Cantrk
The Canadian NTRK (CANTRK) is a ring study to optimize testing for neurotrophic receptor tyrosine kinase (NTRK) fusions in Canadian laboratories. Sixteen diagnostic laboratories used next-generation sequencing (NGS) for NTRK1, NTRK2, or NTRK3 fusions. Each laboratory received 12 formalin-fixed, paraffin-embedded tumor samples with unique NTRK fusions and two control non-NTRK fusion samples (one ALK and one ROS1). Laboratories used validated protocols for NGS fusion detection. Panels included Oncomine Comprehensive Assay v3, Oncomine Focus Assay, Oncomine Precision Assay, AmpliSeq for Illumina Focus, TruSight RNA Pan-Cancer...
Source: Journal of Molecular Diagnostics - December 28, 2022 Category: Pathology Authors: Tracy L. Stockley, Bryan Lo, Adrian Box, Andrea Gomez Corredor, John DeCoteau, Patrice Desmeules, Harriet Feilotter, Daria Grafodatskaya, Wenda Greer, Cynthia Hawkins, Weei Yuarn Huang, Iyare Izevbaye, Guylaine L épine, Sebastiao N. Martins Filho, Andrea Tags: Regular article Source Type: research
CANTRK: A Canadian Ring Study to Optimize Detection of NTRK Gene Fusions by Next Generation RNA Sequencing
CANTRK is a ring study to optimize testing for neurotrophic receptor tyrosine kinase (NTRK) fusions in Canadian laboratories. Sixteen diagnostic laboratories used next generation sequencing (NGS) for NTRK1, NTRK2 or NTRK3 fusions. Each laboratory received 12 formalin fixed, paraffin embedded (FFPE) tumor samples with unique NTRK fusions, and 2 control non-NTRK fusion samples (1 ALK and 1 ROS1). Laboratories used validated protocols for NGS fusion detection. Panels included Oncomine Comprehensive Assay v3, Oncomine Focus, Oncomine Precision, AmpliSeq Focus, TruSight RNA Pan-Cancer Panel, FusionPlex Lung and QIAseq Multimoda...
Source: Journal of Molecular Diagnostics - December 28, 2022 Category: Pathology Authors: Tracy L. Stockley, Bryan Lo, Adrian Box, Andrea Gomez Corredor, John DeCoteau, Patrice Desmeules, Harriet Feilotter, Daria Grafodatskaya, Wenda Greer, Cynthia Hawkins, Weei Yuarn Huang, Iyare Izevbaye, Guylaine L épine, Sebastiao N. Martins Filho, Andrea Tags: Regular Article Source Type: research
A Novel Approach to Detect IDH Point Mutations in Gliomas Using Nanopore Sequencing
The use of standard next-generation sequencing technologies to detect key mutations in IDH genes for glioma diagnosis imposes several challenges, including high capital cost and turnaround delays associated with the need for batch testing. For both glioma testing and testing in other tumor types where highly specific mutation identification is required, the high-throughput nature of next-generation sequencing limits the feasibility of using it as a primary approach in clinical laboratories. We hypothesized that third-generation nanopore sequencing by Oxford Nanopore Technologies has the capability to overcome these limitat...
Source: Journal of Molecular Diagnostics - December 21, 2022 Category: Pathology Authors: Mashiat L. Mimosa, Wafa Al-ameri, Jared T. Simpson, Michael Nakhla, Karel Boissinot, David G. Munoz, Sunit Das, Harriet Feilotter, Ramzi Fattouh, Rola M. Saleeb Tags: Technical advance Source Type: research
A Novel Approach to Detect IDH Point Mutations in Gliomas Using Nanopore Sequencing, Test Validation for the Clinical Laboratory
The use of standard next generation sequencing (NGS) technologies to detect key mutations in isocitrate dehydrogenase (IDH) genes for glioma diagnosis imposes several challenges including high capital cost and turnaround delays associated with the need for batch testing. Both for glioma testing, as well as for testing in other tumor types where highly specific mutation identification is required, the high throughput nature of NGS limits the feasibility of using it as a primary approach in clinical laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 21, 2022 Category: Pathology Authors: Mashiat L. Mimosa, Wafa Al-ameri, Jared T. Simpson, Michael Nakhla, Karel Boissinot, David G. Munoz, Sunit Das, Harriet Feilotter, Ramzi Fattouh, Rola M. Saleeb Tags: Technical Advance Source Type: research
A systematic method for detecting abnormal mRNA splicing and assessing its clinical impact in individuals undergoing genetic testing for hereditary cancer syndromes
Nearly 14% of disease-causing germline variants result from disruption of mRNA splicing. Most (67%) DNA variants predicted in silico to disrupt splicing end up classified as variants of uncertain significance (VUS). We developed and validated an analytic workflow — Splice Effect Event Resolver (SPEER) — that uses mRNA sequencing to reveal significant deviations in splicing, pinpoints the DNA variants potentially responsible, and measures the deleterious effect of the altered splicing on mRNA transcripts, providing evidence to assess the pathogenicity of the variant. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 20, 2022 Category: Pathology Authors: Nick Kamps-Hughes, Victoria E.H. Carlton, Laure Fresard, Steve Osazuwa, Elizabeth Starks, John J. Vincent, Sarah Albritton, Robert L. Nussbaum, Keith Nykamp Tags: Regular Article Source Type: research
