Clinical implementation of MetaFusion for accurate cancer-driving fusion detection from RNA Sequencing
Oncogenic fusion genes may be identified from next-generation sequencing data, typically RNA-Seq. However, in a clinical setting, identifying these alterations is challenging against a background of non-relevant fusion calls that reduce workflow precision and specificity. Furthermore, although numerous algorithms have been developed to detect fusions in RNA-Seq, there are variations in their individual sensitivities. Here this problem was addressed by introducing MetaFusion into clinical use. Its utility was illustrated when applied to both whole transcriptome and targeted sequencing datasets. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 23, 2023 Category: Pathology Authors: Michael Apostolides, Michael Li, Anthony Arnoldo, Michelle Ku, Mia Husi ć, Arun K. Ramani, Michael Brudno, Andrei Turinsky, Cynthia Hawkins, Robert Siddaway Tags: Regular Article Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 15, 2023 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 15, 2023 Category: Pathology Source Type: research
Toward Cytogenomics
The current advances and success of next-generation sequencing hold the potential for the transition of cancer cytogenetics toward comprehensive cytogenomics. However, the conventional use of short reads impedes the resolution of chromosomal aberrations with current next-generation sequencing modalities. Thus, this study evaluated the detection and reproducibility of extensive copy number alterations and chromosomal translocations using long-read Oxford Nanopore Technologies whole-genome sequencing compared with short-read Illumina sequencing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 7, 2023 Category: Pathology Authors: Marcus H øy Hansen, Oriane Cédile, Marie Louise Grube Kjeldsen, Mads Thomassen, Birgitte Preiss, Nils von Neuhoff, Niels Abildgaard, Charlotte Guldborg Nyvold Tags: Technical advance Source Type: research
Development of a Rapid and High-Throughput Multiplex Real-Time PCR Assay for Mycoplasma hominis and Ureaplasma Species
Bacterial commensals of the human genitourinary tract, Mycoplasma hominis and Ureaplasma species (parvum and urealyticum) can be sexually transmitted, with the potential to cause nongonococcal urethritis, pelvic inflammatory disease, and infertility. Mycoplasma hominis and Ureaplasma species may also cause severe invasive infections in immunocompromised patients. Current culture-based methods for Mycoplasma/Ureaplasma identification are costly and laborious, with a turnaround time between 1 and 2 weeks. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 7, 2023 Category: Pathology Authors: June L. Chan, Stacey Cer ón, Stephanie M. Horiuchi, Jewell P. Yap, Erika G. Chihuahua, Allison T. Tsan, Edwin Kamau, Shangxin Yang Tags: Regular article Source Type: research
Toward cytogenomics: Technical assessment of long-read Nanopore whole-genome sequencing for detecting large chromosomal alterations in mantle cell lymphoma
The current advances and success of next-generation sequencing (NGS) hold the potential for the transition of cancer cytogenetics toward comprehensive cytogenomics. However, the conventional usage of short reads impedes the resolution of chromosomal aberrations with current NGS modalities. Thus, this study evaluated the detection and reproducibility of extensive copy-number alterations and chromosomal translocations using long-read Oxford Nanopore Technologies (ONT) whole-genome sequencing compared to short-read Illumina sequencing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 7, 2023 Category: Pathology Authors: Marcus H øy Hansen, Oriane Cédile, Marie Louise Grube Kjeldsen, Mads Thomassen, Birgitte Preiss, Nils von Neuhoff, Niels Abildgaard, Charlotte Guldborg Nyvold Tags: Technical Advance Source Type: research
Development of a Rapid and High Throughput Multiplex Real-time PCR Assay for Mycoplasma hominis and Ureaplasma species
Bacterial commensals of the human genitourinary tract, Mycoplasma hominis and Ureaplasma species (parvum and urealyticum) can be sexually transmitted, with the potential to cause non-gonococcal urethritis, pelvic inflammatory disease, and infertility. M. hominis and Ureaplasma spp. may also cause severe invasive infections in immunocompromised patients. Current culture-based methods for Mycoplasma/Ureaplasma identification are costly and laborious, with a turnaround time between 1-2 weeks. We developed a high-throughput, real-time multiplex PCR assay for the rapid detection of M. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 7, 2023 Category: Pathology Authors: June L. Chan, Stacey Cer ón, Stephanie M. Horiuchi, Jewell P. Yap, Erika G. Chihuahua, Allison T. Tsan, Edwin Kamau, Shangxin Yang Tags: Regular Article Source Type: research
Genetic factors contribute to the phenotypic variability in GJB2-related hearing impairment
Recessive variants in GJB2 are the most important genetic cause of sensorineural hearing impairment (SNHI) worldwide. Phenotypes vary significantly in GJB2-related SNHI, even in patients with identical variants. For instance, patients homozygous for the GJB2 p.V37I variant, which is highly prevalent in the Asian populations, usually present with mild-to-moderate SNHI; yet severe-to-profound SNHI is occasionally observed in approximately 10% of p.V37I homozygotes. To investigate the genomic underpinnings of the phenotypic variability, we performed next-generation sequencing of GJB2 and other deafness genes in 63 p.V37I homo...
