Journal of Molecular Diagnostics最新文献_第2页

Investigating the Pathogenicity of Uncommon KRAS Mutations and Their Association with Clinicopathologic Characteristics in Patients with Colorectal Cancer.

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-12-16 DOI: 10.1016/j.jmoldx.2024.11.007

Riccardo Adorisio, Davide Ciardiello, Alessandra Rappa, Lorenzo Gervaso, Gloria Pelizzari, Laura Marinucci, Nicola Fusco, Maria Giulia Zampino, Nicola Fazio, Konstantinos Venetis, Elena Guerini-Rocco

{"title":"Investigating the Pathogenicity of Uncommon KRAS Mutations and Their Association with Clinicopathologic Characteristics in Patients with Colorectal Cancer.","authors":"Riccardo Adorisio, Davide Ciardiello, Alessandra Rappa, Lorenzo Gervaso, Gloria Pelizzari, Laura Marinucci, Nicola Fusco, Maria Giulia Zampino, Nicola Fazio, Konstantinos Venetis, Elena Guerini-Rocco","doi":"10.1016/j.jmoldx.2024.11.007","DOIUrl":"10.1016/j.jmoldx.2024.11.007","url":null,"abstract":"<p><p>Kirsten rat sarcoma viral oncogene homolog (KRAS) somatic mutations occur in 30% to 40% of patients with colorectal cancer (CRC). These were thought to equally affect prognosis and resistance to anti-epidermal growth factor receptor agents; however, recent data show the activity of KRAS-G12C and pan-RAS inhibitors. The effects of uncommon KRAS (uKRAS) variants are largely unexplored. The distribution and pathogenicity of uKRAS mutations and their relationship with patients' clinicopathologic features were assessed. A total of 2427 CRCs were profiled for KRAS using next-generation sequencing (NGS). The study and control groups included patients with uKRAS (<1% frequency in CRC data sets on cBioPortal) and canonical KRAS mutations, respectively. In silico protein structure modifications and prediction analyses were performed by using PyMOL, trRosetta, and PolyPhen-2. uKRAS mutations affected 35 cases (1.5%), with G13C (28.6%), G12R (20%), and V14I (8.6%) being most common. Missense mutations (D33E, G12W, G12F, Q22H, Q61L, and L19F) occurred in nine cases (25.7%). Duplications (G10dup and L52_G60dup) affected two cases. Pathogenicity analyses showed that G12W, Q22R, L56V, and A130I mutations are probably damaging, with scores between 0.928 and 1.000. No differences were seen in clinicopathologic features. uKRAS mutants had lower event-free survival but no difference in overall survival compared with controls. Although these data are hypothesis generating and need further confirmation, they highlight the importance of NGS-based profiling to identify CRC patients with uKRAS mutations as candidates for personalized therapy.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142856521","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}

引用次数: 0

Validation and Performance of Quantitative BRCA1 and RAD51C Promoter Hypermethylation Testing in Breast and Ovarian Cancers. 乳腺癌和卵巢癌 BRCA1 和 RAD51C Promoter 高甲基化定量检测的验证和性能。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-12-13 DOI: 10.1016/j.jmoldx.2024.11.004

J Lynn Fink, Binny Jaradi, Nathan Stone, Brittany Sanker, Fan Zhang, Alexander Dobrovic, Sophie Kirschner, James Hadfield, Olga Kondrashova, Paul M Waring

{"title":"Validation and Performance of Quantitative BRCA1 and RAD51C Promoter Hypermethylation Testing in Breast and Ovarian Cancers.","authors":"J Lynn Fink, Binny Jaradi, Nathan Stone, Brittany Sanker, Fan Zhang, Alexander Dobrovic, Sophie Kirschner, James Hadfield, Olga Kondrashova, Paul M Waring","doi":"10.1016/j.jmoldx.2024.11.004","DOIUrl":"10.1016/j.jmoldx.2024.11.004","url":null,"abstract":"<p><p>Poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors represent a significant advancement in the treatment of epithelial ovarian cancer, triple-negative breast cancer, pancreatic cancer, and castrate-resistant prostate cancer, and they are poised to improve treatment in an increasing number of other cancer types. PARP inhibitor efficacy as monotherapy has been primarily observed in tumors with deleterious genetic variants in genes involved in the homologous recombination repair pathway. Tumors without these variants have also been shown to respond; notably, those with hypermethylation at all alleles of the BRCA1 or RAD51C promoter can respond to PARP inhibitors. These epigenetic biomarkers therefore represent a patient population that may also benefit from this targeted therapy. However, no robust test has been conducted to identify these biomarkers in routine clinical specimens that is amenable to implementation for decentralized testing. This study describes the analytical and clinical validation of a BRCA1 and RAD51C promoter methylation test that can be run with a single-day library preparation workflow for sequencing on any next-generation sequencing platform. The results show that this test can accurately quantitate the level of promoter methylation at the BRCA1 and RAD51C genes using formalin-fixed, paraffin-embedded samples, even when the extracted DNA is extremely degraded or the input amount is limited. This test increases the precision of diagnostic tests aimed at identifying patients who are likely and unlikely to respond to PARP inhibitor therapy.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142830686","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}

