin. A total of 134 of 139 (96.4%) samples were cultured, and 76 of 134 (56.7%) were positive in culture. An increase in positive swabs was noted. Four patients developed disseminated infections following a positive surveillance swab. Whole-genome sequencing classified all isolates as clade I, except for one isolate identified as clade III. Resistance to fluconazole was detected in 80% of isolates. Although the positivity rate remained low in this patient population, the recent increase in cases of C. auris nationwide underlies the need for active surveillance to prevent spread of this multidrug-resistant organism.
{"title":"Yield of an Active Candida auris Molecular Surveillance Program at a Tertiary Care Cancer Center","authors":"Krupa Jani , Tracy McMillen , Cindy Lee , Edwin Miranda , Stephanie Rizzo , Anoshe Aslam , Tania Bubb , Mini Kamboj , N. Esther Babady","doi":"10.1016/j.jmoldx.2025.09.009","DOIUrl":"10.1016/j.jmoldx.2025.09.009","url":null,"abstract":"<div><div><em>Candida auris</em> is a high-priority multidrug-resistant yeast. In New York, <em>C. auris</em> is reportable, and surveillance screening is recommended for high-risk patients. This study provides a retrospective review of the yield and characteristics of <em>C. auris</em> cases detected through active surveillance testing at a tertiary cancer care center. Testing for <em>C. auris</em> was performed using a laboratory-developed real-time PCR test on patients admitted to the intensive care unit. Sample sources included axilla, groin, and nares swabs. <em>Candida auris–</em>positive PCR samples were further tested by culture with recovered isolates identified and further characterized by whole-genome sequencing and antifungal susceptibility testing. From 2019 to 2023, 27,299 samples were tested, with 139 positive samples (0.5%) on 16 unique patients. Positive swabs included 40 of 139 (28.7%) axilla, 44 of 139 (31.7%) nares, and 55 of 139 (39.5%) groin. A total of 134 of 139 (96.4%) samples were cultured, and 76 of 134 (56.7%) were positive in culture. An increase in positive swabs was noted. Four patients developed disseminated infections following a positive surveillance swab. Whole-genome sequencing classified all isolates as clade I, except for one isolate identified as clade III. Resistance to fluconazole was detected in 80% of isolates. Although the positivity rate remained low in this patient population, the recent increase in cases of <em>C. auris</em> nationwide underlies the need for active surveillance to prevent spread of this multidrug-resistant organism.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1224-1231"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145356661","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 : 2025-12-01Epub Date: 2025-09-26DOI: 10.1016/j.jmoldx.2025.09.001
Haley J. Abel , Mohamed Mahgoub , Nidhi Davarapalli , Rohan Kodgule , Christopher A. Miller , Robert S. Fulton , Catrina Fronick , Christopher Markovic , Sharon Heath , Jacqueline E. Payton , Meagan A. Jacoby , Daniel C. Link , Matthew J. Walter , Eric J. Duncavage , Timothy J. Ley , David H. Spencer
Whole-genome sequencing (WGS) is a comprehensive approach for the genomic evaluation of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). We recently described a streamlined tumor-only WGS assay (ChromoSeq) that uses Illumina short-read sequencing with targeted analysis to detect the full range of clinically relevant somatic mutations. Here we sought to determine the performance of this targeted analysis approach using long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Samples from 26 patients with AML and MDS were sequenced to a mean of 52× coverage. Head-to-head comparison of reportable somatic variants to standard WGS revealed more than 96% recall and 91% precision for single nucleotide variants for both long-read platforms. Performance was lower for insertion/deletions (66% recall and 42% precision), especially in regions with few phased reads that facilitate accurate variant detection. The long-read platforms were 95% accurate for copy number calls, and they detected all recurrent structural variants with no false-positive findings. In addition, long reads properly identified intronic insertions near repetitive elements that were incorrectly identified as interchromosomal structural rearrangements by standard WGS. These results indicate that targeted, tumor-only analysis of long-read sequence data is a feasible approach for the genomic evaluation of myeloid cancers, and they show the utility of incorporating variants discovered via long-read sequencing to improve variant interpretation in short-read WGS.
