Pub Date : 2025-06-13DOI: 10.1016/j.jmoldx.2025.05.003
Susan J. Hsiao , Destin Black , Kelly A. Devereaux , Ian S. Hagemann , Lawrence J. Jennings , Diana Mandelker , Vera A. Paulson , Michelle Shiller , Tracy L. Stockley , Eric Vail , Praveen Vikas , Anna Yemelyanova
Homologous recombination deficiency (HRD) is a genomic feature present in some malignant neoplasms and is attributed to the failure of the homologous recombination repair pathway. Tumors with an HRD-positive status may have a distinct prognosis and/or response to therapies, including poly (ADP-ribose) polymerase inhibitors. The Association for Molecular Pathology assembled an expert panel to examine current practice and perform a scoping review of the medical literature pertaining to the molecular detection of HRD in the clinical setting. The expert panel examined the following topics: components of existing and proposed HRD and genomic instability biomarkers (including mutational signatures, loss of heterozygosity, mutations in homologous recombination repair–associated genes, and epigenetic silencing of RAD51C, BRCA1, or BRCA2); technical considerations for identifying genomic scars from tumor and germline next-generation sequencing results; guidelines on interpretation and caveats when reporting assessments of genomic instability and HRD scores; and the clinical significance of HRD. The panel formulated a set of expert consensus opinion recommendations regarding HRD assay design and validation to guide laboratories in developing HRD tests to ensure high-quality and reproducible results.
{"title":"Recommendations for Clinical Molecular Laboratories for Detection of Homologous Recombination Deficiency in Cancer","authors":"Susan J. Hsiao , Destin Black , Kelly A. Devereaux , Ian S. Hagemann , Lawrence J. Jennings , Diana Mandelker , Vera A. Paulson , Michelle Shiller , Tracy L. Stockley , Eric Vail , Praveen Vikas , Anna Yemelyanova","doi":"10.1016/j.jmoldx.2025.05.003","DOIUrl":"10.1016/j.jmoldx.2025.05.003","url":null,"abstract":"<div><div>Homologous recombination deficiency (HRD) is a genomic feature present in some malignant neoplasms and is attributed to the failure of the homologous recombination repair pathway. Tumors with an HRD-positive status may have a distinct prognosis and/or response to therapies, including poly (ADP-ribose) polymerase inhibitors. The Association for Molecular Pathology assembled an expert panel to examine current practice and perform a scoping review of the medical literature pertaining to the molecular detection of HRD in the clinical setting. The expert panel examined the following topics: components of existing and proposed HRD and genomic instability biomarkers (including mutational signatures, loss of heterozygosity, mutations in homologous recombination repair–associated genes, and epigenetic silencing of <em>RAD51C</em>, <em>BRCA1</em>, or <em>BRCA2</em>); technical considerations for identifying genomic scars from tumor and germline next-generation sequencing results; guidelines on interpretation and caveats when reporting assessments of genomic instability and HRD scores; and the clinical significance of HRD. The panel formulated a set of expert consensus opinion recommendations regarding HRD assay design and validation to guide laboratories in developing HRD tests to ensure high-quality and reproducible results.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 685-704"},"PeriodicalIF":3.4,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-13DOI: 10.1016/j.jmoldx.2025.04.012
Hsin-Fu Lin , Pei-Miao Chien , Chinyi Cheng , Tzu-Hang Yuan , Yu-Bin Wang , Pei-Lung Chen , Chien-Yu Chen , Jia-Hsin Huang , Jacob Shujui Hsu
Evaluating robustness of somatic mutation detections is essential when using whole-exome sequencing (WES) for treatment decision-making. A comprehensive evaluation was conducted using tumor WES from the US Food and Drug Administration–led Sequencing Quality Control Phase 2 project, in which multiple library kits sequenced identical DNA materials across three laboratories to benchmark analytical validity. These workflows included various read aligner (BWA, Bowtie2, DRAGEN-Aligner, DRAGMAP, and HISAT2) and mutation caller (Mutect2, TNscope, DRAGEN-Caller, and DeepVariant) combinations. The results revealed that DRAGEN exhibited superior performance, achieving mean F1 scores of 0.966 and 0.791 for single-nucleotide variant and insertion/deletion detection, respectively. Among open-source software, BWA Mutect2 and HISAT2 Mutect2 combinations showed the highest mean F1 scores for single-nucleotide variant (0.949) and insertion/deletion (0.722), respectively. The analyses indicated that high-quality data can be analyzed as having worse results, and vice versa. Evaluations of Catalog of Somatic Mutations in Cancer reported mutations unveiled discrepancies across enrichment kits. Integrated DNA Technologies enrichment kits showed a higher false-negative rate, whereas Agilent WES kits tended to miss mutations in CBL and IDH1, and Roche library kits tended to miss the mutations in PIK3CB. Sentieon TNscope tended to underestimate tumor mutation burden and overlook FLT3:c.G1879A for cytarabine resistance in leukemia and MAP2K1:c.G199A for BRAF inhibitors in melanoma. The findings highlight the importance of robust bioinformatic analysis in guiding clinical decision-making.
