Journal of Molecular Diagnostics最新文献

{"title":"Morphological Bone Score as a Predictive Tool for Molecular Profiling Success","authors":"Kirill Kriukov ,&nbsp;Dmitry Ivchenkov ,&nbsp;Anna Bejanyan ,&nbsp;Aleksandr Sarachakov ,&nbsp;Aleksandra Kviatkovskaia ,&nbsp;Gleb Khegai ,&nbsp;Dominique Knipper-Davis ,&nbsp;Amber Berlinski ,&nbsp;Tayla Soares ,&nbsp;Jochen K. Lennerz ,&nbsp;Vladimir Kushnarev","doi":"10.1016/j.jmoldx.2025.04.013","DOIUrl":"10.1016/j.jmoldx.2025.04.013","url":null,"abstract":"<div><div>Decalcification of bone-containing tumor samples serves to soften tissues before histologic processing. However, it can lead to nucleic acid degradation, resulting in next-generation sequencing failures that impede diagnostic solutions for patients. The Morphological Bone Score (MBS) described herein optimizes the assessment of decalcified tissue samples, consequently improving both diagnostic accuracy and cost efficiency in molecular genetic laboratories. The MBS, constructed using five key morphologic features, assigns scores from 0 to 11, reflecting low to high tissue damage and direct proportionality with nucleic acid yields per cell. The MBS threshold can be adjusted depending on the aims of a specific analysis while balancing between sensitivity and accuracy. In our next-generation sequencing workflow, the exclusion of poor-quality samples from downstream processing using MBS led to a savings of $1500 per sample. The MBS provides a cost-effective approach for maximizing tissue utilization and optimizing downstream profiling in precision oncology because its objectivity and consistency in evaluating pathologic samples ensure reliable and reproducible outcomes. With additional verification, this tool could be implemented in computational models for converting morphologic features into measurable units.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 747-756"},"PeriodicalIF":3.4,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303455","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}

{"title":"A Comparative Study of Medium-Coverage Genome Sequencing and SNP Array Technology in Identifying Chromosomal Abnormalities to Advance Prenatal and Postnatal Diagnosis","authors":"Jialun Pang ,&nbsp;Lin Zhou ,&nbsp;Jiancheng Hu ,&nbsp;Hanzhe Kuang ,&nbsp;Hui Xi ,&nbsp;Na Ma ,&nbsp;Shuting Yang ,&nbsp;Wenxian Yu ,&nbsp;Yanan Zhang ,&nbsp;Qian Zhang ,&nbsp;Victor Wei Zhang ,&nbsp;Jing Chen ,&nbsp;Ying Peng","doi":"10.1016/j.jmoldx.2025.04.009","DOIUrl":"10.1016/j.jmoldx.2025.04.009","url":null,"abstract":"<div><div>This study compared the performance of 5-fold genome sequencing (GS) with single nucleotide polymorphism (SNP) array technology in detecting chromosomal abnormalities, particularly in the context of prenatal and postnatal diagnostics. A total of 42 samples, previously analyzed by SNP array, were re-examined using 5-fold GS to evaluate the detection of clinically significant copy number variations (CNVs), mosaicism, and absence of heterozygosity (AOH). The results revealed a 100% concordance between the two methods for the identification of clinically relevant CNVs, with both technologies detecting similar CNV size ranges. However, 5-fold GS demonstrated better precision in defining CNV breakpoints and exhibited a lower false-positive rate, as confirmed by quantitative PCR validation. Additionally, 5-fold GS detected mosaicism with comparable sensitivity to SNP array, capturing mosaic levels as low as 17%, whereas SNP array identified levels between 15% and 84%. For AOH detection, 5-fold GS identified all candidate AOH regions with a slightly better sensitivity, achieving a detection size limit of 4.8 Mb compared with SNP array's 5.08 Mb. Overall, 5-fold GS shows potential as a reliable method for chromosomal abnormality detection, offering high accuracy and clinical utility in both prenatal and postnatal genetic testing.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 736-746"},"PeriodicalIF":3.4,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250605","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}

