Evaluation of Sensitive Urine DNA-based PENK Methylation Test for Detecting Bladder Cancer in Patients with Hematuria
This study introduces and validates a highly sensitive urine-based DNA methylation test. The test improves sensitivity in detecting PENK methylation in urine DNA using Linear Target Enrichment (LTE) followed by quantitative methylation-specific PCR (qMSP) (mePENK-LTE/qMSP). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 14, 2023 Category: Pathology Authors: Tae Jeong Oh, Ji Yong Lee, Yangyei Seo, Min A. Woo, Jae Sung Lim, Yong Gil Na, Ki Hak Song, Bo-Ram Bang, Justin Junguek Lee, Ju Hyun Shin, Sungwhan An Tags: Regular Article Source Type: research
Partitioning for Easy Multiplexing
Clinical genome-wide next-generation sequencing (NGS) has brought new challenges to genetic laboratories. The identification of numerous patient-specific variants that may require to be screened for on multiple other samples poses an issue when striving for time and cost-effectiveness. Here, we propose d-multiSeq, a straightforward method utilizing the advantages of droplet PCR for multiplexing combined with amplicon-based NGS. By comparing d-multiSeq with a standard multiplex amplicon-based NGS, we showed that partitioning prevents the amplification competition seen when multiplexing and leads to a homogeneous representat...
Source: Journal of Molecular Diagnostics - June 9, 2023 Category: Pathology Authors: Alexia Kinoo, Aur élie Caye-Eude, Yoann Vial, Hélène Cavé, Chloé Arfeuille Tags: Regular article Source Type: research
Partitioning for easy multiplexing: a versatile droplet PCR application for clone monitoring in tumors
Clinical genome-wide next generation sequencing (NGS) has brought new challenges to genetic laboratories. The identification of numerous patient-specific variants which may require to be screened for on multiple other samples poses an issue when striving for time and cost effectiveness. Here we propose d-multiSeq, a straightforward method utilizing the advantages of droplet PCR (dPCR) for multiplexing combined with amplicon-based NGS. By comparing d-multiSeq with a standard multiplex amplicon-based NGS we showed that partitioning prevents the amplification competition seen when multiplexing and lead to a homogeneous repres...
Source: Journal of Molecular Diagnostics - June 9, 2023 Category: Pathology Authors: Alexia Kinoo, Aur élie Caye-Eude, Yoann Vial, Hélène Cavé, Chloé Arfeuille Tags: Regular Article Source Type: research
Abstracts of the AMP Europe 2023 Congress
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 1, 2023 Category: Pathology Source Type: research
Author Index
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 1, 2023 Category: Pathology Source Type: research
MICon Contamination Detection Workflow for Next-Generation Sequencing Laboratories Using Microhaplotype Loci and Supervised Learning
Innovation in sequencing instrumentation is increasing the per-batch data volumes and decreasing the per-base costs. Multiplexed chemistry protocols after the addition of index tags have further contributed to efficient and cost-effective sequencer utilization. With these pooled processing strategies, however, comes an increased risk of sample contamination. Sample contamination poses a risk of missing critical variants in a patient sample or wrongly reporting variants derived from the contaminant, which are particularly relevant issues in oncology specimen testing in which low variant allele frequencies have clinical rele...
Source: Journal of Molecular Diagnostics - May 24, 2023 Category: Pathology Authors: Jagadheshwar Balan, Tejaswi Koganti, Shubham Basu, Michelle A. Dina, Cody J. Artymiuk, Emily G. Barr Fritcher, Katie E. Halverson, Xianglin Wu, Garrett Jenkinson, David S. Viswanatha Tags: Regular articles Source Type: research
MICon
Innovation in sequencing instrumentation is increasing the per-batch data volumes and decreasing the per-base costs. Multiplexed chemistry protocols after the addition of index tags have further contributed to efficient and cost-effective sequencer utilization. With these pooled processing strategies, however, comes an increased risk of sample contamination. Sample contamination poses a risk of missing critical variants in a patient sample or wrongly reporting variants derived from the contaminant, which are particularly relevant issues in oncology specimen testing in which low variant allele frequencies have clinical rele...
Source: Journal of Molecular Diagnostics - May 24, 2023 Category: Pathology Authors: Jagadheshwar Balan, Tejaswi Koganti, Shubham Basu, Michelle A. Dina, Cody J. Artymiuk, Emily G. Barr Fritcher, Katie E. Halverson, Xianglin Wu, Garrett Jenkinson, David S. Viswanatha Tags: Regular article Source Type: research
MICon – A Contamination Detection Workflow for NGS Laboratories using Microhaplotype Locus and Supervised Learning.
