The Journal of Molecular Diagnostics

25/07/2024

Quality-assured analysis of PIK3CA mutations in HR+/HER2- breast cancer tissue – A story about the need for proficiency testing for high-quality molecular biomarker reporting in precision medicine. Authors from FAU Erlangen-Nürnberg, BZKF, QuIP, Uniklinikum Erlangen, Philipps-Universität Marburg, Medizinische Hochschule Hannover/ MHHnova and Charité - Universitätsmedizin Berlin.

text: https://www.jmdjournal.org/article/S1525-1578(24)00088-6/fulltext

24/07/2024

: Comparison of Real-Time PCR and Digital PCR for Detection of Plasma Virus DNA in Nasopharyngeal Carcinoma. From Association for Molecular Pathology member Dr. Benjamin Pinsky and colleagues from Stanford Pathology and Stanford Medicine.

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Plasma Epstein-Barr virus (EBV) DNA is an established biomarker for endemic nasopharyngeal carcinoma. However, existing real-time quantitative PCR (qPCR) assays are limited by poor interlaboratory reproducibility. This is a barrier to biomarker integration into staging systems and management. It was...

23/07/2024

A Streamlined PENK Methylation Test in Urine DNA, EarlyTect BCD, Effectively Detects Bladder Cancer in Patients with . Authors from VA Greater Los Angeles Healthcare System, Genomictree, Inc, Chungnam National University College of
Medicine, and David Geffen School of Medicine at UCLA.

text: https://loom.ly/g0fUva0

The current noninvasive diagnostic approaches for detecting bladder cancer (BC) often exhibit limited clinical performance, especially for the initial diagnosis. This study aims to evaluate the validity of a streamlined urine-based PENK methylation test called EarlyTect BCD in detecting BC in patien...

23/07/2024

: Multisite Evaluation and Validation of Optical Genome Mapping for Prenatal Genetic Testing. From Association for Molecular Pathology member author Dr. Ravindra Kolhe and colleagues from Columbia University Irving Medical Center, Cincinnati Children's, University of Cincinnati, UR Medicine, UCSF, Brigham and Women's Hospital, Harvard Medical School, Quest Diagnostics, and the Medical College of Georgia.

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Prenatal diagnostic testing of amniotic fluid, chorionic villi, or more rarely, fetal cord blood, is recommended following a positive or unreportable noninvasive cell-free fetal DNA test, abnormal maternal biochemical serum screen, abnormal ultrasound or increased genetic risk for a cytogenomic abno...

22/07/2024

: Validation of the Labcorp Plasma Focus Test to Facilitate Precision Oncology Through Cell-Free DNA Genomic Profiling of Solid Tumors.

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Genomic profiling is critical for precision oncology to guide treatment decisions. Liquid biopsy testing is a complementary approach to tissue testing, particularly when tissue is not readily available. The Labcorp Plasma Focus test is a circulating cell-free DNA genomic profiling test that identifi...

22/07/2024

article: Analytical Validation of the Multitarget Stool RNA Test for Colorectal Cancer Screening. Authors from Washington University School of Medicine in St. Louis, Geneoscopy,

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The multitarget stool RNA (mt-sRNA) test (ColoSense) is a noninvasive diagnostic test that screens for colorectal cancer and advanced adenomas in average-risk individuals aged 45 years and older. The mt-sRNA test incorporates a commercially available f***l immunochemical test, concentration of eight...

19/07/2024

: Assessment of Droplet Digital PCR for the Detection and Absolute Quantification of . Authors from Sorbonne Université, Université de Montpellier, Université de Limoges and Hôpital Pitié Salpêtrière, AP-HP.



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Accurate tools for Toxoplasma gondii detection and quantification can be valuable for the early and effective management of toxoplasmosis. Droplet digital PCR (ddPCR) is a next-generation end-point PCR technique with high performance. The objective of the study was to evaluate the performance of ddP...

18/07/2024

: The Utility of Real-time PCR, Metagenomic Next-generation Sequencing, and Culture in Bronchoalveolar Lavage Fluid for Diagnosis of Pulmonary .