{"title":"Evaluation of Long-Read Genome Sequencing for Genomic Profiling of Myeloid Cancers","authors":"Haley J. Abel , Mohamed Mahgoub , Nidhi Davarapalli , Rohan Kodgule , Christopher A. Miller , Robert S. Fulton , Catrina Fronick , Christopher Markovic , Sharon Heath , Jacqueline E. Payton , Meagan A. Jacoby , Daniel C. Link , Matthew J. Walter , Eric J. Duncavage , Timothy J. Ley , David H. Spencer","doi":"10.1016/j.jmoldx.2025.09.001","DOIUrl":"10.1016/j.jmoldx.2025.09.001","url":null,"abstract":"<div><div>Whole-genome sequencing (WGS) is a comprehensive approach for the genomic evaluation of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). We recently described a streamlined tumor-only WGS assay (ChromoSeq) that uses Illumina short-read sequencing with targeted analysis to detect the full range of clinically relevant somatic mutations. Here we sought to determine the performance of this targeted analysis approach using long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Samples from 26 patients with AML and MDS were sequenced to a mean of 52× coverage. Head-to-head comparison of reportable somatic variants to standard WGS revealed more than 96% recall and 91% precision for single nucleotide variants for both long-read platforms. Performance was lower for insertion/deletions (66% recall and 42% precision), especially in regions with few phased reads that facilitate accurate variant detection. The long-read platforms were 95% accurate for copy number calls, and they detected all recurrent structural variants with no false-positive findings. In addition, long reads properly identified intronic insertions near repetitive elements that were incorrectly identified as interchromosomal structural rearrangements by standard WGS. These results indicate that targeted, tumor-only analysis of long-read sequence data is a feasible approach for the genomic evaluation of myeloid cancers, and they show the utility of incorporating variants discovered via long-read sequencing to improve variant interpretation in short-read WGS.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1242-1254"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145187385","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 : 2025-12-01Epub Date: 2025-09-25DOI: 10.1016/j.jmoldx.2025.08.009
Nisha Kanwar , Michael B. Campion , Amber R. Schneider , Dragana Milosevic , Carlos Sosa , Antonina A. Wojcik , Kevin C. Halling , Kandelaria M. Rumilla , Ying-Chun Lo , Zhiyv Niu , Katherine B. Geiersbach , Margaret A. DiGuardo , Benjamin R. Kipp , Gang Zheng
The feasibility of circulating tumor (ct)-DNA assays in first-approach pan-cancer genomic profiling is not well established. Furthermore, low ctDNA levels limit assay sensitivity, which challenges adaptation to clinical genomic profiling. In this study, a 33-gene next-generation sequencing–based ctDNA panel was validated, and these issues were investigated using real-world clinical data. The cohorts included 123 patients who underwent first-approach ctDNA testing, and 48 patients for whom matched tissue was tested at the same time-point. The overall ctDNA assay failure rate was 0%. Insufficient tumor tissue was the main reason for liquid biopsy (69%). The most common primary cancer profiled was lung (39.0%), followed by colon (13.8%), bile duct (8.9%), pancreas (8.1%), and breast and prostate (each 4.1%). Tier I variants were detected in 33.3% of patients, and Tier I or II variants were detected in 65.0% (including 54.5% cholangiocarcinomas, in which tissue biopsy may be challenging due to anatomic location). Compared with matched tissue, ctDNA showed 76% sensitivity for Tier I variants. Actionable variants were increased by 14.3% with ctDNA versus tissue testing alone. ctDNA results preceded tissue results by an average of 21 days. High feasibility, actionability, and sensitivity support ctDNA assays as a potential first-line genomic test, especially in specific tumor types for advanced tumors with insufficient or unavailable tissue.
