Phylogenetic analysis of Trypanosoma cruzi from pregnant women and newborns from Argentina, Honduras, and Mexico suggests an association of parasite haplotypes with congenital transmission of the parasite
Trypanosoma cruzi, the causative agent of Chagas disease, exhibits a high genetic variability and has been classified into six discrete typing units (DTUs) named TcI-TcVI. This genetic diversity is believed to be associated with clinical characteristics and outcomes, but evidences supporting such associations have been limited. Here we performed a phylogenetic analysis of T. cruzi sequences of the mini-exon intergenic region obtained from a large cohort of pregnant women and newborns from Argentina, Honduras, and Mexico, to assess parasite genetic diversity and possible associations with congenital transmission. (Source: J...
Source: Journal of Molecular Diagnostics - August 23, 2019 Category: Pathology Authors: Claudia Herrera, Carine Truyens, Eric Dumonteil, Jackeline Alger, Sergio Sosa-Estani, Maria Luisa Cafferata, Luz Gibbons, Alvaro Ciganda, Maria Luisa Matute, Concepcion Zuniga, Yves Carlier, Pierre Buekens Tags: Regular Article Source Type: research

A Novel Next-Generation Sequencing Approach to Detecting Microsatellite Instability (MSI) and Pan-Tumor Characterization of One Thousand MSI-High Cases in 67,000 Patient Samples
Microsatellite instability (MSI) is an important biomarker for predicting response to immune checkpoint inhibitor therapy, as emphasized by the recent checkpoint inhibitor approval for MSI-H solid tumors. Here we describe and validate a novel method for determining MSI status from a next-generation sequencing comprehensive genomic profiling assay using formalin-fixed, paraffin-embedded samples. This method is 97% (65/67) concordant with current standards, PCR and immunohistochemistry. We further apply this method to over 67,000 patient tumor samples to identify genes and pathways that are enriched in MSI-stable (MSS) or MS...
Source: Journal of Molecular Diagnostics - August 22, 2019 Category: Pathology Authors: Sally E. Trabucco, Kyle Gowen, Sophia L. Maund, Eric Sanford, David A. Fabrizio, Michael J. Hall, Evgeny Yakirevich, Jeffrey P. Gregg, Phil J. Stephens, Garrett M. Frampton, Priti S. Hegde, Vincent A. Miller, Jeffrey S. Ross, Ryan J. Hartmaier, Shih-Min A Source Type: research

Multicenter Evaluation of the Fully Automated PCR-Based Idylla EGFR Mutation Assay on Formalin-Fixed, Paraffin-Embedded Tissue of Human Lung Cancer
Before initiating treatment of advanced non –small-cell lung cancer with tyrosine kinase inhibitors (eg, erlotinib, gefitinib, osimertinib, and afatinib), which inhibit the catalytic activity of epidermal growth factor receptor (EGFR), clinical guidelines require determining the EGFR mutational status for activating (EGFR exons 18, 19, 20, or 21) and resistance (EGFR exon 20) mutations. The EGFR resistance mutation T790M should be monitored at cancer progression. The Idylla EGFR Mutation Assay, performed on the Idylla molecular diagnostics platform, is a fully automated ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 21, 2019 Category: Pathology Authors: Sol ène M. Evrard, Estelle T. Clermont, Isabelle Rouquette, Samuel Murray, Sebastian Dintner, Yun-Chung Nam-Apostolopoulos, Beatriz Bellosillo, Mar V. Rodriguez, Ernest Nadal, Klaus H. Wiedorn, Linea Melchior, Emma Andrew, Mary Jones, Jennifer Ridgway, C Source Type: research

