Comparison of Real-Time PCR and Digital PCR for Detection of Plasma Epstein-Barr Virus DNA in Nasopharyngeal Carcinoma
Plasma Epstein-Barr Virus (EBV) DNA is an established biomarker for endemic nasopharyngeal carcinoma (NPC). However, existing real-time PCR (qPCR) assays are limited by poor inter-laboratory reproducibility. This is a barrier to biomarker integration into staging systems and management.It was hypothesized that EBV digital PCR (dPCR) would have similar sensitivity but improved precision relative to qPCR. Using the WHO EBV standard and patient specimens, the NRG BamHI-W qPCR, two commercial EBNA-1 qPCR assays, and two laboratory-developed dPCR assays amplifying the BamHI-W, EBNA-1, and EBER targets were compared. (Source: Jo...
Source: Journal of Molecular Diagnostics - April 14, 2023 Category: Pathology Authors: Jacob A. Miller, ChunHong Huang, Fumiko Yamamoto, Malaya K. Sahoo, Quynh-Thu Le, Benjamin A. Pinsky Tags: Regular Article Source Type: research
Validation of the Labcorp Plasma Focus Test to Facilitate Precision Oncology Through Cell-free DNA Genomic Profiling of Solid Tumors
This study highlights the analytical validation of the test, including accuracy compared to orthogonal methods, sensitivity, specificity, precision, reproducibility, and repeatability. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 14, 2023 Category: Pathology Authors: Ellen L. Verner, Jennifer B. Jackson, Eric Severson, Kenneth C. Valkenburg, Amy E. Greer, David R. Riley, Mark Sausen, Cynthia Maddox, Paul M. McGregor, Aanavi Karandikar, Stephanie B. Hastings, Rebecca A. Previs, Venkataprasanth P. Reddy, Taylor J. Jense Tags: Regular Article Source Type: research
Preanalytic Methodological Considerations and Sample Quality Control of Circulating miRNAs
This study comprehensively analyzed the profiles of 356 miRNAs by quantitative real-time RT-PCR in various blood sample types, with various processing protocols. The comprehensive analysis investigated the correlations of individual miRNAs with certain confounding factors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 6, 2023 Category: Pathology Authors: Suit-Fong Chan, He Cheng, Karen Goh Kai-Rui, Ruiyang Zou Tags: Regular article Source Type: research
Pre-analytic Methodological Considerations and Sample Quality Control of Circulating miRNAs
This study comprehensively analyzed the profiles of 356 miRNAs by quantitative RT-PCR in various blood sample types, with various processing protocols. The comprehensive analysis investigated the correlations of individual miRNAs with certain confounding factors. Based on these profiles, a panel of 7 miRNAs was established for the quality control of samples corresponding to hemolysis and platelet contamination. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 6, 2023 Category: Pathology Authors: Suit-Fong Chan, He Cheng, Karen Goh Kai-Rui, Ruiyang Zou Tags: Regular Article Source Type: research
Multiplex digital PCR assay to detect multiple KRAS and GNAS mutations associated with pancreatic carcinogenesis from minimal specimen amounts
Digital PCR (dPCR) allows for highly sensitive quantification of low-frequency mutations and facilitates early detection of cancer. However, low throughput targeting of single hotspots in dPCR hinders variant specification when multiple probes are used. Here we developed a dPCR method to simultaneously identify major variants related to pancreatic carcinogenesis. Using a 2-D plot of droplet fluorescence under the optimized concentration of two fluorescent probe pools, we determined the absolute quantification of different KRAS and GNAS variants. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 23, 2023 Category: Pathology Authors: Maeda Chiho, Yusuke Ono, Akihiro Hayashi, Kenji Takahashi, Kenzui Taniue, Rika Kakisaka, Miyuki Mori, Takahiro Ishii, Hiroki Sato, Tetsuhiro Okada, Hidemasa Kawabata, Takuma Goto, Nobue Tamamura, Yuko Omori, Kuniyuki Takahashi, Akio Katanuma, Hidenori Kar Tags: Regular Article Source Type: research
Droplet digital PCR development for adenovirus load monitoring in children after hematopoietic stem cell transplantation
In this study, ddPCR was developed for AdV DNA and compared its performance characteristics with qPCR. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 23, 2023 Category: Pathology Authors: Kazunori Haruta, Suguru Takeuchi, Makoto Yamaguchi, Kazuhiro Horiba, Takako Suzuki, Yuka Torii, Atsushi Narita, Hideki Muramatsu, Yoshiyuki Takahashi, Yoshinori Ito, Jun-ichi Kawada Tags: Regular Article Source Type: research
Clonal Characterization and Somatic Hypermutation Assessment by Next-Generation Sequencing in Chronic Lymphocytic Leukemia/Small Lymphocytic Lymphoma
Somatic hypermutation status of the IGHV gene is essential for treating patients with chronic lymphocytic leukemia/small lymphocytic lymphoma. Unlike the conventional low-throughput method, assessment of somatic hypermutation by next-generation sequencing (NGS) has potential for uniformity and scalability; however, it lacks standardization or guidelines for routine clinical use. We critically assessed the performance of an amplicon-based NGS assay across 458 samples. Using a validation cohort (35 samples), the comparison of two platforms (Ion Torrent versus Illumina) and two primer sets [leader versus framework region 1 (F...