{"title":"Validation of Human Papillomavirus Genotyping by Oxford Nanopore Sequencing in Formalin-Fixed, Paraffin-Embedded Tissues and ThinPrep Anal and Gynecologic Samples","authors":"Carolina Hernandez ,&nbsp;Luz H. Patiño ,&nbsp;Milena Camargo ,&nbsp;Ching Yi Wang ,&nbsp;Feng Chen ,&nbsp;Bernadette Liggayu ,&nbsp;Liyong Cao ,&nbsp;Carlos Cordon-Cardo ,&nbsp;Emilia M. Sordillo ,&nbsp;Alberto Paniz-Mondolfi ,&nbsp;Juan D. Ramírez","doi":"10.1016/j.jmoldx.2025.04.010","DOIUrl":"10.1016/j.jmoldx.2025.04.010","url":null,"abstract":"<div><div>Human papillomavirus (HPV) is linked to various cancers, including cervical, anal, and head and neck cancers. Conventional methods for HPV genotyping and commercial platforms are limited to detecting high-risk HPV genotypes primarily in gynecologic samples. Because of changing trends in the epidemiology and pathogenesis, there is a growing need for HPV genotyping techniques applicable to emerging clinical contexts involving diverse sample types, such as head and neck or anal samples, particularly for formalin-fixed, paraffin-embedded (FFPE) tissues. This study aimed to validate amplicon-based sequencing with Oxford Nanopore Technologies (ONT) for the detection and genotyping of HPV in 181 samples, including FFPE head and neck samples, and ThinPrep liquid-based cytology samples from anal and gynecologic tissues. Sanger sequencing was used as a reference for genotyping accuracy. The ONT sequencing method demonstrated a limit of detection of 1 copy/μL for HPV16 and HPV18. Perfect agreement (κ coefficient = 1.0) was observed for HPV detection across all sample types. Genotyping accuracy exceeded 95%, and ONT identified additional genotypes in certain anal and gynecologic samples that were undetected by Sanger sequencing. The assay showed high reproducibility, with consistent results across intrarun and interrun analyses. This study is the first to validate ONT sequencing for HPV genotyping in FFPE head and neck samples. ONT provides a rapid, cost-effective method for comprehensive HPV genotyping in diverse sample types.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 757-767"},"PeriodicalIF":3.4,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250607","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}

{"title":"Comparison of the Mutational Profile between BCL2- and BCL6-Rearrangement Positive Follicular Lymphoma","authors":"Haruka Ikoma ,&nbsp;Joaquim Carreras ,&nbsp;Yara Yukie Kikuti ,&nbsp;Masashi Miyaoka ,&nbsp;Shunsuke Nagase ,&nbsp;Yusuke Kondo ,&nbsp;Atsushi Ito ,&nbsp;Makoto Orita ,&nbsp;Sakura Tomita ,&nbsp;Shinichiro Hiraiwa ,&nbsp;Hiroshi Kawada ,&nbsp;Juan F. Garcia ,&nbsp;Giovanna Roncador ,&nbsp;Elias Campo ,&nbsp;Naoya Nakamura","doi":"10.1016/j.jmoldx.2025.05.002","DOIUrl":"10.1016/j.jmoldx.2025.05.002","url":null,"abstract":"<div><div>It was recently reported that follicular lymphoma (FL) with <em>BCL6</em> rearrangement (R) is associated with favorable progression-free survival, whereas <em>BCL2</em>-R and <em>BCL2-6</em>-R cases are associated with disease progression. However, the pathologic mechanism remained unexplored. This study analyzed the mutational landscape and immune microenvironment of 31 FL cases, including 16 <em>BCL2</em>-R, 11 <em>BCL6</em>-R, and 4 <em>BCL2-6-</em>R FL cases. The method included an in-house next-generation targeted sequencing panel of 168 genes associated with aggressive B-cell lymphoma and FL, whole genome copy number change microarray (OncoScan), and immunohistochemistry for the immune microenvironment focused on M2-like tumor-associated macrophages, regulatory T lymphocytes, and programmed cell death protein 1 (PDCD1; alias PD-1)–positive follicular T helper cells. The resulting mutational profile was compatible with a previously reported conventional FL series featuring frequent mutations in <em>CREBBP</em>, <em>KMT2D</em>, <em>TNFRSF14</em>, <em>STAT6</em>, and <em>CD36</em>. Moreover, <em>BCL6</em>-R cases had mutations in <em>ARID1B</em>, <em>ARID5B</em>, and <em>RHOA</em>; low frequency of mutations in other genes, such as <em>OSBPL10</em>, <em>PTPRD</em>, <em>ATM</em>, and <em>HLA-B</em>; 6q loss; and absence of disease progression. In comparison with <em>BCL6</em>-R cases, <em>BCL2</em>-R and <em>BCL2-6-</em>R cases had mutations in <em>EZH2</em>, chromosome 18 copy number gain, and disease progression in some cases. The immune microenvironment profile was heterogeneous; however, <em>BCL6</em>-R cases demonstrated higher infiltration of colony-stimulating factor 1 receptor– and leukocyte immunoglobulin like receptor B3 (LILRB3; alias CD85a)–positive cells. In conclusion, compared with <em>BCL</em>2-R, FL with <em>BCL</em>6-R exhibited some differences in mutational profiles and immune microenvironment.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 796-807"},"PeriodicalIF":3.4,"publicationDate":"2025-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144250606","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}