{"title":"Evaluating Discordant Somatic Calls Across Mutation Discovery Approaches to Minimize False-Negative Drug-Resistant Findings","authors":"Hsin-Fu Lin , Pei-Miao Chien , Chinyi Cheng , Tzu-Hang Yuan , Yu-Bin Wang , Pei-Lung Chen , Chien-Yu Chen , Jia-Hsin Huang , Jacob Shujui Hsu","doi":"10.1016/j.jmoldx.2025.04.012","DOIUrl":"10.1016/j.jmoldx.2025.04.012","url":null,"abstract":"<div><div>Evaluating robustness of somatic mutation detections is essential when using whole-exome sequencing (WES) for treatment decision-making. A comprehensive evaluation was conducted using tumor WES from the US Food and Drug Administration–led Sequencing Quality Control Phase 2 project, in which multiple library kits sequenced identical DNA materials across three laboratories to benchmark analytical validity. These workflows included various read aligner (BWA, Bowtie2, DRAGEN-Aligner, DRAGMAP, and HISAT2) and mutation caller (Mutect2, TNscope, DRAGEN-Caller, and DeepVariant) combinations. The results revealed that DRAGEN exhibited superior performance, achieving mean F1 scores of 0.966 and 0.791 for single-nucleotide variant and insertion/deletion detection, respectively. Among open-source software, BWA Mutect2 and HISAT2 Mutect2 combinations showed the highest mean F1 scores for single-nucleotide variant (0.949) and insertion/deletion (0.722), respectively. The analyses indicated that high-quality data can be analyzed as having worse results, and vice versa. Evaluations of Catalog of Somatic Mutations in Cancer reported mutations unveiled discrepancies across enrichment kits. Integrated DNA Technologies enrichment kits showed a higher false-negative rate, whereas Agilent WES kits tended to miss mutations in <em>CBL</em> and <em>IDH1</em>, and Roche library kits tended to miss the mutations in <em>PIK3CB</em>. Sentieon TNscope tended to underestimate tumor mutation burden and overlook <em>FLT3</em><em>:</em>c.G1879A for cytarabine resistance in leukemia and <em>MAP2K1</em><em>:</em>c.G199A for <em>BRAF</em> inhibitors in melanoma. The findings highlight the importance of robust bioinformatic analysis in guiding clinical decision-making.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 8","pages":"Pages 768-782"},"PeriodicalIF":3.4,"publicationDate":"2025-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-06-13DOI: 10.1016/j.jmoldx.2025.04.013
Kirill Kriukov , Dmitry Ivchenkov , Anna Bejanyan , Aleksandr Sarachakov , Aleksandra Kviatkovskaia , Gleb Khegai , Dominique Knipper-Davis , Amber Berlinski , Tayla Soares , Jochen K. Lennerz , Vladimir Kushnarev
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.
{"title":"Morphological Bone Score as a Predictive Tool for Molecular Profiling Success","authors":"Kirill Kriukov , Dmitry Ivchenkov , Anna Bejanyan , Aleksandr Sarachakov , Aleksandra Kviatkovskaia , Gleb Khegai , Dominique Knipper-Davis , Amber Berlinski , Tayla Soares , Jochen K. Lennerz , 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}
Pub Date : 2025-06-06DOI: 10.1016/j.jmoldx.2025.04.009
Jialun Pang , Lin Zhou , Jiancheng Hu , Hanzhe Kuang , Hui Xi , Na Ma , Shuting Yang , Wenxian Yu , Yanan Zhang , Qian Zhang , Victor Wei Zhang , Jing Chen , Ying Peng
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.
{"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 , Lin Zhou , Jiancheng Hu , Hanzhe Kuang , Hui Xi , Na Ma , Shuting Yang , Wenxian Yu , Yanan Zhang , Qian Zhang , Victor Wei Zhang , Jing Chen , 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}
Pub Date : 2025-06-05DOI: 10.1016/j.jmoldx.2025.04.010
Carolina Hernandez , Luz H. Patiño , Milena Camargo , Ching Yi Wang , Feng Chen , Bernadette Liggayu , Liyong Cao , Carlos Cordon-Cardo , Emilia M. Sordillo , Alberto Paniz-Mondolfi , Juan D. Ramírez
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.