Short DNA Probes Developed for Sample Tracking and Quality Assurance in Gene Panel  Testing
Both multiplexing and target-enrichment technologies are key to reducing the cost of genetic testing using next-generation sequencing (NGS). Many diagnostic laboratories routinely handle thousands of targeted resequencing samples, leading to an increased risk of accidental sample mix-ups and cross contamination. Herein, we present a short DNA fragment that can be spiked into the original genomic DNA (gDNA) or whole blood sample and tracked through to the final targeted resequencing data. This DNA fragment comprises a 15-bp unique index sequence assembled with a 120-bp fixed sequence designed for recovery in a hybridization...
Source: Journal of Molecular Diagnostics - August 21, 2019 Category: Pathology Authors: Ryoji Fujiki, Makoto Ikeda, Osamu Ohara Source Type: research

Multi-Center Evaluation of the Fully Automated PCR-Based Idylla EGFR Mutation Assay on Formalin-Fixed, Paraffin-Embedded Tissue of Human Lung Cancer
Before initiating treatment of advanced non –small-cell lung cancer with tyrosine kinase inhibitors (eg, erlotinib, gefitinib, osimertinib, afatinib), which inhibit the catalytic activity of epidermal growth factor receptor (EGFR), clinical guidelines require determining the EGFR mutational status for activating (EGFR exons 18, 19, 20, or 2 1) and resistance mutations (EGFR exon 20). The EGFR resistance mutation T790M should be monitored at cancer progression. The Idylla EGFR Mutation Assay performed on the Idylla molecular diagnostics platform is a fully automated ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 21, 2019 Category: Pathology Authors: Sol ène M. Evrard, Estelle Taranchon Clermont, Isabelle Rouquette, Samuel Murray, Sebastian Dintner, Yun-Chung Nam-Apostolopoulos, Beatriz Bellosillo, Mar Varela Rodriguez, Ernest Nadal, Klaus Hermann Wiedorn, Linea Melchior, Emma Andrew, Mary Jones, Jen Source Type: research

Short DNA Probes Developed for Sample Tracking and Quality Assurance in Gene Panel Testing
Both multiplexing and target-enrichment technologies are key to reducing the cost of genetic testing using next-generation sequencing (NGS). Many diagnostic laboratories routinely handle thousands of targeted re-sequencing samples, leading to an increased risk of accidental sample mix-ups and cross-contamination. Here, we present a short DNA fragment that can be spiked into the original genomic DNA (gDNA) or whole blood sample and tracked through to the final targeted re-sequencing data. This DNA fragment comprises a 15 bp unique index sequence assembled with a 120 bp fixed sequence designed for recovery in a hybridization...
Source: Journal of Molecular Diagnostics - August 21, 2019 Category: Pathology Authors: Ryoji Fujiki, Makoto Ikeda, Osamu Ohara Source Type: research

Evaluation, Validation, and Implementation of the Idylla System as Rapid Molecular Testing for Precision Medicine
We describe our evaluation, validation, and implementation of this system for routine testing of BRAF, EGFR, KRAS, and NRAS using formalin-fixed, paraffin-embedded cancer samples. All four Idylla test systems showed excellent concordance with reference methods. The analytical sensitivity ranged from 94.66% to 100%, depending on the cartridge, and specificity was 100%. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Authors: Huiya Huang, Stephanie Springborn, Kiefer Haug, Kaitlyn Bartow, Hasan Samra, Smitha Menon, Alexander C. Mackinnon Tags: Regular article Source Type: research

Integration Standardization and Diagnostics Oversight of Laboratory Testing
This editorial highlights the article by Schreier et  al that emphasizes on reforming the process for regulating laboratory developed testing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Authors: Barbara Zehnbauer Tags: Editorial Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Source Type: research

Gene Mosaicism Screening Using Single-Molecule Molecular Inversion Probes in Routine Diagnostics for Systemic Autoinflammatory Diseases
Diagnosis of systemic autoinflammatory diseases (SAIDs) is often difficult to achieve and can delay the start of proper treatments and result in irreversible organ damage. In several patients with dominantly inherited SAID, postzygotic mutations have been detected as the disease-causing gene defects. Mutations with allele frequencies (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Authors: Benjamin Kant, Ellen C. Carbo, Iris Kokmeijer, Jelske J.M. Oosterman, Joost Frenkel, Morris A. Swertz, Johannes K. Ploos van Amstel, Juan I. Ar óstegui, Marco J. Koudijs, Mariëlle Elisabeth van Gijn Tags: Technical advance Source Type: research

