Rapid and Automated Semiconductor-Based Next-Generation Sequencing for Simultaneous Detection of Somatic DNA and RNA Aberrations in Myeloid Neoplasms
Evaluation of suspected myeloid neoplasms involves testing for recurrent, diagnostically and therapeutically relevant genetic alterations. Current molecular testing requires multiple technologies, different domains of expertise, and unconnected workflows, resulting in variable, lengthy turnaround times that can delay treatment. To address this unmet clinical need, the Oncomine Myeloid Assay GX panel on the Ion Torrent Genexus platform, a rapid ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 7, 2022 Category: Pathology Authors: Christopher M. Sande, Rui Wu, Guang Yang, Robyn T. Sussman, Ashkan Bigdeli, Chase Rushton, Akshay Chitturi, Jay Patel, Philippe Szankasi, Jennifer J.D. Morrissette, Megan S. Lim, Kojo S.J. Elenitoba-Johnson Tags: Regular article Source Type: research
Assessments of Somatic Variant Classification Using the AMP/ASCO/CAP Guidelines: A Report from the Association for Molecular Pathology
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 AMP 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
Rapid and Automated Semiconductor-Based Next Generation Sequencing for Simultaneous Detection of Somatic DNA and RNA Aberrations in Myeloid Neoplasms
Evaluation of suspected myeloid neoplasms involves testing for recurrent, diagnostically and therapeutically relevant genetic alterations. Current molecular testing requires multiple technologies, different domains of expertise, and unconnected workflows, resulting in variable, lengthy turnaround times (TATs) that can delay treatment. To address this unmet clinical need, the Oncomine Myeloid Assay GX panel on the Ion Torrent Genexus platform, a rapid ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 7, 2022 Category: Pathology Authors: Christopher M. Sande, Rui Wu, Guang Yang, Robyn T. Sussman, Ashkan Bigdeli, Chase Rushton, Akshay Chitturi, Jay Patel, Philippe Szankasi, Jennifer JD. Morrissette, Megan S. Lim, Kojo SJ. Elenitoba-Johnson Tags: Regular Article Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 1, 2022 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 1, 2022 Category: Pathology Source Type: research
Minigene assay as an effective molecular diagnostic strategy in determining the pathogenicity of non-canonical splice-site variants in FLCN
Primary spontaneous pneumothorax (PSP) or pulmonary cyst is one of the manifestations of Birt-Hogg-Dube syndrome, which is caused by pathogenic variants in FLCN gene. Genetic testing in PSP patients identifies a certain number of missense or intronic variants. These variants are usually considered as variants of uncertain significance (VUS) whose functional interpretations pose a challenge in clinical genetics. To improve recognition of pathogenic splice-altering variants in FLCN gene, computational tools are used to prioritize potential splice-altering variants and then a hybrid minigene assay is performed to verify the R...
Source: Journal of Molecular Diagnostics - November 18, 2022 Category: Pathology Authors: Xinxin Zhang, Minghui Cai, Yuanchun Ma, Jie Chen, Shaoping Huang, Mengru Cai, Yibing Ding, Dehua Ma, Qian Gao, Xiaowen Hu, Chengchu Zhu, Long Yi Tags: Regular Article Source Type: research
A Micro-Costing Framework for Circulating Tumor DNA Testing in Dutch Clinical Practice
Circulating tumor DNA (ctDNA) is a promising new biomarker with multiple potential applications in cancer care. Estimating total cost of ctDNA testing is necessary for reimbursement and implementation, but challenging because of variations in workflow. We aimed to develop a micro-costing framework for consistent cost calculation of ctDNA testing. First, the foundation of the framework was built, based on the complete step-wise diagnostic workflow of ctDNA testing. Second, the costing method was set up, including costs for personnel, materials, equipment, overhead, housing, and failures. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 16, 2022 Category: Pathology Authors: Astrid Kramer, Ed Schuuring, Daan C.L. Vessies, Paul van der Leest, Maartje J. Geerlings, Pim Rozendal, Mirthe Lanfermeijer, Theodora C. Linders, L éon C. van Kempen, Remond J.A. Fijneman, Marjolijn J.L. Ligtenberg, Gerrit A. Meijer, Daan van den Broek, Tags: Regular article Source Type: research
A Micro-Costing Framework for Circulating Tumor DNA testing In Dutch Clinical Practice.