{"title":"Clinical Bioinformatician Body of Knowledge—Bioinformatics and Software Core","authors":"Sabah Kadri ,&nbsp;Kelly E. Craven ,&nbsp;Amber M. Fussell ,&nbsp;Elaine P.S. Gee ,&nbsp;Danielle Jordan ,&nbsp;Eric W. Klee ,&nbsp;Niklas Krumm ,&nbsp;Robyn L. Temple-Smolkin ,&nbsp;Ahmet Zehir ,&nbsp;Weiwei Zhang ,&nbsp;Andrea Sboner","doi":"10.1016/j.jmoldx.2025.04.008","DOIUrl":"10.1016/j.jmoldx.2025.04.008","url":null,"abstract":"<div><div>With the evolution of next-generation sequencing–based testing in molecular diagnostics laboratories, the clinical role of bioinformaticians has also evolved. The Association for Molecular Pathology's Clinical Bioinformatician Body of Knowledge aims to define the various roles the clinical bioinformatician operates individually or within a clinical bioinformatics team, along with proficiencies and skill sets that may be required or desirable across these roles. One of the most common professional responsibilities of a clinical bioinformatician is to implement bioinformatics pipelines, either vendor supplied or custom built for the assays in the molecular diagnostics laboratory, along with analysis and quality control of clinical genomics data. This second article in the series describes the various stages in the life cycle of a clinical bioinformatics pipeline and the considerations, areas of expertise, and skill sets required in each stage. This information may help laboratory professionals to better work with clinical bioinformaticians and laboratory directors to hire the appropriate expertise based on the specific needs of the laboratory.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 7","pages":"Pages 566-582"},"PeriodicalIF":3.4,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144121464","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}

{"title":"Standardizing Laboratory Practices in Pharmacogenomics (STRIPE) Consensus Conference","authors":"Victoria M. Pratt ,&nbsp;Betsy Bove ,&nbsp;Raymond A. Lorenz ,&nbsp;Annette K. Taylor ,&nbsp;Bronwyn Ramey","doi":"10.1016/j.jmoldx.2025.04.006","DOIUrl":"10.1016/j.jmoldx.2025.04.006","url":null,"abstract":"","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 674-676"},"PeriodicalIF":3.4,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103001","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}

{"title":"Path to Health Equity and Improved Outcomes through Inclusive Sex and Gender Data Collection in Genomic Testing","authors":"Marco L. Leung ,&nbsp;Ina Amarillo ,&nbsp;Danielle Jordan ,&nbsp;Matthew S. Lebo ,&nbsp;Rizwan C. Naeem ,&nbsp;David I. Suster ,&nbsp;Robyn L. Temple-Smolkin ,&nbsp;Cigdem H. Ussakli ,&nbsp;Honey V. Reddi","doi":"10.1016/j.jmoldx.2025.04.004","DOIUrl":"10.1016/j.jmoldx.2025.04.004","url":null,"abstract":"<div><div>As the demand for health services among sexual and gender diverse (SGD) individuals rises, there is a growing need for comprehensive and equitable standards of care across the health care system. Despite progress in various research areas, there is a relative lag in genetics and genomics. In this Perspective, the Association for Molecular Pathology Working Group presents survey data on how the sex and gender identity of patients, including SGD individuals, is collected, interpreted, and reported within current genomic laboratory practices during the preanalytical, analytical, and postanalytical phases. Recommendations and guidelines related to the care of the SGD community are explored, identifying knowledge and practice gaps in each phase. On the basis of the survey results, review of existing available literature, and collective professional experience, the Working Group provides future considerations to enhance affirmative and inclusive processes, improve test quality, advance health equity, and enhance patient outcomes.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 677-684"},"PeriodicalIF":3.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095509","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}

