Journal of Molecular Diagnostics最新文献_第2页

Impact and Reproducibility of In-House Targeted Next-Generation Sequencing Biomarker Testing in Non-Small-Cell Lung Cancer: An Italian Multi-Institutional Experience.

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-27 DOI: 10.1016/j.jmoldx.2025.02.001

Ida Rapa, Francesca Bertola, Gaia Roversi, Davide Seminati, Federica Panebianco, Cecília Durães, Enzo Gallo, Biagio E Leone, Aldo Palange, Luisella Righi, Paolo Visca, Marco Volante, Simonetta Buglioni

{"title":"Impact and Reproducibility of In-House Targeted Next-Generation Sequencing Biomarker Testing in Non-Small-Cell Lung Cancer: An Italian Multi-Institutional Experience.","authors":"Ida Rapa, Francesca Bertola, Gaia Roversi, Davide Seminati, Federica Panebianco, Cecília Durães, Enzo Gallo, Biagio E Leone, Aldo Palange, Luisella Righi, Paolo Visca, Marco Volante, Simonetta Buglioni","doi":"10.1016/j.jmoldx.2025.02.001","DOIUrl":"10.1016/j.jmoldx.2025.02.001","url":null,"abstract":"<p><p>Next-generation sequencing (NGS) allows the detection of multiple genetic targets in different tumor types. This study aimed to confirm the benefits of implementing in-house NGS testing for non-small-cell lung cancer (NSCLC) samples in molecular pathology laboratories. A multi-institutional study was conducted to evaluate the analytical performance, turnaround time, and feasibility of in-house NGS testing of 50 genes from 283 NSCLC samples. The first phase was a retrospective study with interlaboratory testing (21 samples), and the second phase was a prospective study with intralaboratory testing (262 samples). The retrospective study showed a 100% sequencing success rate for DNA and RNA, high interlaboratory concordance (95.2%), and a strong correlation (R<sup>2</sup> = 0.94) between observed and expected single-nucleotide variant/insertion and/or deletion variant allele fraction. The prospective study showed a sequencing success rate of 99.2% for DNA and 98% for RNA. NGS identified 285 relevant variants (81.1% single-nucleotide variants/insertion and/or deletion variants, 9.8% copy number variants, and 9.1% gene fusions). Co-mutations with potential clinical relevance were detected in 20.5% of samples positive for the main oncogenic drivers in NSCLC. Additionally, 11% of samples wild type for the main oncogenic drivers carried alterations in other relevant genes. The in-house NGS testing had a median turnaround time from sample processing to molecular report of 4 days. This study demonstrates the advantages of implementing in-house NGS testing in molecular pathology laboratories.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537514","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

Reviewer Acknowledgment

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-24 DOI: 10.1016/j.jmoldx.2025.01.001

引用次数: 0

Retaining Clinical Genomics Technologists in the Post–COVID-19 Era

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-24 DOI: 10.1016/j.jmoldx.2024.10.005

Marco L. Leung , Barbara Anderson

引用次数: 0

Repurposing the Whole Expression Transcriptome Assay for the Genetic Diagnosis of T-Cell Acute Lymphoblastic Leukemia and Lymphoma.

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-19 DOI: 10.1016/j.jmoldx.2025.01.006

Valentina Bardelli, Silvia Arniani, Valentina Pierini, Carlotta Nardelli, Caterina Matteucci, Anair Graciela Lema Fernandez, Maria Crocioni, Marco Cerrano, Prassede Salutari, Cristina Papayanidis, Silvia Trappolini, Fabio Giglio, Sara Mastaglio, Patrizia Zappasodi, Crescenza Pasciolla, Marzia Defina, Matteo Piccini, Giuseppe Lanzarone, Danika Di Giacomo, Simona Sica, Lindsey E Montefiori, Charles G Mullighan, Cristina Mecucci, Roberta La Starza