引用次数: 0

Clinical Implementation of a High-Throughput Automated Comprehensive Genomic Profiling Test: TruSight Oncology 500 HT. 高通量自动化综合基因组分析测试 - TruSight Oncology 500 HT 的临床实施。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-12-12 DOI: 10.1016/j.jmoldx.2024.11.005

Markus Ball, Eva Romanovsky, Fabian Schnecko, Martina Kirchner, Olaf Neumann, Regine Brandt, Susanne Beck, Huriye Seker-Cin, Klaus Kluck, Iordanis Ourailidis, Hannah Goldschmid, Annette Fink, Anna-Lena Volckmar, Michael Menzel, Michael Allgäuer, Peter Schirmacher, Jan Budczies, Albrecht Stenzinger, Daniel Kazdal

{"title":"Clinical Implementation of a High-Throughput Automated Comprehensive Genomic Profiling Test: TruSight Oncology 500 HT.","authors":"Markus Ball, Eva Romanovsky, Fabian Schnecko, Martina Kirchner, Olaf Neumann, Regine Brandt, Susanne Beck, Huriye Seker-Cin, Klaus Kluck, Iordanis Ourailidis, Hannah Goldschmid, Annette Fink, Anna-Lena Volckmar, Michael Menzel, Michael Allgäuer, Peter Schirmacher, Jan Budczies, Albrecht Stenzinger, Daniel Kazdal","doi":"10.1016/j.jmoldx.2024.11.005","DOIUrl":"10.1016/j.jmoldx.2024.11.005","url":null,"abstract":"<p><p>The adoption of comprehensive genomic profiling in oncology has rapidly increased the demand for standardized tumor sample processing in diagnostic laboratories. Automation of DNA and RNA library preparation workflows offers the possibility to scale-up and standardize sample processing. We report on the clinical implementation of the automated TruSight Oncology 500 High-Throughput library preparation workflow from formalin-fixed, paraffin-embedded tumor samples using the Biomek i7 hybrid Workstation. Using the same input amount, the automated workflow was validated against manual library preparation. Quality control metrics (total and mapped reads, median insert size, and median exon coverage) and the detection of tumor mutational burden, a complex biomarker, were concordant between the manual and automated workflows. The automated workflow was implemented on a total of 2997 pan-cancer clinical samples to detect genomic variants and complex biomarkers. Workflow automation resulted in a 4-fold reduction in hands-on time and a 1.7-fold reduction in total runtime compared with manual library preparation (6 hours vs. 23 hours; 24 hours vs. 42.5 hours, respectively) for a 48 DNA + 48 RNA sample batch. The automated workflow required one technician versus three technicians to manually prepare the same number of libraries. This study shows that implementation of the automated TruSight Oncology 500 High-Throughput workflow significantly reduced hands-on time and processing time per sample compared with manual library preparation.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142824659","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}

引用次数: 0

The Validation of Digital PCR-Based Minimal Residual Disease Detection for the Common Mutations in IDH1 and IDH2 Genes in Patients with Acute Myeloid Leukemia.

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-29 DOI: 10.1016/j.jmoldx.2024.11.002

Jing Di, Tao Sheng, Ranjana Arora, Jennifer Stocks-Candelaria, Sainan Wei, Charles Lutz, Fevzi F Yalniz, Shulin Zhang

{"title":"The Validation of Digital PCR-Based Minimal Residual Disease Detection for the Common Mutations in IDH1 and IDH2 Genes in Patients with Acute Myeloid Leukemia.","authors":"Jing Di, Tao Sheng, Ranjana Arora, Jennifer Stocks-Candelaria, Sainan Wei, Charles Lutz, Fevzi F Yalniz, Shulin Zhang","doi":"10.1016/j.jmoldx.2024.11.002","DOIUrl":"10.1016/j.jmoldx.2024.11.002","url":null,"abstract":"<p><p>Accurate monitoring of minimal residual disease (MRD) is crucial for effective management of patients with acute myeloid leukemia (AML). This study aims to validate MRD detection of the seven most common IDH1 and IDH2 mutations in patients with AML using a QuantStudio 3D digital PCR platform. This assay demonstrated a high concordance for the variant allele frequencies between digital PCR and next-generation sequencing assays. Precision analysis revealed only small variation (<0.5 log10) for all mutations near or at the limit of detection level. This validation also showed a great reproducibility for interrun and intrarun comparisons (28 runs, variation ranges from 0 to 0.48 log10), ensuring comparable results for patient follow-ups. The limit of detection was determined to be 0.1% for all mutations, except the IDH2 R140Q mutation, which was 0.5%. Controls and acceptable ranges were also established for each mutation during validation. This study suggests that the QuantStudio 3D digital PCR assay is a quantitative, sensitive, and reproducible platform for monitoring MRD in patients with AML.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774302","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}