{"title":"Validation and Clinical Utility of a Pan-Cancer Circulating Tumor DNA Assay as a First-Approach Test","authors":"Nisha Kanwar , Michael B. Campion , Amber R. Schneider , Dragana Milosevic , Carlos Sosa , Antonina A. Wojcik , Kevin C. Halling , Kandelaria M. Rumilla , Ying-Chun Lo , Zhiyv Niu , Katherine B. Geiersbach , Margaret A. DiGuardo , Benjamin R. Kipp , Gang Zheng","doi":"10.1016/j.jmoldx.2025.08.009","DOIUrl":"10.1016/j.jmoldx.2025.08.009","url":null,"abstract":"<div><div>The feasibility of circulating tumor (ct)-DNA assays in first-approach pan-cancer genomic profiling is not well established. Furthermore, low ctDNA levels limit assay sensitivity, which challenges adaptation to clinical genomic profiling. In this study, a 33-gene next-generation sequencing–based ctDNA panel was validated, and these issues were investigated using real-world clinical data. The cohorts included 123 patients who underwent first-approach ctDNA testing, and 48 patients for whom matched tissue was tested at the same time-point. The overall ctDNA assay failure rate was 0%. Insufficient tumor tissue was the main reason for liquid biopsy (69%). The most common primary cancer profiled was lung (39.0%), followed by colon (13.8%), bile duct (8.9%), pancreas (8.1%), and breast and prostate (each 4.1%). Tier I variants were detected in 33.3% of patients, and Tier I or II variants were detected in 65.0% (including 54.5% cholangiocarcinomas, in which tissue biopsy may be challenging due to anatomic location). Compared with matched tissue, ctDNA showed 76% sensitivity for Tier I variants. Actionable variants were increased by 14.3% with ctDNA versus tissue testing alone. ctDNA results preceded tissue results by an average of 21 days. High feasibility, actionability, and sensitivity support ctDNA assays as a potential first-line genomic test, especially in specific tumor types for advanced tumors with insufficient or unavailable tissue.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 12","pages":"Pages 1213-1223"},"PeriodicalIF":3.4,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145182369","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 : 2025-11-01Epub Date: 2025-09-01DOI: 10.1016/j.jmoldx.2025.08.003
Krupa Jani , Taheefa Stephen , Cindy Lee , Arianna Pinto , Tracy McMillen , June L. Chan , N. Esther Babady
Human adenoviruses (HAdVs) can result in significant morbidity and mortality in immunocompromised patients. The AltoStar Adenovirus PCR Kit 1.5 (AltoStar HAdV PCR) is a real-time PCR test for the detection and quantification of HAdV DNA. In this study, the performance of the AltoStar HAdV PCR was evaluated compared with a laboratory-developed HAdV PCR based on MultiCode HAdV reagents (MultiCode HAdV PCR) using plasma and stool specimens. Performance of the AltoStar HAdV PCR was established by determining the linearity, lower limit of detection, precision, specificity, accuracy, and inclusivity of the assay. Accuracy was determined by testing plasma and stool clinical samples previously tested by the MultiCode HAdV PCR and inclusivity evaluated by using several HAdV genotypes. A time-and-motion study was performed to compare the workflows of both PCRs. The limit of detection was <200 copies/mL for both sample types. Overall agreement with the MultiCode HAdV PCR was 91% for plasma samples and 85.5% for stool samples. Quantitative agreement between the two tests was moderate. Specificity and precision in both sample types were high. All major HAdV species tested were detected. Hands-on-time was significantly less for the semi-automated AltoStar HAdV PCR. The AltoStar HAdV PCR showed great performance for the detection and/or quantitation of HAdV in clinical samples.
{"title":"Analytical and Clinical Evaluation of the AltoStar Adenovirus PCR Kit 1.5 and the AltoStar Automation System AM16 for Adenovirus Detection in Plasma and Stool Samples","authors":"Krupa Jani , Taheefa Stephen , Cindy Lee , Arianna Pinto , Tracy McMillen , June L. Chan , N. Esther Babady","doi":"10.1016/j.jmoldx.2025.08.003","DOIUrl":"10.1016/j.jmoldx.2025.08.003","url":null,"abstract":"<div><div>Human adenoviruses (HAdVs) can result in significant morbidity and mortality in immunocompromised patients. The AltoStar Adenovirus PCR Kit 1.5 (AltoStar HAdV PCR) is a real-time PCR test for the detection and quantification of HAdV DNA. In this study, the performance of the AltoStar HAdV PCR was evaluated compared with a laboratory-developed HAdV PCR based on MultiCode HAdV reagents (MultiCode HAdV PCR) using plasma and stool specimens. Performance of the AltoStar HAdV PCR was established by determining the linearity, lower limit of detection, precision, specificity, accuracy, and inclusivity of the assay. Accuracy was determined by testing plasma and stool clinical samples previously tested by the MultiCode HAdV PCR and inclusivity evaluated by using several HAdV genotypes. A time-and-motion study was performed to compare the workflows of both PCRs. The limit of detection was <200 copies/mL for both sample types. Overall agreement with the MultiCode HAdV PCR was 91% for plasma samples and 85.5% for stool samples. Quantitative agreement between the two tests was moderate. Specificity and precision in both sample types were high. All major HAdV species tested were detected. Hands-on-time was significantly less for the semi-automated AltoStar HAdV PCR. The AltoStar HAdV PCR showed great performance for the detection and/or quantitation of HAdV in clinical samples.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 11","pages":"Pages 1115-1122"},"PeriodicalIF":3.4,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144993690","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 : 2025-11-01Epub Date: 2025-08-20DOI: 10.1016/j.jmoldx.2025.07.004