{"title":"Repurposing the Whole Expression Transcriptome Assay for the Genetic Diagnosis of T-Cell Acute Lymphoblastic Leukemia and Lymphoma.","authors":"Valentina Bardelli, Silvia Arniani, Valentina Pierini, Carlotta Nardelli, Caterina Matteucci, Anair Graciela Lema Fernandez, Maria Crocioni, Marco Cerrano, Prassede Salutari, Cristina Papayanidis, Silvia Trappolini, Fabio Giglio, Sara Mastaglio, Patrizia Zappasodi, Crescenza Pasciolla, Marzia Defina, Matteo Piccini, Giuseppe Lanzarone, Danika Di Giacomo, Simona Sica, Lindsey E Montefiori, Charles G Mullighan, Cristina Mecucci, Roberta La Starza","doi":"10.1016/j.jmoldx.2025.01.006","DOIUrl":"10.1016/j.jmoldx.2025.01.006","url":null,"abstract":"<p><p>Unlike other cases of acute leukemia, the diagnosis of T-cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL) is uniquely based on morphology and flow cytometry. Although the genomic background has been broadly uncovered, the large spectrum of genes involved and the variability of the molecular mechanisms underlying gene deregulation have delayed the introduction of molecular cytogenetics into diagnostic flowcharts. To overcome these limitations and implement a genetic diagnosis of T-ALL/LBLs, a whole transcriptome expression assay (WTEa) was repurposed as a \"priority test\" to classify T-ALL/LBLs into the major genetic subtypes. A WTEa classifier based on a set of 312 probes on 215 T-ALL/LBLs was set up and applied, which properly assigned >95% of cases with subtype-defining alterations to the corresponding subgroups (ie, TAL/LMO, HOXA, TLX1, TLX3, BCL11B). It pinpointed cases that harbored cryptic alterations, such as noncoding mutations that generate new enhancer at TAL1 and LMO2 loci (8% of TAL/LMO), and duplications of noncoding element downstream BCL11B (BETA) (18% of BCL11B). It was also suitable to classify lymphoma cases for which only formalin-fixed embedded tissues were available, as confirmed in cases harboring TLX1 or TLX3 rearrangements, and distinguished new putative subtypes. WTEa offers a unifying tool to provide a genetic classification of T-ALL/LBLs. If introduced in multicenter prospective studies, it will facilitate evaluation of the clinical impact of genetic classification.</p>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":" ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472983","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

A Perspective on Artificial Intelligence for Molecular Pathologists.

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-13 DOI: 10.1016/j.jmoldx.2025.01.005

Timothy J O'Leary, Brendan J O'Leary, Dianne P O'Leary

引用次数: 0

Biomimetic Digital Twins and Multiomics

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-13 DOI: 10.1016/j.jmoldx.2024.12.012

William G. Kearns , Joe Glick , Lawrence Baisch , Andrew Benner , Dalton Brough , Luke Du , Chandra Germain , Laura Kearns , Georgios Stamoulis

{"title":"Biomimetic Digital Twins and Multiomics","authors":"William G. Kearns , Joe Glick , Lawrence Baisch , Andrew Benner , Dalton Brough , Luke Du , Chandra Germain , Laura Kearns , Georgios Stamoulis","doi":"10.1016/j.jmoldx.2024.12.012","DOIUrl":"10.1016/j.jmoldx.2024.12.012","url":null,"abstract":"<div><div>The National Academies of Sciences, Engineering, and Medicine issued a report on December 15, 2023, “Foundational Research Gaps and Future Directions for Digital Twins.” This described the importance of using biomimetic digital twins and multiomics in research. These were incorporated in the current analysis of patients with rheumatoid arthritis (RA). Exome sequencing, genotype-phenotype ranking, and biomimetic digital twin analysis were used to identify five pathogenic and one likely pathogenic DNA variants in patient samples analyzed, which were absent from controls. The variants identified in these genes, <em>P2RX7</em>, <em>HTRA2</em>, <em>PTPN22</em>, <em>FLG</em>, <em>CD46</em>, and <em>EIF4G1</em>, play a role in the development of RA. Additionally, 3172 variants of unknown clinical significance (VUSs) were identified in patient samples, which were absent from controls. All VUSs appeared to be associated with RA. Hidden or dark data were identified from six genes. These genes, often found in patient samples, included <em>HIF1A</em>, <em>HLA-DOA</em>, <em>PTGER3</em>, <em>HIPK3</em>, <em>TGFBR3</em>, and <em>HIF1A-AS3</em>. VUSs identified in genes <em>HIF1A</em>, <em>HLA-DOA</em>, <em>PTGER3</em>, and <em>HIPK3</em> were directly related to the pathogenesis of RA, whereas VUSs identified in genes <em>TGFBR3</em> and <em>HIF1A-AS3</em> were indirectly related. The current results suggest that biomimetic digital twins and multiomics can provide further insight into the development of RA. This may also potentially help with the process of reclassifying VUSs. The reclassification of VUSs will play a critical role in complex molecular diagnostics and drug development.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 4","pages":"Pages 256-269"},"PeriodicalIF":3.4,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426565","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