Innovation in sequencing instrumentation is increasing the per-batch data volumes and decreasing the per-base costs. Multiplexed chemistry protocols after the addition of index tags have further contributed to efficient and cost-effective sequencer utilization. With these pooled processing strategies, however, comes an increased risk of sample contamination. Sample contamination poses a risk of missing critical variants in a patient sample or wrongly reporting variants derived from the contaminant, which are particularly relevant issues in oncology specimen testing where low variant allele frequencies have clinical relevan...
Source: Journal of Molecular Diagnostics - May 24, 2023 Category: Pathology Authors: Jagadheshwar Balan, Tejaswi Koganti, Shubham Basu, Michelle A. Dina, Cody J. Artymiuk, Emily G. Barr Fritcher, Katie E. Halverson, Xianglin Wu, Garrett Jenkinson, David S. Viswanatha Tags: Regular Article Source Type: research
Molecular and cytogenetic features of NTRK fusions enriched in BRAF and RET double-negative papillary thyroid cancer
Rare NTRK-driven malignant neoplasms can be effectively inhibited by anti-TRK agents. The discovery of NTRK1/2/3-rich tumours in papillary thyroid cancer (PTC) patients is a precondition for the rapid identification of NTRK fusion tumours. Knowledge of NTRK gene activation is critical to accurately detect NTRK status. A total of 229 BRAF V600E-negative samples from PTC patients were analysed in this study. Break-apart fluorescence in situ hybridisation (FISH) was performed to detect RET fusion. NTRK status was analysed using FISH, DNA- and RNA-based next-generation sequencing (NGS), and quantitative reverse transcription-p...
Source: Journal of Molecular Diagnostics - May 24, 2023 Category: Pathology Authors: Shafei Wu, Yuanyuan Liu, Kaimi. Li, Zhiyong Liang, Xuan Zeng Tags: Regular Article Source Type: research
Comparison of the Diagnostic Performance of MeltPro and Next-Generation Sequencing in Determining Fluoroquinolone Resistance in Multidrug-Resistant Tuberculosis Isolates
This study systematically investigated the performance of MeltPro and next-generation sequencing in the diagnosis of fluoroquinolone (FQ) resistance among multidrug-resistant tuberculosis patients and explored the relationship between nucleotide alteration and the level of phenotypic susceptibility to FQs. From March 2019 to June 2020, a feasibility and validation study with both MeltPro and next-generation sequencing was performed in 126 patients with multidrug-resistant tuberculosis. Using phenotypic drug susceptibility testing as the gold standard, 95.3% (82 of 86) of ofloxacin-resistant isolates were identified correct...
Source: Journal of Molecular Diagnostics - May 17, 2023 Category: Pathology Authors: Yan Hu, Yuqing Chi, Xin Feng, Fengping Yu, Haoran Li, Yuanyuan Shang, Junhua Pan, Yu Pang Tags: Regular articles Source Type: research
Analysis of Clinical Laboratory Detecting Challenging Variants from Exome Sequencing Using Simulated Patient –Parent Trio Sample
To date, there has been no systematic analysis for the clinical laboratory in detecting technically challenging variants using the trio-based exome sequencing (ES) approach. Here, we present an interlaboratory pilot proficiency testing study that used synthetic patient –parent specimens to assess the detection of challenging variants with de novo dominant inheritance modes for neurodevelopmental disorders using various trio-based ES. In total, 27 clinical laboratories that performed diagnostic exome analyses participated in the survey. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 17, 2023 Category: Pathology Authors: Kuo Zhang, Guigao Lin, Yanxi Han, Rongxue Peng, Jinming Li Tags: Regular articles Source Type: research
Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 17, 2023 Category: Pathology Source Type: research
Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 17, 2023 Category: Pathology Source Type: research
Recommendations for Next-Generation Sequencing Germline Variant Confirmation
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 sustained discussion in the field is whether and to what extent orthogonal con firmation of genetic variants identified by NGS are necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirm...
Source: Journal of Molecular Diagnostics - May 17, 2023 Category: Pathology Authors: Kristy R. Crooks, Kelly D. Farwell Hagman, Diana Mandelker, Avni Santani, Ryan J. Schmidt, Robyn L. Temple-Smolkin, Stephen E. Lincoln Tags: Special article Source Type: research
Recommendations for Next-Generation Sequencing Germline Variant Confirmation: A Joint Report of the Association for Molecular Pathology and National Society of Genetic Counselors
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 sustained discussion in the field is whether and to what extent orthogonal confirmation of genetic variants identified by NGS is necessary or helpful. The Association for Molecular Pathology Clinical Practice Committee convened the NGS Germline Variant Confirmation Working Group to assess current evidence regarding orthogonal confirmation...
Source: Journal of Molecular Diagnostics - May 17, 2023 Category: Pathology Authors: Kristy R. Crooks, Kelly D. Farwell Hagman, Diana Mandelker, Avni Santani, Ryan J. Schmidt, Robyn L. Temple-Smolkin, Stephen E. Lincoln Tags: Special Article Source Type: research
