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
Minimal/measurable residual disease (MRD) 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 seen at our institution. (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 Article Source Type: research
Deep intronic PAH variants explain missing heritability in hyperphenylalaninemia
Phenylalanine hydroxylase (PAH) deficiency or phenylketonuria (PKU) is the most common cause of hyperphenylalaninemia (HPA), and approximately 5% of patients remain genetically unsolved. Identifying deep intronic PAH variants may help improve their molecular diagnostic rate. Next-generation sequencing was utilized to detect the whole PAH gene in 96 genetically unsolved HPA patients from 2013 to 2022. The effects of deep intronic variants on pre-mRNA splicing were investigated by minigene-based assay. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 25, 2023 Category: Pathology Authors: Xiaomei Luo, Ruifang Wang, Yu Sun, Wenjuan Qiu, Deyun Lu, Yu Wang, Zhuwen Gong, Huiwen Zhang, Lianshu Han, Lili Liang, Xuefan Gu, Yongguo Yu, Bing Xiao Tags: Regular Article Source Type: research
CRISPR-Cas9 Targeted Enrichment and Next-Generation Sequencing for Mutation Detection
Despite the rapid application of next-generation sequencing (NGS) technologies, target sequencing in regions of the genome is often required to diagnose many genetic diseases. Target enrichment can be an effective factor in reducing the cost of sequencing and the duration of sequencing. Recently, several clustered system regularly interspaced short palindromic repeats (CRISPR) –based methods (amplification-free sequencing) have been developed to target enrichment in combination with one of the NGS platforms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 23, 2023 Category: Pathology Authors: Mehrdad Malekshoar, Sajad Ataei Azimi, Arastoo Kaki, Leila Mousazadeh, Jamshid Motaei, Majid Vatankhah Tags: Review Source Type: research
CRISPR-Cas9 Targeted Enrichment and Next Generation Sequencing for Mutations Detection
Despite the rapid application of next-generation sequencing (NGS) technologies, target sequencing in regions of the genome is often required to diagnose many genetic diseases. Target enrichment can be a very effective factor in reducing the cost of sequencing and the duration of sequencing. Recently, several CRISPR-based methods (amplification-free sequencing) have been developed to target enrichment in combination with one of the NGS platforms. CRISPR-based target enrichment strategies act as an auxiliary tool to improve NGS analytical performance, thereby indirectly facilitating nucleic acid detection. (Source: Journal o...
Source: Journal of Molecular Diagnostics - February 23, 2023 Category: Pathology Authors: Mehrdad Malekshoar, Sajad Ataei Azimi, Arastoo Kaki, Leila Mousazadeh, Jamshid Motaei, Majid Vatankhah Tags: Review Source Type: research
Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests
This report describes the results from the JFDI (Just Freaking Do It) study, a BLOODPAC initiative to develop standards on the use of contrived materials mimicking cell-free circulating tumor DNA, to comparatively evaluate clinical laboratory testing procedures. Nine independent laboratories tested the concordance, sensitivity, and specificity of commercially available contrived materials with known variant-allele frequencies (VAFs) ranging from 0.1% to 5.0%. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 22, 2023 Category: Pathology Authors: Kyle M. Hernandez, Kelli S. Bramlett, Phaedra Agius, Jonathan Baden, Ru Cao, Omoshile Clement, Adam S. Corner, Jonathan Craft, Dennis A. Dean, Jonathan R. Dry, Kristina Grigaityte, Robert L. Grossman, James Hicks, Nikki Higa, Timothy R. Holzer, Jeffrey Je Tags: Regular article Source Type: research
Reviewer Acknowledgment
The Editors gratefully acknowledge the generous assistance of the following reviewers who served The Journal of Molecular Diagnostics between January 1 and December 31, 2022. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 22, 2023 Category: Pathology Tags: Reviewer acknowledgment Source Type: research
Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases
This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 22, 2023 Category: Pathology Authors: M. Anwar Iqbal, Ulrich Broeckel, Brynn Levy, Steven Skinner, Nikhil S. Sahajpal, Vanessa Rodriguez, Aaron Stence, Kamel Awayda, Gunter Scharer, Cindy Skinner, Roger Stevenson, Aaron Bossler, Peter L. Nagy, Ravindra Kolhe Tags: Regular article Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 22, 2023 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 22, 2023 Category: Pathology Source Type: research
Next-CLL, a New Next-Generation Sequencing –Based Method for Assessment of IGHV Gene Mutational Status in Chronic Lymphoid Leukemia
We present a new method called Next-CLL, a ready-to-use strategy to evaluate IGHV gene mutation status using any NGS device (including 2 × 150 bp sequenc ers) in routine diagnostic laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 9, 2023 Category: Pathology Authors: Estelle Bourbon, Kaddour Chabane, Isabelle Mosnier, Anne Bouvard, Florian Thonier, Emmanuelle Ferrant, Anne-Sophie Michallet, St éphanie Poulain, Sandrine Hayette, Pierre Sujobert, Sarah Huet Tags: Regular article Source Type: research
Next-CLL
We present a new method called Next-CLL, a ready-to-use strategy to evaluate IGHV gene mutation status using any NGS device (including 2 × 150 bp sequenc ers) in routine diagnostic laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 9, 2023 Category: Pathology Authors: Estelle Bourbon, Kaddour Chabane, Isabelle Mosnier, Anne Bouvard, Florian Thonier, Emmanuelle Ferrant, Anne-Sophie Michallet, St éphanie Poulain, Sandrine Hayette, Pierre Sujobert, Sarah Huet Tags: Regular article Source Type: research
Minimizing sample failure rates for challenging clinical tumor samples
Identification of somatic variants in cancer by high-throughput sequencing has become common clinical practice largely because many of these variants may be predictive biomarkers for targeted therapies. However, there can be high sample quality control (QC) failure rates for some tests preventing the return of results.SLIMamp is a patented technology that has been incorporated into commercially available cancer NGS testing kits with the claimed advantage that these kits can interrogate challenging formalin-fixed paraffin-embedded tissue (FFPET) samples with low tumor purity, poor DNA quality, and/or low input DNA, resultin...
Source: Journal of Molecular Diagnostics - February 9, 2023 Category: Pathology Authors: J. Lynn Fink, Binny Jaradi, Nathan Stone, Lisa Anderson, Paul J. Leo, Mhairi Marshall, Jonathan Ellis, Paul M. Waring, Kenneth O ’Byrne Tags: Regular Article Source Type: research
Next-CLL: a new next generation sequencing-based method for assessment of IGHV gene mutational status in chronic lymphoid leukemia
Current guidelines for patients with Chronic Lymphocytic Leukemia (CLL) recommend mutation status determination of the clonotypic IGHV gene prior to treatment initiation in order to guide the choice of the first-line therapy. Currently, commercially available next-generation sequencing (NGS) solutions have technical constraints, as they necessitate at least a 2x300 bp sequencing, which restricts their use for routine practice. The cost of the commercial kits also represents an important drawback. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 9, 2023 Category: Pathology Authors: Estelle Bourbon, Kaddour Chabane, Isabelle Mosnier, Anne Bouvard, Florian Thonier, Emmanuelle Ferrant, Anne-Sophie Michallet, St éphanie Poulain, Sandrine Hayette, Pierre Sujobert, Sarah Huet Tags: Regular Article Source Type: research
Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing
The standard-of-care (SOC) diagnostic prenatal testing includes a combination of cytogenetic methods such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA) using either direct or cultured amniocytes or chorionic villi sampling (CVS). However, each technology has its limitations: karyotyping has a low resolution (>5Mb), FISH is targeted, and CMA does not detect balanced structural variants (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially to reach a genetic diagnosis. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 7, 2023 Category: Pathology Authors: Nikhil Shri Sahajpal, Ashis K. Mondal, Timothy Fee, Benjamin Hilton, Lawrence Layman, Alex R. Hastie, Alka Chaubey, Barbara R. DuPont, Ravindra Kolhe Tags: Regular Article Source Type: research