Single-Tube, Switched Temperature Amplicon Barcoding for Multiplex Detection of Rare Mutations in Circulating Tumor DNA

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-12 DOI: 10.1016/j.jmoldx.2025.01.004

Tony E. Godfrey , Ekaterina Kintsurashvili , Gordana Rasic , Jessalyn Kaur , Christopher D'Amato , Robert H. Meltzer

{"title":"Single-Tube, Switched Temperature Amplicon Barcoding for Multiplex Detection of Rare Mutations in Circulating Tumor DNA","authors":"Tony E. Godfrey , Ekaterina Kintsurashvili , Gordana Rasic , Jessalyn Kaur , Christopher D'Amato , Robert H. Meltzer","doi":"10.1016/j.jmoldx.2025.01.004","DOIUrl":"10.1016/j.jmoldx.2025.01.004","url":null,"abstract":"<div><div>Detection and analysis of circulating tumor DNA (ctDNA) as a biomarker for cancer is a promising approach. Applications for ctDNA analysis include screening, diagnosis, treatment selection, treatment monitoring, minimal residual disease detection, and recurrence monitoring. Detection of ctDNA is challenging and requires highly sensitive methods. Approaches such as digital PCR are appropriate when only a small number of targets is being interrogated, whereas next-generation sequencing (NGS) is typically used when more targets are being analyzed. There are several NGS methods available, some of which are published and can be implemented in laboratories with the required expertise while other, commercial approaches are proprietary and are only available as a service. Of the published methods, most use some kind of unique molecular identifiers (or barcodes) to facilitate NGS error correction and detection of rare mutations at mutant allele frequencies of <0.1%. However, incorporation of barcodes and amplification of the resulting libraries are not trivial and typically require multiple steps and considerable hands-on time by an experienced molecular biologist. Herein, a novel approach for switched temperature amplicon barcoding was used, in which barcoding and library amplification were performed in the same tube using a two-stage PCR protocol with no additional manipulation. Total hands-on time was 10 to 15 minutes for reaction setup; the library was then cleaned and was ready for sequencing.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 4","pages":"Pages 237-246"},"PeriodicalIF":3.4,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426566","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 基于数字pcr的IDH1和IDH2基因常见突变的最小残留疾病检测在急性髓系白血病患者中的验证

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-01 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":"<div><div>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 <em>IDH1</em> and <em>IDH2</em> 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 <em>IDH2 R140Q</em> 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.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 2","pages":"Pages 100-108"},"PeriodicalIF":3.4,"publicationDate":"2025-02-01","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

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 : 2025-02-01 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":"<div><div>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 <em>BRCA1</em> or <em>RAD51C</em> 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 <em>BRCA1</em> and <em>RAD51C</em> 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 <em>BRCA1</em> and <em>RAD51C</em> 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.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 2","pages":"Pages 139-153"},"PeriodicalIF":3.4,"publicationDate":"2025-02-01","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

Investigating the Pathogenicity of Uncommon KRAS Mutations and Their Association with Clinicopathologic Characteristics in Patients with Colorectal Cancer 探讨结直肠癌患者罕见KRAS突变的致病性及其与临床病理特征的关系。

IF 3.4 3区医学

Journal of Molecular Diagnostics Pub Date : 2025-02-01 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":"<div><div>Kirsten rat sarcoma viral oncogene homolog <em>(KRAS</em>) 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 <em>KRAS</em> (u<em>KRAS</em>) variants are largely unexplored. The distribution and pathogenicity of u<em>KRAS</em> mutations and their relationship with patients’ clinicopathologic features were assessed. A total of 2427 CRCs were profiled for <em>KRAS</em> using next-generation sequencing (NGS). The study and control groups included patients with u<em>KRAS</em> (<1% frequency in CRC data sets on cBioPortal) and canonical <em>KRAS</em> mutations, respectively. <em>In silico</em> protein structure modifications and prediction analyses were performed by using PyMOL, trRosetta, and PolyPhen-2. u<em>KRAS</em> 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. u<em>KRAS</em> 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 u<em>KRAS</em> mutations as candidates for personalized therapy.</div></div>","PeriodicalId":50128,"journal":{"name":"Journal of Molecular Diagnostics","volume":"27 2","pages":"Pages 130-138"},"PeriodicalIF":3.4,"publicationDate":"2025-02-01","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