引用次数: 0

BCR::ABL1 Deep Molecular Response Quantification and Transcript Type Identification in Chronic Myeloid Leukemia Using a US Food and Drug Administration-Approved Droplet-Based Digital PCR Assay.

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-29 DOI: 10.1016/j.jmoldx.2024.11.003

Camille Kockerols, Peter J M Valk, Pauline Hogenbirk, Jan J Cornelissen, Peter E Westerweel

{"title":"BCR::ABL1 Deep Molecular Response Quantification and Transcript Type Identification in Chronic Myeloid Leukemia Using a US Food and Drug Administration-Approved Droplet-Based Digital PCR Assay.","authors":"Camille Kockerols, Peter J M Valk, Pauline Hogenbirk, Jan J Cornelissen, Peter E Westerweel","doi":"10.1016/j.jmoldx.2024.11.003","DOIUrl":"10.1016/j.jmoldx.2024.11.003","url":null,"abstract":"<p><p>BCR::ABL1 digital PCR is a promising technique for the quantification of deep molecular responses (DMRs) in chronic myeloid leukemia. It provides an improved precision and sensitivity compared with conventional real-time quantitative PCR (qPCR), which is particularly relevant in the context of prediction of successful treatment-free remission. This study assessed the feasibility of BCR::ABL1 digital PCR in clinical practice. A total of 168 DMR samples of patients with chronic myeloid leukemia aiming for a treatment-free remission attempt were assessed by both digital PCR and qPCR. Digital PCR was performed with the droplet-based Bio-Rad QXDx BCR-ABL %IS assay, using eight replicates per sample. qPCR was performed with the fully automized Cepheid Xpert BCR-ABL Ultra assay. Various technical and practical aspects of BCR::ABL1 quantification using digital PCR were assessed. The reported limit of detection of the qPCR is molecular response 4.5, requiring an equivalent of 32,000 ABL1 transcripts. Using digital PCR, a median number of ABL1 of approximately 300,000 were obtained. BCR::ABL1 was quantifiable by digital PCR in 68% of the samples below qPCR's limit of detection. In addition, e13a2 and e14a2 BCR::ABL1 transcript types could be discriminated based on the mean fluorescence intensity of BCR::ABL1-positive droplets. BCR::ABL1 digital PCR is feasible for DMR quantification in clinical practice and offers an increased sensitivity over qPCR.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774371","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}

引用次数: 0

Twenty-Five Years of Germline Genetic Testing and What May Lie Ahead 25 年来的种系遗传检测及未来展望

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-25 DOI: 10.1016/j.jmoldx.2024.06.013

Victoria M. Pratt , Sara Akhavanfard , Jane Houldsworth , Jennifer J. Laffin , Ann M. Moyer , Honey V. Reddi , Stuart A. Scott , Matthew S. Lebo

引用次数: 0

A New Serotyping Method of Streptococcus pneumoniae Based on CRISPR/Cas9–Targeted Sequencing 基于 CRISPR/Cas9 靶向测序的肺炎链球菌血清分型新方法

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-25 DOI: 10.1016/j.jmoldx.2024.08.009

Yustinus Maladan , Endah Retnaningrum , Budi Setiadi Daryono , Rosantia Sarassari , Ratna Fathma Sari , Sarah Azhari Balqis , Ghina Athyah Wahid , Dodi Safari