{"title":"Smart Nonuniformity for Calibrating Sequencing Depth of a Targeted Gene Panel to Simultaneously Detect Somatic and Germline Variants","authors":"Robert L. O'Reilly ,&nbsp;Philip Harraka ,&nbsp;Jared Burke ,&nbsp;Daniele Belluoccio ,&nbsp;Paul Yeh ,&nbsp;Kerryn Howlett ,&nbsp;Kiarash Behrouzfar ,&nbsp;Amanda Rewse ,&nbsp;Helen Tsimiklis ,&nbsp;Graham G. Giles ,&nbsp;John L. Hopper ,&nbsp;Kristen J. Bubb ,&nbsp;Stephen J. Nicholls ,&nbsp;Roger L. Milne ,&nbsp;Melissa C. Southey","doi":"10.1016/j.jmoldx.2025.04.007","DOIUrl":"10.1016/j.jmoldx.2025.04.007","url":null,"abstract":"<div><div>Targeted gene panel sequencing that measures genomic variation at different depths has potential diagnostic application. A targeted gene panel, smart nonuniformity sequencing, was developed to detect somatic variants associated with clonal hematopoiesis of indeterminate potential (CHIP), which requires an optimal sequencing depth of &gt;500×; and germline variants requiring a lower ≥50× depth (panel 1). This was achieved by adjusting probe ratios for genomic regions relevant to identifying CHIP in comparison to those relevant to germline variation analysis. An additional custom panel containing only the genomic regions relevant to the identification of CHIP (panel 2) was also manufactured to confirm that panel 1 did not miss variants because of the complex design. Both panels were used to sequence 150 blood-derived DNAs; 94 DNAs from research participants aged 64 to 75 years; 16 DNAs with known germline variants; 16 DNAs with known germline variants (titrated from 0% to 100%); 24 DNAs from individuals aged &lt;40 years; and 3 commercial CHIP controls and 3 high-molecular-weight DNA controls. The sequencing median depth ratio between the CHIP and germline relevant genomic regions was 4.7:1. Fourteen CHIP-associated variants were called in both panel 1 (1382× median variant depth) and panel 2 (1665× median variant depth). All known germline variants were identified (251× median variant depth). Smart nonuniformity sequencing reliably detects variants with allele frequency in the range &gt;0.01 to 1 in one workflow.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 705-712"},"PeriodicalIF":3.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095511","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}