Source: Journal of Molecular Diagnostics - September 7, 2023 Category: Pathology Authors: Yu-Ting Chiang, Pei-Hsuan Lin, Ming-Yu Lo, Hsin-Lin Chen, Chen-Yu Lee, Cheng-Yu Tsai, Yin-Hung Lin, Shih-Feng Tsai, Tien-Chen Liu, Chuan-Jen Hsu, Pei-Lung Chen, Jacob Shu-Jui Hsu, Chen-Chi Wu Tags: Regular Article Source Type: research
Mutational Signatures in Cancer
Patterns of somatic mutations have emerged from the broad sequencing of human cancer genomes. These mutational signatures reflect mechanisms of mutagenesis and DNA repair defects and represent an emerging class of cancer biomarkers. The appropriate interpretation of mutational signatures from sequencing assays holds implications in the reporting of molecular diagnostic results for patients with cancer. This brief review describes the scientific principles, laboratory considerations, and emerging clinical applications of mutational signature analysis from clinical cancer genomes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 24, 2023 Category: Pathology Authors: Fei Dong, Kurtis D. Davies Tags: Special Article Source Type: research
Mutational Signatures in Cancer: Laboratory Considerations and Emerging Applications
Patterns of somatic mutations have emerged from the broad sequencing of human cancer genomes. These mutational signatures reflect mechanisms of mutagenesis and DNA repair defects and represent an emerging class of cancer biomarkers. The appropriate interpretation of mutational signatures from sequencing assays holds implications in the reporting of molecular diagnostic results for patients with cancer. This brief review describes the scientific principles, laboratory considerations, and emerging clinical applications of mutational signature analysis from clinical cancer genomes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 24, 2023 Category: Pathology Authors: Fei Dong, Kurtis D. Davies Tags: Review Source Type: research
Noninvasive Evaluation of Fetal Zygosity in Twin Pregnancies Involving a Binary Analysis of Single-Nucleotide Polymorphisms
Twin pregnancy constitutes significant risks for maternal and fetal health, which is usually detected by ultrasound examination at early gestation. However, the imaging-based approach may not accurately identify all twins confounded by practical or clinical variables. The analysis of fetal cell-free DNA in noninvasive prenatal screening assays can completement the ultrasound method for twin detection, which differentiates fraternal or identical twins based on their distinct genotypes. Here, a new noninvasive prenatal screening employing high-coverage next-generation sequencing for targeted nucleotide polymorphisms was deve...
Source: Journal of Molecular Diagnostics - August 19, 2023 Category: Pathology Authors: Yanlin Wang, Xiang Qiu, Songchang Chen, Dong Pan, Renyi Hua, Shuyuan Li, Yiyao Chen, Nina Pan, Xiaoqiang Cai, Jianli Li, Xin Zhao, Jing Wang, Ruilin Jing, Guangxin Xiang, Zhiwei Zhang, He-Feng Huang, Chenming Xu, Jinglan Zhang Tags: Regular article Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 19, 2023 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 19, 2023 Category: Pathology Source Type: research
Circulating Tumor DNA
For patients with BRAF wild-type stage III and IV melanoma, there is an urgent clinical need to identify prognostic biomarkers and biomarkers predictive of treatment response. Circulating tumor DNA (ctDNA) is emerging as a blood-based biomarker and has shown promising results for many cancers, including melanoma. The purpose of this study was to identify targetable, tumor-derived mutations in patient blood that may lead to treatment alternatives and improved outcomes for patients with BRAF-negative melanoma. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 4, 2023 Category: Pathology Authors: Lauren G. Aoude, Sandra Brosda, Jessica Ng, James M. Lonie, Clemence J. Belle, Kalpana Patel, Lambros T. Koufariotis, Scott Wood, Victoria Atkinson, B. Mark Smithers, John V. Pearson, Nicola Waddell, Andrew P. Barbour, Vanessa F. Bonazzi Tags: Regular article Source Type: research
A Highly Sensitive Pan-Cancer Test for Microsatellite Instability
Microsatellite instability (MSI) is an evolving biomarker for cancer detection and treatment. MSI was first used to identify patients with Lynch syndrome, a hereditary form of colorectal cancer (CRC), but has recently become indispensable in predicting patient response to immunotherapy. To address the need for pan-cancer MSI detection, a new multiplex assay was developed that utilizes novel long mononucleotide repeat markers (LMR) to improve sensitivity. 469 tumor samples from 20 different cancer types, including 319 from patients with Lynch syndrome, were tested for MSI using the new LMR MSI Analysis System. (Source: Jour...
Source: Journal of Molecular Diagnostics - August 4, 2023 Category: Pathology Authors: Jeffery W. Bacher, Eshwar B. Udho, Ethan E. Strauss, Irina Vyazunova, Steven Gallinger, Daniel D. Buchanan, Rish K. Pai, Allyson S. Templeton, Douglas R. Storts, James R. Eshleman, Richard B. Halberg Tags: Regular Article Source Type: research