Douglas A. Mata , Angela A. Kou , Andreas M. Heilmann , Julius Honecker , Benjamin R. Kroger , Thomas Wieland , Erik A. Williams , Soo-Ryum Yang , Jamal K. Benhamida , Chad Vanderbilt , Chelsea Marcus , Irene Shyu , Caleb Ho , Matthew C. Hiemenz , Tyler Janovitz , Ethan S. Sokol , Zoe Fleischmann , Dexter Jin , Ryon P. Graf , Richard A. Hickman , Brennan Decker
This study evaluated a UV mutational signature classifier applied to circulating tumor DNA (ctDNA) in cell-free DNA liquid biopsies, using the FoundationOne Liquid CDx platform. Among 73,790 samples, 12.9% (9527) met the variant threshold for signature analysis, with UV signatures detected in 3.8% (365) of cases. Of these, 51.5% (188) were initially submitted as cutaneous, 8.5% (31) as unspecified primary, and 40.0% (146) as extracutaneous tumors. The UV classifier demonstrated high specificity (99.7%) and variable sensitivity, reaching up to 37.5% and 67.6% in samples with elevated ctDNA levels and mutational loads, respectively. Molecular pathologist review confirmed that 74.0% (270/365) of UV calls were true positives and enabled resolution of false positives and ambiguous findings through integration of genomic and clinicopathologic features. This refined sensitivity estimates to 41.9% and 70.2% in cases with elevated ctDNA levels and mutational loads, respectively. Confirmed UV-positive tumors exhibited genomic alterations characteristic of sun-exposed skin cancers. In 175 matched liquid and tissue biopsy pairs, the positive percent agreement for UV signature detection was 38.7% overall, increasing to 87.5% and 90.6% in subsets with elevated ctDNA levels and mutational load, respectively. These results underline the utility of FoundationOne Liquid CDx, complemented by molecular pathologist oversight, in identifying cancers of cutaneous origin to refine diagnoses and guide treatment for patients with advanced cancers.
{"title":"High-Specificity Detection of UV Mutational Signatures in Circulating Tumor DNA for Diagnostic Classification of Cutaneous and Unknown Primary Tumors Using FoundationOne Liquid CDx","authors":"Douglas A. Mata , Angela A. Kou , Andreas M. Heilmann , Julius Honecker , Benjamin R. Kroger , Thomas Wieland , Erik A. Williams , Soo-Ryum Yang , Jamal K. Benhamida , Chad Vanderbilt , Chelsea Marcus , Irene Shyu , Caleb Ho , Matthew C. Hiemenz , Tyler Janovitz , Ethan S. Sokol , Zoe Fleischmann , Dexter Jin , Ryon P. Graf , Richard A. Hickman , Brennan Decker","doi":"10.1016/j.jmoldx.2025.07.004","DOIUrl":"10.1016/j.jmoldx.2025.07.004","url":null,"abstract":"<div><div>This study evaluated a UV mutational signature classifier applied to circulating tumor DNA (ctDNA) in cell-free DNA liquid biopsies, using the FoundationOne Liquid CDx platform. Among 73,790 samples, 12.9% (9527) met the variant threshold for signature analysis, with UV signatures detected in 3.8% (365) of cases. Of these, 51.5% (188) were initially submitted as cutaneous, 8.5% (31) as unspecified primary, and 40.0% (146) as extracutaneous tumors. The UV classifier demonstrated high specificity (99.7%) and variable sensitivity, reaching up to 37.5% and 67.6% in samples with elevated ctDNA levels and mutational loads, respectively. Molecular pathologist review confirmed that 74.0% (270/365) of UV calls were true positives and enabled resolution of false positives and ambiguous findings through integration of genomic and clinicopathologic features. This refined sensitivity estimates to 41.9% and 70.2% in cases with elevated ctDNA levels and mutational loads, respectively. Confirmed UV-positive tumors exhibited genomic alterations characteristic of sun-exposed skin cancers. In 175 matched liquid and tissue biopsy pairs, the positive percent agreement for UV signature detection was 38.7% overall, increasing to 87.5% and 90.6% in subsets with elevated ctDNA levels and mutational load, respectively. These results underline the utility of FoundationOne Liquid CDx, complemented by molecular pathologist oversight, in identifying cancers of cutaneous origin to refine diagnoses and guide treatment for patients with advanced cancers.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 11","pages":"Pages 1039-1053"},"PeriodicalIF":3.4,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144976933","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 : 2025-11-01Epub Date: 2025-08-20DOI: 10.1016/j.jmoldx.2025.07.007