{"title":"Leveraging RNA from DNA Extraction Lysate to Rescue “Insufficient” Samples for More Comprehensive Genomic Profiling in Patients with Scant Tumor Specimens","authors":"Mark D. Ewalt ,&nbsp;Sara E. DiNapoli ,&nbsp;Kerry Mullaney ,&nbsp;Alison Urvalek ,&nbsp;Minji Kim Uh ,&nbsp;Purvil Sukhadia ,&nbsp;J. Keith Killian ,&nbsp;Michael Zaidinski ,&nbsp;Hun Jae Jung ,&nbsp;Tiffany McFarlane ,&nbsp;Kelly Rios-Papachristos ,&nbsp;Alexander Drilon ,&nbsp;Mark G. Kris ,&nbsp;Khedoudja Nafa ,&nbsp;Maria E. Arcila ,&nbsp;Marc Ladanyi ,&nbsp;Ahmet Zehir ,&nbsp;Michael Offin ,&nbsp;Ryma Benayed","doi":"10.1016/j.jmoldx.2025.04.005","DOIUrl":"10.1016/j.jmoldx.2025.04.005","url":null,"abstract":"<div><div>Tissue availability is often a limiting factor in obtaining comprehensive genomic profiling to identify actionable oncogenic drivers in tumors from patients with cancer. The utility of performing complementary DNA and RNA sequencing to better identify targetable gene fusions was previously reported. Here, we report our experience using RNA recovered from lysate material, following DNA extraction, to perform targeted RNA sequencing and identify gene fusions and oncogenic transcript variants in a large cohort of patients with solid tumors. To validate this approach, RNA-sequencing results of lysate-extracted RNA and direct formalin-fixed, paraffin-embedded (FFPE) extracted RNA from the same tumors were compared. After finding equivalent identification of oncogenic gene fusions and transcript variants, efforts were expanded to a larger cohort across more diverse tumor types. Lysate-extracted RNA performed comparably to freshly FFPE extract RNA, with 97% and 96% success rates, respectively. Within the lysate-extracted group, it was documented that lysate was the only material available for RNA extraction (<em>n</em> = 1862, 42% of all tested samples) and, within this subgroup, 364 (20%) samples were positive for actionable fusions or oncogenic isoforms. Using RNA recovered from lysate can permit sequential or simultaneous comprehensive DNA/RNA sequencing from scant FFPE samples in laboratories where dual sample extraction is not logistically possible, allowing more complete profiling to enhance the identification of actionable oncogenic gene fusions to guide care.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 713-721"},"PeriodicalIF":3.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095416","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}

{"title":"Analytical Performance of the NCI-myeloMATCH Assay","authors":"Cecilia C.S. Yeung ,&nbsp;Srikrishna K. Narava ,&nbsp;Ting-Chia Chang ,&nbsp;Maria Saeed ,&nbsp;Lauri Aicher ,&nbsp;Lan W. Beppu ,&nbsp;Marvin S. Majano ,&nbsp;Erin M. Taylor ,&nbsp;Corinne E. Camalier ,&nbsp;Pooja Sandhuria ,&nbsp;Olga Sala-Torra ,&nbsp;Jessica Li ,&nbsp;Laura M. Yee ,&nbsp;Lisa M. McShane ,&nbsp;Chris Karlovich ,&nbsp;Richard F. Little ,&nbsp;Lyndsay Harris ,&nbsp;James H. Doroshow ,&nbsp;Paul M. Williams ,&nbsp;Jerald P. Radich ,&nbsp;Shahanawaz Jiwani","doi":"10.1016/j.jmoldx.2025.05.001","DOIUrl":"10.1016/j.jmoldx.2025.05.001","url":null,"abstract":"<div><div>myeloMATCH is a National Cancer Institute (NCI) precision medicine clinical trial initiative to evaluate treatments for acute myeloid leukemia and myelodysplastic syndrome based on a leukemia’s diagnostic molecular–genetic profile. The NCI myeloid assay version 2 (NMAv2) uses the Genexus System, an automated platform with &lt;48-hour turnaround from specimen receipt to reporting, to provide harmonized regulatory-compliant use for myeloMATCH across two independent clinical laboratories. Using clinical specimens, cell lines, and contrived reference materials, NMAv2 exhibited 99% sensitivity for 291 known mutations and 100% specificity. High reproducibility detecting all reportable variants was observed, with &gt;98% mean positive percentage agreement and 100% negative percent agreement across six reproducibility assessments. Reproducibility experiments of companion diagnostic biomarkers (1 to 1.5× clinical limit of reporting) showed 100% positive percentage agreement and negative percent agreement. The limit of detection was 0.06% for hotspot single-nucleotide variants, 0.16% for non-hotspot single-nucleotide variants, 0.51% for hotspot insertion/deletions, approximately 1% for non-hotspot insertion/deletions, 0.23% for <em>FLT3</em>–internal tandem duplications, and ≤40 reads at 0.1% tumor content for fusions. Concordance of 99.39% was observed in orthogonal assays testing 76 blinded myeloid specimens in the sensitivity study, and 100% concordance was observed in testing 54 <em>FLT3</em>–internal tandem duplication specimens. The results show that NMAv2 has high specificity, sensitivity, accuracy, and reproducibility, and can rapidly characterize genomic alterations in acute myeloid leukemia and myelodysplastic syndrome.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 783-795"},"PeriodicalIF":3.4,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144095415","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}