{"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 , Luz H. Patiño , Milena Camargo , Ching Yi Wang , Feng Chen , Bernadette Liggayu , Liyong Cao , Carlos Cordon-Cardo , Emilia M. Sordillo , Alberto Paniz-Mondolfi , 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}
Pub Date : 2025-06-05DOI: 10.1016/j.jmoldx.2025.05.002
Haruka Ikoma , Joaquim Carreras , Yara Yukie Kikuti , Masashi Miyaoka , Shunsuke Nagase , Yusuke Kondo , Atsushi Ito , Makoto Orita , Sakura Tomita , Shinichiro Hiraiwa , Hiroshi Kawada , Juan F. Garcia , Giovanna Roncador , Elias Campo , Naoya Nakamura
It was recently reported that follicular lymphoma (FL) with BCL6 rearrangement (R) is associated with favorable progression-free survival, whereas BCL2-R and BCL2-6-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 BCL2-R, 11 BCL6-R, and 4 BCL2-6-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 CREBBP, KMT2D, TNFRSF14, STAT6, and CD36. Moreover, BCL6-R cases had mutations in ARID1B, ARID5B, and RHOA; low frequency of mutations in other genes, such as OSBPL10, PTPRD, ATM, and HLA-B; 6q loss; and absence of disease progression. In comparison with BCL6-R cases, BCL2-R and BCL2-6-R cases had mutations in EZH2, chromosome 18 copy number gain, and disease progression in some cases. The immune microenvironment profile was heterogeneous; however, BCL6-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 BCL2-R, FL with BCL6-R exhibited some differences in mutational profiles and immune microenvironment.
{"title":"Comparison of the Mutational Profile between BCL2- and BCL6-Rearrangement Positive Follicular Lymphoma","authors":"Haruka Ikoma , Joaquim Carreras , Yara Yukie Kikuti , Masashi Miyaoka , Shunsuke Nagase , Yusuke Kondo , Atsushi Ito , Makoto Orita , Sakura Tomita , Shinichiro Hiraiwa , Hiroshi Kawada , Juan F. Garcia , Giovanna Roncador , Elias Campo , 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}
Pub Date : 2025-05-19DOI: 10.1016/j.jmoldx.2025.04.008
Sabah Kadri , Kelly E. Craven , Amber M. Fussell , Elaine P.S. Gee , Danielle Jordan , Eric W. Klee , Niklas Krumm , Robyn L. Temple-Smolkin , Ahmet Zehir , Weiwei Zhang , Andrea Sboner
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.
{"title":"Clinical Bioinformatician Body of Knowledge—Bioinformatics and Software Core","authors":"Sabah Kadri , Kelly E. Craven , Amber M. Fussell , Elaine P.S. Gee , Danielle Jordan , Eric W. Klee , Niklas Krumm , Robyn L. Temple-Smolkin , Ahmet Zehir , Weiwei Zhang , 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}
Pub Date : 2025-05-17DOI: 10.1016/j.jmoldx.2025.04.006
Victoria M. Pratt , Betsy Bove , Raymond A. Lorenz , Annette K. Taylor , Bronwyn Ramey
{"title":"Standardizing Laboratory Practices in Pharmacogenomics (STRIPE) Consensus Conference","authors":"Victoria M. Pratt , Betsy Bove , Raymond A. Lorenz , Annette K. Taylor , 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}
Pub Date : 2025-05-15DOI: 10.1016/j.jmoldx.2025.04.004
Marco L. Leung , Ina Amarillo , Danielle Jordan , Matthew S. Lebo , Rizwan C. Naeem , David I. Suster , Robyn L. Temple-Smolkin , Cigdem H. Ussakli , Honey V. Reddi
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.
{"title":"Path to Health Equity and Improved Outcomes through Inclusive Sex and Gender Data Collection in Genomic Testing","authors":"Marco L. Leung , Ina Amarillo , Danielle Jordan , Matthew S. Lebo , Rizwan C. Naeem , David I. Suster , Robyn L. Temple-Smolkin , Cigdem H. Ussakli , 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}
Pub Date : 2025-05-15DOI: 10.1016/j.jmoldx.2025.04.007
Robert L. O'Reilly , Philip Harraka , Jared Burke , Daniele Belluoccio , Paul Yeh , Kerryn Howlett , Kiarash Behrouzfar , Amanda Rewse , Helen Tsimiklis , Graham G. Giles , John L. Hopper , Kristen J. Bubb , Stephen J. Nicholls , Roger L. Milne , Melissa C. Southey
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 >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 <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 >0.01 to 1 in one workflow.
{"title":"Smart Nonuniformity for Calibrating Sequencing Depth of a Targeted Gene Panel to Simultaneously Detect Somatic and Germline Variants","authors":"Robert L. O'Reilly , Philip Harraka , Jared Burke , Daniele Belluoccio , Paul Yeh , Kerryn Howlett , Kiarash Behrouzfar , Amanda Rewse , Helen Tsimiklis , Graham G. Giles , John L. Hopper , Kristen J. Bubb , Stephen J. Nicholls , Roger L. Milne , 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 >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 <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 >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}
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