Machine learning analysis using RNA-seq to distinguish neuromyelitis optica from multiple sclerosis and identify therapeutic candidates
This study aims to identify RNA biomarkers distinguishing neuromyelitis optica (NMO) from relapsing-remitting multiple sclerosis (RRMS) and explore potential therapeutic applications leveraging machine learning (ML). An ensemble approach was developed using differential gene expression analysis and competitive ML methodologies, interrogating total RNA sequencing datasets from peripheral whole blood of treatment-na ïve RRMS and NMO patients and healthy individuals. Pathway analysis of candidate biomarkers informed the biological context of disease, transcription factor activity, and small-molecule therapeutic potential. (S...
Source: Journal of Molecular Diagnostics - March 21, 2024 Category: Pathology Authors: Lukasz S. Wylezinski, Cheryl L. Sesler, Guzel I. Shaginurova, Elena V. Grigorenko, Jay G. Wohlgemuth, Franklin R. Cockerill, Michael K. Racke, Charles F. Spurlock Tags: Regular Article Source Type: research
Leveraging off-target reads in panel sequencing for homologous recombination repair deficiency screening in tumor
This study aims to develop an approach for robust copy number variant (CNV) calling in tumor samples using only off-target region (OTR) reads. We also established a clinical use case for homologous recombination deficiency (HRD) score estimation (HRDest) using the sum of telomeric allelic imbalance (TAI) and large-scale state transitions (LST) scores without the need for loss of heterozygosity (LOH) information. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 21, 2024 Category: Pathology Authors: Markus Ball, Iordanis Ourailidis, Klaus Kluck, Michael Menzel, Martina Kirchner, Michael Allg äuer, Timothy Kwang Yong Tay, Fabian Schnecko, Anna-Lena Volckmar, Hannah Goldschmid, Olaf Neuman, Stefan Fröhling, Peter Schirmacher, Jan Budczies, Albrecht S Tags: Regular Article Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 18, 2024 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 18, 2024 Category: Pathology Source Type: research
Panel Comparative Analysis Tool
Multigene next-generation sequencing (NGS) panels have become a routine diagnostic method in the contemporary practice of personalized medicine. To avoid inadequate test choice or interpretation, a detailed understanding of the precise panel target regions is required. However, the necessary bioinformatic expertise is not always available, and publicly accessible and easily interpretable analyses of target regions are scarce. To address this critical knowledge gap, we present the Panel Comparative Analysis Tool (PanelCAT), an open-source application to analyze, visualize, and compare NGS panel DNA target regions. (Source: ...
Source: Journal of Molecular Diagnostics - March 18, 2024 Category: Pathology Authors: Andr é Oszwald, Lucia Zisser, Eva Compérat, Leonhard Müllauer Tags: Regular article Source Type: research
PanelCAT: an Open-Source Comparative Analysis Tool for Next-Generation Sequencing Panel Target Regions
Multi-gene next-generation sequencing (NGS) panels have become a routine diagnostic method in the contemporary practice of personalized medicine. To avoid inadequate test choice or interpretation, a detailed understanding of the precise panel target regions is required. However, the necessary bioinformatic expertise is not always available, and publicly accessible and easily interpretable analyses of target regions are scarce. To address this critical knowledge gap, we present the Panel Comparative Analysis Tool (PanelCAT) an open-source application to analyze, visualize and compare NGS panel DNA target regions. (Source: J...
Source: Journal of Molecular Diagnostics - March 18, 2024 Category: Pathology Authors: Andr é Oszwald, Lucia Zisser, Eva Compérat, Leonhard Müllauer Tags: Regular Article Source Type: research
Evaluation of Pre-Analytical Variables for Human Papillomavirus Primary Screening from Self-Collected Vaginal Swabs
Human papillomavirus (HPV) primary screening is an effective approach to assessing cervical cancer risk. Self-collected vaginal swabs have shown promise to expand testing access, but there are limited data defining analytical performance criteria necessary for adoption of self-collected specimens, especially for those occurring outside the clinic, where the swab remains dry during transport. Here, we evaluated the performance of self-collected vaginal swabs for HPV detection using the Cobas 6800. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 15, 2024 Category: Pathology Authors: Michelle Qi, Anissa R. Naranjo, Abigail J. Duque, Thomas S. Lorey, Jeffrey M. Schapiro, Betty J. Suh-Burgmann, Michael Rummel, Stephen J. Salipante, Nicolas Wentzensen, Dina N. Greene Tags: Regular article Source Type: research
DNA reference reagents for genotyping RH variants
Patients who carry RH blood group variants may develop Rh alloantibodies requiring matched red cell transfusions. Serologic reagents for Rh variants often fail to specifically identify variant Rh antigens and are in limited supply. Therefore, red cell genotyping assays are essential for managing transfusions in patients with clinically relevant Rh variants. Well-characterized DNA reference reagents are needed to ensure quality and accuracy of the molecular tests. Eight lyophilized DNA reference reagents, representing 21 polymorphisms in RHD and RHCE, were produced from an existing repository of immortalized B-lymphoblastoi...
Source: Journal of Molecular Diagnostics - March 15, 2024 Category: Pathology Authors: Emilia Sippert, Evgeniya Volkova, Meagan Rippee-Brooks, Gregory A. Denomme, Willy A. Flegel, Christine Lee, Richardae Araojo, Orieji Illoh, Zhugong Liu, Maria Rios, Collaborative Study Group Tags: Regular Article Source Type: research
Evaluation of Pre-Analytical variables for HPV Primary Screening from Self-Collected Vaginal Swabs
HPV primary screening is an effective approach to assessing cervical cancer risk. Self-collected vaginal swabs have shown promise to expand testing access, but there are limited data defining analytical performance criteria necessary for adoption of self-collected specimens, especially for those occurring outside the clinic where the swab remains dry during transport. Here, we evaluated the performance of self-collected vaginal swabs for HPV detection using the Roche Cobas 6800. There was insignificant variability between swabs self-collected by the same individual (n=15 participants collecting 5 swabs/participant), measur...