Xueting Zhu, Shuang Yao, Jun Zhang, Lili Pan, Guanghua Luo, Lu Zheng
This study aimed to establish a two-dimensional PCR (2D-PCR) methodology capable of simultaneously identifying HLA-A∗31:01, HLA-B∗15:02, HLA-B∗57:01, and HLA-B∗58:01 alleles to prevent adverse drug reactions and guide safe clinical medication use. To achieve this goal, key nucleotide sites were first selected through multiple sequence alignment for the purpose of identifying HLA alleles: c.243T and c.290T for HLA-A∗31:01; c.206C, c.256G, and c.285G for HLA-B∗58:01; c.362T and c.419C for HLA-B∗57:01; and c.1012 + 104T (rs144012689) for HLA-B∗15:02. Using universal tag sequences linked to the 5′ end of primers and base-quenched probes, high-throughput identification of multiple target genes was achieved through PCR amplification and melting curve analysis, followed by methodologic optimization and evaluation. Results indicated that the 2D-PCR method has a detection limit of approximately 101 copies and achieves high specificity and accuracy. The entire detection process can be completed in approximately 100 minutes, with a cost of less than $1 (USD). Furthermore, 2D-PCR overcomes the limitations of traditional fluorescent channels, providing technical support for the identification of multiple target genes. In conclusion, this study shows that 2D-PCR offers a convenient and rapid approach for human leukocyte antigen allele identification to prevent adverse drug reactions and holds potential for clinical application.
{"title":"Two-Dimensional PCR for Identifying the HLA Alleles Associated with Adverse Drug Reactions","authors":"Xueting Zhu, Shuang Yao, Jun Zhang, Lili Pan, Guanghua Luo, Lu Zheng","doi":"10.1016/j.jmoldx.2025.07.007","DOIUrl":"10.1016/j.jmoldx.2025.07.007","url":null,"abstract":"<div><div>This study aimed to establish a two-dimensional PCR (2D-PCR) methodology capable of simultaneously identifying <em>HLA-A∗31:01</em>, <em>HLA-B∗15:02</em>, <em>HLA-B∗57:01</em>, and <em>HLA-B∗58:01</em> alleles to prevent adverse drug reactions and guide safe clinical medication use. To achieve this goal, key nucleotide sites were first selected through multiple sequence alignment for the purpose of identifying <em>HLA</em> alleles: c.243T and c.290T for <em>HLA-A∗31:01</em>; c.206C, c.256G, and c.285G for <em>HLA-B∗58:01</em>; c.362T and c.419C for <em>HLA-B∗57:01</em>; and c.1012 + 104T (rs144012689) for <em>HLA-B∗15:02</em>. Using universal tag sequences linked to the 5′ end of primers and base-quenched probes, high-throughput identification of multiple target genes was achieved through PCR amplification and melting curve analysis, followed by methodologic optimization and evaluation. Results indicated that the 2D-PCR method has a detection limit of approximately 10<sup>1</sup> copies and achieves high specificity and accuracy. The entire detection process can be completed in approximately 100 minutes, with a cost of less than $1 (USD). Furthermore, 2D-PCR overcomes the limitations of traditional fluorescent channels, providing technical support for the identification of multiple target genes. In conclusion, this study shows that 2D-PCR offers a convenient and rapid approach for human leukocyte antigen allele identification to prevent adverse drug reactions and holds potential for clinical application.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 11","pages":"Pages 1084-1097"},"PeriodicalIF":3.4,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144976908","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 : 2025-11-01Epub Date: 2025-09-01DOI: 10.1016/j.jmoldx.2025.08.002
Tom Bisson , Stefan Kaluziak , Norman Zerbe , Jochen K. Lennerz
Following recommendations from various consortia and professional societies, the double colon symbol (::) has become an integral part of gene fusion nomenclature (eg, EML4::ALK). Although widely adopted, its use presents technical challenges, as many common operating systems restrict the use of colons (:) in file and directory names. Consequently, the double colon (::) is often replaced with an underscore (_) or other allowed characters, introducing ambiguity and inconsistency. The first objective of this work is to raise awareness of this issue. The second objective is to propose a simple technical solution, that is, replacing the command-carrying symbol with a visually similar and functionally distinct ASCII character. The technical solution includes confirmation of functional compatibility and visual compliance with the established fusion nomenclature. The proposal also includes using Unicode characters to replace the slash (/) for alternative variants, the greater than symbol (>) for substitutions, and the asterisk (∗) for nonsense variants, for example. To support consistency, keyboard shortcuts or custom scripts may be used to automate these substitutions. The straightforward solution presented in this paper counterbalances unintended technical consequences and thereby promotes harmonization towards a unified genomic variant nomenclature.