{"title":"A New Serotyping Method of Streptococcus pneumoniae Based on CRISPR/Cas9–Targeted Sequencing","authors":"Yustinus Maladan , Endah Retnaningrum , Budi Setiadi Daryono , Rosantia Sarassari , Ratna Fathma Sari , Sarah Azhari Balqis , Ghina Athyah Wahid , Dodi Safari","doi":"10.1016/j.jmoldx.2024.08.009","DOIUrl":"10.1016/j.jmoldx.2024.08.009","url":null,"abstract":"<div><div>Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) application for targeted sequencing has made a breakthrough in the genomic research era. High diversity in the capsular polysaccharide (<em>cps</em>) locus of <em>Streptococcus pneumoniae</em> has hampered identification of the serotype. This study developed a new serotyping method for <em>S. pneumoniae</em> using CRISPR/Cas9–targeted sequencing with the Oxford Nanopore Technologies platform. A probe was designed at the position of the <em>cps</em> locus using an excision approach on two sides flanking genes between the <em>dexB</em> and <em>aliA</em> genes with approximately 20 kb. A native barcoding method was used for multiplexing. The probe will attach to a specific side followed by attachment of CRISPR/Cas9 to cut the recognition area. The study used <em>de novo</em> assembly to reconstruct sequence reads, which were analyzed using PneumoCRISPR, a new serotyping pipeline for Oxford Nanopore Technologies sequencing data output. Four CRISPR/Cas9 probes have been designed and recognize the <em>cps</em> locus of <em>S. pneumoniae</em>. Serotyping results align precisely with serotyping data from whole-genome sequencing. This serotyping method also allows researchers to use multiple samples in a single run. The new serotyping method based on CRISPR/Cas9–targeted sequencing holds immense promise for serotype identification of <em>S. pneumoniae</em>.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 12","pages":"Pages 1045-1054"},"PeriodicalIF":3.4,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721844","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}

引用次数: 0

Changes and Challenges in Molecular Diagnostics 分子诊断的变化与挑战

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-25 DOI: 10.1016/j.jmoldx.2024.06.012

Karen L. Kaul , Timothy J. O'Leary , Barbara Zehnbauer

引用次数: 0

Sensitivity and Specificity of Chimerism Tests in Predicting Leukemia Relapse Using Increasing Mixed Chimerism 利用不断增加的混合嵌合体预测白血病复发的嵌合体检验灵敏度和特异性

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-25 DOI: 10.1016/j.jmoldx.2024.09.003

Ruoheng Zhang , Yimeng Shang , Joseph Cioccio , Kevin Rakszawski , Myles Nickolich , Christopher Ehmann , Yoshitaka Inoue , Seema Naik , Witold Rybka , Hong Zheng , Joseph Mierski , Brooke Silar , Jason Liao , Robert Greiner , Valerie Brown , David Claxton , Jing Ning , Shouhao Zhou , Shin Mineishi , Kentaro Minagawa , Hiroko Shike

{"title":"Sensitivity and Specificity of Chimerism Tests in Predicting Leukemia Relapse Using Increasing Mixed Chimerism","authors":"Ruoheng Zhang , Yimeng Shang , Joseph Cioccio , Kevin Rakszawski , Myles Nickolich , Christopher Ehmann , Yoshitaka Inoue , Seema Naik , Witold Rybka , Hong Zheng , Joseph Mierski , Brooke Silar , Jason Liao , Robert Greiner , Valerie Brown , David Claxton , Jing Ning , Shouhao Zhou , Shin Mineishi , Kentaro Minagawa , Hiroko Shike","doi":"10.1016/j.jmoldx.2024.09.003","DOIUrl":"10.1016/j.jmoldx.2024.09.003","url":null,"abstract":"<div><div>Chimerism test was evaluated to predict leukemia relapse. Increasing mixed chimerism (IMC), defined as recipient increase ≥0.1% in peripheral blood total cell chimerism, was used as a surrogate of disease activity. Combination of quantitative PCR and short-tandem repeat method was applied to achieve high assay sensitivity. Total of 184 patients received stem cell transplant for acute myeloid leukemia (N = 110), acute lymphocytic leukemia (N = 41), myelodysplastic syndrome (N = 30), and 2389 chimerism tests (median follow-up, 1054 days). Sixty-six patients relapsed, and 118 patients did not. Cumulative incidence of relapse increased after 1 IMC or ≥2 consecutive IMCs (hazard ratios, 9.9 and 44.4, respectively). Predicted percentage relapse by day 30 after IMC was 0% (0 IMC), 10% (1 IMC), and 40% (≥2 IMCs). The last chimerism results before relapse detected IMC in 57 of 66 relapsed patients (sensitivity, 86.4%). Nine patients had no IMC before relapse (false negative) because of rapidly evolving relapse (N = 4) or extramural relapse (N = 5). In 118 patients without relapse, 158 of 1873 tests detected IMC (false positive, 8.4%; specificity, 91.6%). The false-positive rates increased with higher percentage recipient T-cell chimerism levels, indicating T-cell contamination as a cause. Chimerism monitoring predicts relapse. However, caution must be taken for false-positive or false-negative IMCs. T-cell removal can improve chimerism test specificity in patients with mixed T-cell chimerism.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"26 12","pages":"Pages 1159-1170"},"PeriodicalIF":3.4,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142721941","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}

引用次数: 0

Title page 扉页

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2024-11-01 DOI: 10.1016/S1525-1578(24)00230-7

引用次数: 0