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Timely detection of Aspergillus infection is crucial given the high mortality rate of pulmonary aspergillosis (PA). Here, the diagnostic performances for PA of mycological culture, Aspergillus real-time PCR, and metagenomic next-generation sequencing (mNGS) assay from bronchoalveolar lavage fluid, w...

17/07/2024

Targeted linked-read sequencing for direct haplotype phasing of parental GJB2/SLC26A4 alleles: A universal and dependable noninvasive prenatal diagnosis method applied to autosomal recessive nonsyndromic in at-risk families.

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Noninvasive prenatal diagnosis (NIPD) for autosomal recessive nonsyndromic hearing loss (ARNSHL) has been rarely reported until recent years. Additionally, the existing method can not be used for challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on....

16/07/2024

: RNA Sequencing Identifies Novel NRG1 Fusions in Solid Tumors that Lack Co-Occurring Oncogenic Drivers. Authors from Labcorp, Duke Cancer Institute, Illumina, and Wake Forest University School of Medicine

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15/07/2024

: Validation and Implementation of a Somatic only Tumor Exome for Routine Clinical Application. From Association for Molecular Pathology members at Dartmouth Hitchcock Medical Center.

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Next-generation sequencing–based genomic testing is standard of care for tumor workflows. However, its application across different institutions continues to be challenging given the diversity of needs and resource availability among different institutions globally. Moreover, the use of a variety ...

12/07/2024

Performance Characteristics of a Real-Time PCR assay for Direct Detection of Streptococcus pneumoniae in Clinical Specimens. From Association for Molecular Pathology member author Dr. Leslie A. Wolf and colleagues from University of Louisville.

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Community-acquired pneumonia and complications, such as bacteremia and meningitis due to Streptococcus pneumoniae infection, still occur in at-risk populations, despite the availability of effective vaccines. Laboratory confirmation of S. pneumoniae remains challenging despite advances in blood cult...

12/07/2024

Include a set of Key Points with your next submission to The Journal of Molecular Diagnostics. This short, bulleted list, can summarize the purpose, methods or conclusions presented in the manuscript.

See this sample from a current from Association for Molecular Pathology member author Theresa Boyle.

https://www.jmdjournal.org/article/S1525-1578(24)00101-6/fulltext

11/07/2024

: Preanalytic Methodological Considerations and Sample Quality Control of Circulating miRNAs. Authors from Mirxes.

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As miRNAs emerge as potential circulating biomarkers for the diagnosis or prognosis of a wide variety of diseases, the quantification of miRNA necessitates careful preanalytic considerations and sample quality control becomes crucial. This study comprehensively analyzed the profiles of 356 miRNAs by...

11/07/2024

: Development, validation and implementation of an augmented multi-well, multi-target quantitative PCR-HPV genotyping analysis through software automation, data science and artificial intelligence. Authors from UAntwerpen, Universiteit Gent

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The value of human papillomavirus (HPV) testing for cervical cancer screening is well established, where its use as a primary screening option or as a reflex test after atypical cytology results has recently gained wide acceptance. The importance of full genotyping and viral load determination has b...

10/07/2024

Clinical Validation of a Targeted Next Generation Sequencing Panel for Lymphoid Malignancies. From Association for Molecular Pathology member author Dr. David Viswanatha and colleagues from Mayo Clinic.

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Lymphoid malignancies are a heterogeneous group of hematological disorders characterized by a diverse range of morphologic, immunophenotypic, and clinical features. Next-generation sequencing (NGS) is increasingly being applied to delineate the complex nature of these malignancies and identify high-...

09/07/2024

: Assessing the risk stratification of polygenic risk scores in a Brazilian cohort. Authors from USP - Universidade de São Paulo, Hospital Israelita Albert Einstein, and Bryn Mawr College.

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Polygenic risk scores (PRS) for breast cancer (BC) have a clear clinical utility in risk prediction. PRS transferability across populations and ancestry groups is hampered by population-specific factors, ultimately leading to differences in variant effects, such as linkage disequilibrium (LD) and di...

08/07/2024

: Real-Time, Multiplexed for in Vitro Diagnostics. Authors from Sherlock Biosciences, Inc.

Free in the :

The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has highlighted the need for simple, low-cost, and scalable diagnostics that can be widely deployed for rapid testing. Clustered regularly interspaced short palindromic repeats (CRISPR)–based diagnostics have emerg...