Updates and Initiatives from The Journal of Molecular Diagnostics
It has been about ten months since I've become the Editor-in-Chief (EIC) of The Journal of Molecular Diagnostics (JMD), and customarily the editor introduces achievements of the year prior. After successfully transitioning into the EIC role I was pleased to welcome Dr. Lynette Sholl to the Senior Associate Editor role and Dr. Rondell Graham as the Associate Editor overseeing solid tumor submissions. There were also eight new members added to the Editorial Board: Gregory Berry, Alanna Church, Avinash Dharmadhikari, Valentina Nardi, Lauren Ritterhouse, Somak Roy, Ryan Schmidt, and Laura Tafe. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 13, 2022 Category: Pathology Authors: Ronald M. Przygodzki Tags: Editorial Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 13, 2022 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 13, 2022 Category: Pathology Source Type: research
Instructions to Authors
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 13, 2022 Category: Pathology Source Type: research
Scientific Integrity Policy
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 13, 2022 Category: Pathology Source Type: research
Correction
The authors of the article entitled, “Development and Clinical Validation of a 90-Gene Expression Assay for Identifying Tumor Tissue Origin” (Volume 22, pages 1139–1150 of the September 2020 issue of The Journal of Molecular Diagnostics; DOI: https://doi.org/10.1016/j.jmoldx.2020.06.005) have discovered an omission in the publish ed funding statement. Funding from the Clinical Research Project of Shanghai Municipal Health Committee 20194Y0348 (M.X.) is being added to the complete funding information. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2022 Category: Pathology Tags: Correction Source Type: research
Corrections
The authors of the article entitled, “Development and Clinical Validation of a 90-Gene Expression Assay for Identifying Tumor Tissue Origin” (Volume 22, pages 1139-1150 of the September 2020 issue of The Journal of Molecular Diagnostics; DOI: https://doi.org/10.1016/j.jmoldx.2020.06.005) have discovered an omission in the published funding statement. Funding from the Clinical Research Project of Shanghai Municipal Health Committee 20194Y0348 (M.X.) is being added to the complete funding information. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2022 Category: Pathology Tags: Correction Source Type: research
Diagnosis of Fusion-Associated Sarcomas by Exon Expression Imbalance and Gene Expression
Sarcomas are a diverse group of tumors, with>70 subtypes in the current World Health Organization classification, each with distinct biological behavior requiring specific clinical management. A significant portion of sarcomas are molecularly defined by expression of a driver fusion gene; identification of such fusions is the basis of molecular diagnostics in sarcomas, which is of increasing complexity due to the ongoing discovery of new gene fusions. Recently, a multiplex NanoString platform –based assay was developed and clinically implemented, with fusion junction–spanning probes that detect the majority of sarcoma ...
Source: Journal of Molecular Diagnostics - December 8, 2022 Category: Pathology Authors: Angela Goytain, Kenneth Tou En Chang, Jian Yuan Goh, Torsten O. Nielsen, Tony L. Ng Tags: Regular article Source Type: research
Diagnosis of Fusion Associated Sarcomas by Exon Expression Imbalance and Gene Expression
Sarcomas are a diverse group of tumors, with greater than 70 subtypes in the current World Health Organization classification, each with distinct biological behavior requiring specific clinical management. A significant proportion of sarcomas are molecularly defined by expression of a driver fusion gene; identification of such fusions is the basis of molecular diagnostics in sarcomas, which is of increasing complexity due to the ongoing discovery of new gene fusions. Recently, we developed and clinically implemented a multiplex Nanostring platform-based assay with fusion junction-spanning probes that detects the majority o...
Source: Journal of Molecular Diagnostics - December 8, 2022 Category: Pathology Authors: Angela Goytain, Kenneth Tou En Chang, Jian Yuan Goh, Torsten O. Nielsen, Tony L. Ng Tags: Regular Article Source Type: research
Assessments of Somatic Variant Classification Using the Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists Guidelines
To assess the clinical implementation of the 2017 Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists, identify content that may result in classification inconsistencies, and evaluate implementation barriers, an Association for Molecular Pathology Working Group conducted variant interpretation challenges and a guideline implementation survey. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 7, 2022 Category: Pathology Authors: Marilyn M. Li, Catherine E. Cottrell, Mrudula Pullambhatla, Somak Roy, Robyn L. Temple-Smolkin, Scott A. Turner, Kai Wang, Yunyun Zhou, Cindy L. Vnencak-Jones Tags: Special article Source Type: research