Source: Journal of Molecular Diagnostics - March 15, 2024 Category: Pathology Authors: Michelle Qi, Anissa R. Naranjo, Abigail J. Duque, Thomas S. Lorey, Jeffrey M. Schapiro, Betty J. Suh-Burgmann, Michael Rummel, Stephen J. Salipante, Nicolas Wentzensen, Dina N. Greene Tags: Regular Article Source Type: research
Correction
The authors of the article entitled, “Minigene Assay as an Effective Molecular Diagnostic Strategy in Determining the Pathogenicity of Noncanonical Splice-Site Variants in FLCN” (Volume 25, pages 110–120 of the February 2023 issue of The Journal of Molecular Diagnostics; DOI: https://doi.org/10.1016/j.jmoldx.2022.10.005) contacte d the editorial office after noticing an error in the labeling of Figure 2C. The exons in this panel should be Exon 10 and Exon 12, the labeling of Exon 11 in the original is a clerical mistake. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 14, 2024 Category: Pathology Tags: Correction Source Type: research
Deconvoluting the Complexity of Congenital Sideroblastic Anemias through Genetic and Functional Profiling
In this edition, we highlight the research of Sharma et al. [1] on congenital sideroblastic anemias (CSA), a group of rare disorders. Their work harnesses a large cohort of childhood anemia patients to advance our understanding of both CSA and the broader implications for iron deficiency anemia (IDA). Their focused study leverages targeted genetic analyses to identify novel genetic variants in key genes such as ALAS2, paving the way for improved treatments, a deeper biological understanding of metal metabolism, and improved diagnostic techniques to enhance patient outcomes in hematologic diseases. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 14, 2024 Category: Pathology Authors: F.N.U. Alnoor, Robert S. Ohgami Tags: Commentary Source Type: research
Assay Validation of Cell-Free DNA Shallow Whole-Genome Sequencing to Determine Tumor Fraction in Advanced Cancers
We describe assay validation of this approach to facilitate broad clinical application, including evaluation of assay sensitivity, precision, repeatability, reproducibility, pre-analytic factors, and DNA quality/quantity. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 13, 2024 Category: Pathology Authors: Micah Rickles-Young, Gabriel Tinoco, Junko Tsuji, Sam Pollock, Marcy Haynam, Heather Lefebvre, Kristyn Glover, Dwight H. Owen, Katharine A. Collier, Gavin Ha, Viktor A. Adalsteinsson, Carrie Cibulskis, Niall J. Lennon, Daniel G. Stover Tags: Regular article Source Type: research
Assay Validation of Cell-Free DNA Shallow Whole Genome Sequencing To Determine Tumor Fraction in Advanced Cancers
We describe assay validation of this approach to facilitate broad clinical application, including evaluation of assay sensitivity, precision, repeatability, reproducibility, pre-analytic factors, and DNA quality/quantity. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 13, 2024 Category: Pathology Authors: Micah Rickles-Young, Gabriel Tinoco, Junko Tsuji, Sam Pollock, Marcy Haynam, Heather Lefebvre, Kristyn Glover, Dwight H. Owen, Katharine A. Collier, Gavin Ha, Viktor A. Adalsteinsson, Carrie Cibulskis, Niall J. Lennon, Daniel G. Stover Tags: Regular Article Source Type: research
Diagnosis of challenging spinal muscular atrophy cases with long-read sequencing
This study assesses the diagnostic potential of Long-Read Sequencing (LRS) in three SMA patients. For Patient 1, who has a heterozygous SMN1 deletion, LRS unveiled a missense mutation in SMN1 exon 5. In Patient 2, an Alu/Alu-mediated rearrangement covering the SMN1 promoter and exon 1 was identified through a blend of Multiplex Ligation-Dependent Probe Amplification (MLPA), LRS, and Gap-PCR. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 13, 2024 Category: Pathology Authors: Ningning Wang, Kexin Jiao, Jin He, Bochen Zhu, Nachuan Cheng, Jian Sun, Lan Chen, Wanjin Chen, Lingyun Gong, Kai Qiao, Jianying Xi, Qihan Wu, Chongbo Zhao, Wenhua Zhu Tags: Regular Article Source Type: research
Optical Genome Mapping for Comprehensive Cytogenetic Analysis of Soft-Tissue and Bone Tumors for Diagnostic Purposes
Soft-tissue and bone tumors represent a heterogeneous group of tumors encompassing more than 100 histologic subtypes today. Identifying genetic aberrations increasingly is important in these tumors for accurate diagnosis. Although gene mutations typically are detected by second-generation sequencing, the identification of structural variants (SVs) and copy number alterations (CNAs) remains challenging and requires various cytogenetic techniques including karyotyping, fluorescence in situ hybridization, and arrays, each with important limitations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 21, 2024 Category: Pathology Authors: Jef Baelen, Barbara Dewaele, Maria Debiec-Rychter, Raphael Sciot, Patrick Sch öffski, Daphne Hompes, Friedl Sinnaeve, Hazem Wafa, Isabelle Vanden Bempt Tags: Regular article Source Type: research