04/07/2024

: Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors.

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Clinical laboratory implementation of next-generation sequencing (NGS)–based constitutional genetic testing has been rapid and widespread. In the absence of widely adopted comprehensive guidance, there remains substantial variability among laboratories in the practice of NGS. One issue of sustaine...

03/07/2024

: Mono- and biallelic replication-coupled gene editing discriminates dominant-negative and loss-of-function variants of DNA mismatch repair genes. Authors from Antoni van Leeuwenhoek and the Hubrecht Institute.

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Replication-coupled gene editing using locked-nucleic-acid-modified single-stranded oligodeoxyribonucleotides (LMOs) can genetically engineer mammalian cells with high precision at single nucleotide resolution. Based on this method, we developed oligonucleotide-directed mutation screening (ODMS) to....

02/07/2024

The Application of Knowledge Engineering via the use of a Biomimetic Digital Twin Ecosystem, Phenotype Driven Variant Analysis, and Exome Sequencing to Understand the Molecular Mechanisms of Disease. From Association for Molecular Pathology member Dr. William Kearns and colleagues from QIAGEN and Brigham and Women's Hospital.

text: https://www.jmdjournal.org/article/S1525-1578(24)00062-X/fulltext

01/07/2024

: Variant Detection in 3’ Exons of PMS2 Using Exome Sequencing Data. From Association for Molecular Pathology member author Dr. Wei Shen and colleagues from Mayo Clinic.

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PMS2 is one of the mismatch repair genes included in routine genetic testing for Lynch syndrome, colorectal, ovarian, and endometrial cancers. PMS2 is also included in the American College of Medical Genetics and Genomics (ACMG) secondary findings gene list in the context of clinical exome and genom...

01/07/2024

New month, new !

The July 2023 issue of The Journal of Molecular Diagnostics is now fully free in the : https://www.jmdjournal.org/issue/S1525-1578(22)X0009-3

28/06/2024

Send in your diagnostic advancements for consideration in The Journal of Molecular Diagnostics today! Submission is free and can be done online: https://www.editorialmanager.com/jmdi/default2.aspx.

JMD is the flagship journal of the Association for Molecular Pathology and we feature progress related to , , and .

28/06/2024

: Improved genetic characterization of congenital adrenal hyperplasia by long-read sequencing compared with multiplex ligation-dependent probe amplification plus Sanger sequencing.

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Genetic analysis of congenital adrenal hyperplasia (CAH) has been challenging due to high homology between CYP21A2 and its pseudogene CYP21A1P. This study aimed to evaluate the clinical utility of long-read sequencing (LRS) in diagnosis of CAH due to 21-hydroxylase deficiency by comparing with multi...

27/06/2024

The July 2024 issue of The Journal of Molecular Diagnostics is now live!

Full issue: https://www.jmdjournal.org/issue/S1525-1578(23)X0010-5

27/06/2024

: Plasma protein profiling to discern indolent from advanced systemic . Authors from Karolinska Institutet and Uppsala University.

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Mastocytosis is a heterogeneous disorder characterized by abnormal mast cell accumulation, in which the clinical severity may be explained by distinct molecular mechanisms. This study aimed to explore plasma protein biomarkers associated with systemic mastocytosis subtypes, as well as the cellular o...

26/06/2024

: Analysis of Clinical Laboratory Detecting Challenging Variants from Exome Sequencing Using Simulated Patient–Parent Trio Sample.

Free in the : https://www.jmdjournal.org/article/S1525-1578(23)00058-2/fulltext

26/06/2024

Focused Exome Sequencing Gives a High Diagnostic Yield in The Indian Sub-Continent. From authors at Revvity.

Full text: https://www.jmdjournal.org/article/S1525-1578(24)00063-1/fulltext

25/06/2024

: Advances in host depletion and pathogen enrichment methods for rapid sequencing-based diagnosis of bloodstream infection. Authors from University of Glasgow and NHS Greater Glasgow and Clyde.

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Bloodstream infection remains a major cause of morbidity and death worldwide. Timely and appropriate treatment can reduce mortality among critically ill patients. Current diagnostic methods are too slow to inform precise antibiotic choice leading to the prescription of empirical antibiotics which ma...