Source: Journal of Molecular Diagnostics - March 22, 2023 Category: Pathology Authors: Kseniya Petrova-Drus, Mustafa Syed, Wayne Yu, Kasey Hutt, Alyssa M. Zlotnicki, Ying Huang, Monika Kamalska-Cyganik, Lidia Maciag, Meiyi Wang, Yuanyuan G. Ma, Caleb Ho, Christine Moung, Jinjuan Yao, Khedoudja Nafa, Jeeyeon Baik, Chad M. Vanderbilt, Jamal K Tags: Regular article Source Type: research
Clonal Characterization and Somatic Hypermutation (SHM) Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia/ Small Lymphocytic Lymphoma (CLL/SLL): A Detailed Description of the Technical Performance, Clinical Utility, and Platform Comparison.
Somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene is essential for treating chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL) patients. Unlike the conventional low-throughput method, assessment of SHM by next generation sequencing (NGS) has potential for uniformity and scalability, however it lacks standardization or guidelines for routine clinical use. We critically assessed the performance of an amplicon-based NGS assay across 458 samples. Using a validation cohort (35 samples), the comparison of two platforms (Ion Torrent vs Illumina) and two primer sets (Leader vs FR1) in t...
Source: Journal of Molecular Diagnostics - March 22, 2023 Category: Pathology Authors: Kseniya Petrova-Drus, Mustafa Syed, Wayne Yu, Kasey Hutt, Alyssa M. Zlotnicki, Ying Huang, Monika Kamalska-Cyganik, Lidia Maciag, Meiyi Wang, Yuanyuan G. Ma, Caleb Ho, Christine Moung, Jinjuan Yao, Khedoudja Nafa, Jeeyeon Baik, Chad M. Vanderbilt, Jamal K Tags: Regular Article Source Type: research
Development of multiplex drop-off digital PCR assays for hotspot mutation detection of KRAS, NRAS, BRAF and PIK3CA in the plasma of colorectal cancer patients
The detection of mutations in KRAS, NRAS, BRAF and PIK3CA has become essential in treatment management of metastatic colorectal cancer (mCRC), with the approval of new targeted therapies. We developed novel multiplex drop-off digital PCR (MDO-dPCR) assays, by combining amplitude-/ratio-based multiplexing with drop-off/double drop-off strategies, which allow for detection of at least 69 most frequent hotspot mutations in all four genes with only three reactions. We assessed the analytical performance of the assays using synthetic oligonucleotides, further validated on plasma cfDNA samples from a large cohort of CRC patients...
Source: Journal of Molecular Diagnostics - March 22, 2023 Category: Pathology Authors: Qian Yu, Huiqin Jiang, Xi Su, Zhengxin Jiang, Xue Liang, Chunyan Zhang, Wu Shang, Yiliang Zhang, Hao Chen, Zhijie Yang, Minna Shen, Fei Huang, Xinning Chen, Yihui Yang, Baishen Pan, Beili Wang, Daru Lu, Wei Guo Tags: Regular Article Source Type: research
Improving RNA fusion call confidence and reliability in molecular diagnostic testing
Next-generation sequencing (NGS) is a superior method for detecting known and novel RNA fusions in formalin-fixed paraffin-embedded tissue over FISH and RT-PCR. However, confidence in fusion calling and true negatives may be compromised by poor RNA quality. Using a commercial panel of 507 genes and the recommended 3 million read threshold to accept results, two cases yielded false negatives while exceeding this recommendation during clinical validation. To develop a reliable quality control metric that better reflects internal sample quality and improve call confidence, gene expression across 361 patient tumor samples was ...
Source: Journal of Molecular Diagnostics - March 21, 2023 Category: Pathology Authors: Mariusz Shrestha, Sasha Blay, Sydney Liang, David Swanson, Jordan Lerner-Ellis, Brendan Dickson, Andrew Wong, George S. Charames Tags: Technical Advance Source Type: research
Detection of biallelic loss of DNA repair genes in formalin-fixed, paraffin-embedded tumor samples using a novel tumor-only sequencing panel
This report describes SyNthetic lethal Interactions for Precision Diagnostics (SNiPDx), a targeted next-generation sequencing (NGS) panel for detection of LOH and biallelic LOF alterations in 26 target genes focused on DNA damage response (DDR) pathways, in tumor-only formalin-fixed, paraffin-embedded (FFPE) samples. NGS was performed across all exons of these 26 genes and encompassed a total of 7632 genome-wide single nucleotide polymorphisms (SNPs) on genomic DNA from 80 FFPE solid tumor samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 19, 2023 Category: Pathology Authors: Dominik Glodzik, Pier Selenica, Ryan A. Rogge, Ian M. Silverman, Diana Mandelker, Sam Harris, Jianhua Zhao, Michael Zinda, Artur Veloso, Nirav Malani, Nadeem Riaz, Maria Koehler, Robert D. Daber, Verity Johnson, Victoria Rimkunas, Jorge S. Reis-Filho Tags: Regular Article Source Type: research
Correction
The authors of the article entitled, “Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines: A Report from the Association for Molecular Pathology” (Volume 25, pages 69–86 of the February 2023 issue of The Journ al of Molecular Diagnostics; DOI: https://doi.org/10.1016/j.jmoldx.2022.11.002) have discovered an error in Table 3 related to the Evidence Summary listed for variant 2A. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 16, 2023 Category: Pathology Tags: Correction Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 16, 2023 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 16, 2023 Category: Pathology Source Type: research
Minimal/Measurable Residual Disease Monitoring in Patients with Lymphoid Neoplasms by High-Throughput Sequencing of the T-Cell Receptor
In this study, the performance of the commercially available LymphoTrack high-throughput sequencing assay was assessed for determining residual disease burden in patients with various T-cell malignancies. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 2, 2023 Category: Pathology Authors: Jack K. Tung, Diwash Jangam, Chandler C. Ho, Eula Fung, Michael S. Khodadoust, Youn H. Kim, James L. Zehnder, Henning Stehr, Bing M. Zhang Tags: Regular articles Source Type: research