Circulating tumor DNA (ctDNA) is a promising new biomarker with multiple potential applications in cancer care. Estimating total cost of ctDNA-testing is necessary for reimbursement and implementation, but challenging due to variations in workflow. We aimed to develop a micro-costing framework for consistent cost calculation of ctDNA-testing. First, the foundation of the framework was built, based on the complete step-wise diagnostic workflow of ctDNA-testing. Second, the costing method was set-up, including costs for personnel, materials, equipment, overhead, housing, and failures. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 16, 2022 Category: Pathology Authors: Astrid Kramer, Ed Schuuring, Daan C.L. Vessies, Paul van der Leest, Maartje J. Geerlings, Pim Rozendal, Mirthe Lanfermeijer, Theodora C. Linders, L éon C. van Kempen, Remond J.A. Fijneman, Marjolijn J.L. Ligtenberg, Gerrit A. Meijer, Daan van den Broek, Tags: Regular Article Source Type: research
Evaluating Multiple Next-Generation Sequencing –Derived Tumor Features to Accurately Predict DNA Mismatch Repair Status
Identifying tumor DNA mismatch repair deficiency (dMMR) is important for precision medicine. Tumor features, individually and in combination, derived from whole-exome sequenced (WES) colorectal cancers (CRCs) and panel-sequenced CRCs, endometrial cancers (ECs), and sebaceous skin tumors (SSTs) were assessed for their accuracy in detecting dMMR. CRCs (n = 300) with WES, where mismatch repair status was determined by immunohistochemistry, were assessed for microsatellite instability (MSMuTect, MANTIS, MSIseq, and MSISensor), Catalogue of Somatic Mutations in Cancer tumor mutational signatures, and somatic mutation counts. (S...
Source: Journal of Molecular Diagnostics - November 14, 2022 Category: Pathology Authors: Romy Walker, Peter Georgeson, Khalid Mahmood, Jihoon E. Joo, Enes Makalic, Mark Clendenning, Julia Como, Susan Preston, Sharelle Joseland, Bernard J. Pope, Ryan A. Hutchinson, Kais Kasem, Michael D. Walsh, Finlay A. Macrae, Aung K. Win, John L. Hopper, Dm Tags: Regular article Source Type: research
Evaluating multiple next-generation sequencing derived tumor features to accurately predict DNA mismatch repair status
Identifying tumor DNA mismatch repair deficiency (dMMR) is important for precision medicine. Tumor features, individually and in combination, derived from whole-exome sequenced (WES) colorectal cancers (CRCs) and panel sequenced CRCs, endometrial cancers (ECs) and sebaceous skin tumors (SSTs) were assessed for their accuracy in detecting dMMR. CRCs (n=300) with WES, where MMR status was determined by immunohistochemistry, were assessed for microsatellite instability (MSMuTect, MANTIS, MSIseq, MSISensor), COSMIC tumor mutational signatures (TMS) and somatic mutation counts. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 14, 2022 Category: Pathology Authors: Romy Walker, Peter Georgeson, Khalid Mahmood, Jihoon E. Joo, Enes Makalic, Mark Clendenning, Julia Como, Susan Preston, Sharelle Joseland, Bernard J. Pope, Ryan A. Hutchinson, Kais Kasem, Michael D. Walsh, Finlay A. Macrae, Aung K. Win, John L. Hopper, Dm Tags: Regular Article Source Type: research
Pathogenicity of Intronic and Synonymous Variants of ATP7B in Wilson Disease
This study included such patients from the authors' center and screened for the full-length sequence of ATP7B by next-generation sequencing. Newly identified synonymous and intronic variants were then analyzed with in silico tools. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 4, 2022 Category: Pathology Authors: Wan-Qing Xu, Rou-Min Wang, Yi Dong, Zhi-Ying Wu Tags: Regular article Source Type: research
Pathogenicity of intronic and synonymous variants of ATP7B in Wilson's disease
This study included such patients from the authors ’ center and screened for the full-length sequence of ATP7B by next-generation sequencing (NGS). Newly identified synonymous and intronic variants were then analyzed with in silico tools. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 4, 2022 Category: Pathology Authors: Wan-Qing Xu, Rou-Min Wang, Yi Dong, Zhi-Ying Wu Tags: Regular Article Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 1, 2022 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 1, 2022 Category: Pathology Source Type: research
Clinical Validation and Diagnostic Utility of Optical Genome Mapping for Enhanced Cytogenomic Analysis of Hematological Neoplasms
The current standard-of-care (SOC) cytogenetic techniques for the analysis of hematological malignancies include karyotyping, FISH, and CMA, which are labor-intensive, time and cost-prohibitive, and often do not reveal the genetic complexity of the tumor, demonstrating the need for alternative technology for better characterization of these tumors. Herein, we report the results from our clinical validation study and demonstrate the utility of optical genome mapping (OGM), evaluated using 92 sample runs (including replicates) that included 69 well-characterized unique samples (59 hematological neoplasms and 10 controls). (S...
Source: Journal of Molecular Diagnostics - October 17, 2022 Category: Pathology Authors: Nikhil Shri Sahajpal, Ashis K. Mondal, Tatiana Tvrdik, Jennifer Hauenstein, Huidong Shi, Kristin K. Deeb, Debra Saxe, Alex R. Hastie, Alka Chaubey, Natasha M. Savage, Vamsi Kota, Ravindra Kolhe Tags: Regular Article Source Type: research