{"title":"Solving the :: Fusion Nomenclature Challenge for File and Directory Naming","authors":"Tom Bisson , Stefan Kaluziak , Norman Zerbe , Jochen K. Lennerz","doi":"10.1016/j.jmoldx.2025.08.002","DOIUrl":"10.1016/j.jmoldx.2025.08.002","url":null,"abstract":"<div><div>Following recommendations from various consortia and professional societies, the double colon symbol (::) has become an integral part of gene fusion nomenclature (eg, <em>EML4::ALK</em>). Although widely adopted, its use presents technical challenges, as many common operating systems restrict the use of colons (:) in file and directory names. Consequently, the double colon (::) is often replaced with an underscore (_) or other allowed characters, introducing ambiguity and inconsistency. The first objective of this work is to raise awareness of this issue. The second objective is to propose a simple technical solution, that is, replacing the command-carrying symbol with a visually similar and functionally distinct ASCII character. The technical solution includes confirmation of functional compatibility and visual compliance with the established fusion nomenclature. The proposal also includes using Unicode characters to replace the slash (/) for alternative variants, the greater than symbol (>) for substitutions, and the asterisk (∗) for nonsense variants, for example. To support consistency, keyboard shortcuts or custom scripts may be used to automate these substitutions. The straightforward solution presented in this paper counterbalances unintended technical consequences and thereby promotes harmonization towards a unified genomic variant nomenclature.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 11","pages":"Pages 1070-1073"},"PeriodicalIF":3.4,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144994119","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 : 2025-11-01Epub Date: 2025-08-20DOI: 10.1016/j.jmoldx.2025.07.006
Somak Roy , Martine W. Tremblay , Edward Lockhart , Swaroop Aradhya , Pinar Bayrak-Toydemir , Mark Bowser , Jeana DaRe , Kristin Gibson , Michael Kennemer , Christopher Krueger , Matt Lebo , Rong Mao , Robert Nussbaum , Brendan O'Fallon , Andrew Rosato , Lisa V. Kalman , Birgit Funke
Clinical implementation of whole-genome and whole-exome sequencing by next-generation sequencing (NGS) allows for comprehensive detection of genomic alterations. However, with the growing number of clinically relevant genes and variants, there is an urgent need for reference materials to optimize, validate, and quality control NGS tests. This pilot study documents the paucity of physical reference materials for widely tested genes and demonstrates the utility of in silico mutagenized reference materials to supplement physical samples when developing NGS tests. We examined published, expert curated lists of clinically relevant variants for these widely tested genes and found that publicly available reference materials were available for only 29.4%. We outline the steps for generating in silico resources and used 49 curated variants to conduct a blinded proof-of-concept study with three experienced NGS laboratories. One laboratory detected all added variants, and two detected all but one. This study revealed common scenarios that could lead to false-negative results when common pathogenic variants cannot be tested during analytical validation. This work highlights the need to establish centralized knowledge bases for common, pathogenic variants, demonstrates the utility of in silico reference materials, and provides guidance for generating in silico reference materials in-house. Additional work will be needed to generate turnkey processes for novice laboratories without in-house bioinformatics expertise.
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