Variant Call Format –Diagnostic Annotation and Reporting Tool
In this article, we introduce the variant call format –diagnostic annotation and reporting tool (VCF-DART), a customized analysis pipeline tool for the rapid annotation of variants from exome or genome sequencing and the generation of reports for genetic diagnostics. VCF-DART uses custom gene lists to categorize variants into specific analysis tiers and to subcategorize them on the basis of standard parameters to facilitate the rapid interrogation of potentially pathogenic variants by human operators. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Authors: Miles C. Benton, Robert A. Smith, Larisa M. Haupt, Heidi G. Sutherland, Paul J. Dunn, Cassie L. Albury, Neven Maksemous, Rodney Lea, Lyn Griffiths Tags: Technical advance Source Type: research

Gene Mosaicism Screening Using Single Molecule Molecular Inversion Probes in Routine Diagnostics for Systemic Autoinflammatory Diseases
Diagnosis of systemic autoinflammatory diseases (SAID) is often difficult to achieve and can delay the start of proper treatments and result in irreversible organ damage. In several patients with dominantly-inherited SAID, postzygotic mutations have been detected as the disease-causing gene defects. Mutations with allele frequencies (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Authors: Benjamin Kant, Ellen C. Carbo, Iris Kokmeijer, Jelske J.M. Oosterman, Joost Frenkel, Morris A. Swertz, Johannes Kristian Ploos van Amstel, Juan Ignacio Ar óstegui, Marco J. Koudijs, Mariëlle Elisabeth van Gijn Tags: Technical Advance Source Type: research

Variant Call Format (VCF)-Diagnostic Annotation and Reporting Tool (VCF-DART) A Customizable Analysis Pipeline for Identification of Clinically Relevant Genetic Variants in Next-Generation Sequencing Data
In this paper, we introduce variant call format-diagnostic annotation and reporting tool (VCF-DART), a customized analysis pipeline tool for the rapid annotation of variants from exome or genome sequencing and the generation of reports for genetic diagnostics. VCF-DART uses custom gene lists to categorize variants into specific analysis tiers and to subcategorize them based on standard parameters to facilitate the rapid interrogation of potentially pathogenic variants by human operators. The tool utilizes publicly available databases to identify a range of data to assist with variant classification and curation processes a...
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Authors: Miles C. Benton, Robert A. Smith, Larisa M. Haupt, Heidi G. Sutherland, Paul J. Dunn, Cassie L. Albury, Neven Maksemous, Rodney Lea, Lyn Griffiths Tags: Technical Advance Source Type: research

Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine
Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for detecting cancer mutation, diagnosing infectious disease (eg, tuberculosis), monitoring organ transplantation, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented (30 to 100 nt). The clinical sensitivity of urine cfDNA detection increases with decreasing target length, motivating use of sample preparation methods designed for short fragments. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2019 Category: Pathology Authors: Amy Oreskovic, Norman D. Brault, Nuttada Panpradist, James J. Lai, Barry R. Lutz Source Type: research

Broad-Range Papillomavirus Transcriptome as a Biomarker of Papillomavirus-Associated Cervical High-Grade Cytology
Human papillomaviruses (HPVs) are responsible for>99% of cervical cancers. Molecular diagnostic tests based on the detection of viral DNA or RNA have low positive predictive values for the identification of cancer or precancerous lesions. Triage with the Papanicolaou test lacks sensitivity; and even when combined with molecular detection of high-risk HPV, this results in a significant number of unnecessary colposcopies. We have developed a broad-range detection test of HPV transcripts to take a snapshot of the transcriptome of 16 high-risk or putative high-risk HPVs in cervical lesions (HPVs 16, 18, 31, 33, 35, 39, 45, ...
Source: Journal of Molecular Diagnostics - August 12, 2019 Category: Pathology Authors: Philippe P érot, Anne Biton, Jacques Marchetta, Anne-Gaelle Pourcelot, André Nazac, Henri Marret, Thomas Hébert, Delphine Chrétien, Marie-Christine Demazoin, Michaël Falguières, Laurence Arowas, Hélène Laude, Isabelle Heard, Marc Eloit Tags: Regular article Source Type: research

Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles
Pharmacogenetic testing increasingly is available from clinical and research laboratories. However, only a limited number of quality control and other reference materials currently are available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, CDC-based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories (Camden, NJ), has characterized 179 DNA samples derived from Coriell cell lines. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 9, 2019 Category: Pathology Authors: Andrea Gaedigk, Amy Turner, Robin E. Everts, Stuart A. Scott, Praful Aggarwal, Ulrich Broeckel, Gwendolyn A. McMillin, Roberta Melis, Erin C. Boone, Victoria M. Pratt, Lisa V. Kalman Source Type: research

Characterization of Reference Materials for Genetic Testing of CYP2D6 Alleles A GeT-RM Collaborative Project
Pharmacogenetic (PGx) testing is increasingly available from clinical and research laboratories. However, only a limited number of quality control and other reference materials (RMs) are currently available for the complex rearrangements and rare variants that occur in the CYP2D6 gene. To address this need, the Division of Laboratory Systems, Centers for Disease Control and Prevention based Genetic Testing Reference Material Coordination Program (GeT-RM), in collaboration with members of the pharmacogenetic testing and research communities and the Coriell Cell Repositories, has characterized 179 DNA samples derived from Co...
Source: Journal of Molecular Diagnostics - August 9, 2019 Category: Pathology Authors: Andrea Gaedigk, Amy Turner, Robin E. Everts, Stuart A. Scott, Praful Aggarwal, Ulrich Broeckel, Gwendolyn A. McMillin, Roberta Melis, Erin C. Boone, Victoria M. Pratt, Lisa V. Kalman Source Type: research

Development and Application of Duplex Sequencing Strategy for Cell-Free DNA –Based Longitudinal Monitoring of Stage IV Colorectal Cancer
In this study, we evaluate a systematic approach and identify key components of wet bench and bioinformatics strategies to address these challenges. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 8, 2019 Category: Pathology Authors: Saradhi Mallampati, Stephanie Zalles, Dzifa Y. Duose, Peter C. Hu, L. Jeffrey Medeiros, Ignacio I. Wistuba, Scott Kopetz, Rajyalakshmi Luthra Tags: Regular article Source Type: research

Development and Application of Duplex Sequencing Strategy for Cell-Free DNA (cfDNA) –Based Longitudinal Monitoring of Stage IV Colorectal Cancer
In this study, we demonstrate a systematic approach and identify key components of wet bench and bioinformatics strategies to address these challenges. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 8, 2019 Category: Pathology Authors: Saradhi Mallampati, Stephanie Zalles, Dzifa Y. Duose, Peter C. Hu, L. Jeffrey Medeiros, Ignacio I. Wistuba, Scott Kopetz, Rajyalakshmi Luthra Source Type: research

Prospective Evaluation of the Vela Diagnostics Next-Generation Sequencing Platform for HIV-1 Genotypic Resistance Testing
This study investigates the semi-automated, next-generation sequencing (NGS)-based Vela Diagnostics Sentosa SQ HIV-1 Genotyping Assay in a prospective cohort of HIV-1 infected patients. Two-hundred and sixty-nine samples were successfully sequenced by both NGS and Sanger sequencing. Among the 261 protease/reverse transcriptase (PR/RT) sequences, a mean of 0.37 drug resistance mutations were identified by both Sanger and NGS, 0.08 by NGS alone, and 0.03 by Sanger alone. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 2, 2019 Category: Pathology Authors: Jenna Weber, Ilona Volkova, Malaya K. Sahoo, Philip L. Tzou, Robert W. Shafer, Benjamin A. Pinsky Source Type: research

Interactive Browser-Based Genomics Data Visualization Tools for Translational and Clinical Laboratory Applications
Visualization-driven data exploration is a highly effective modality for interpreting and discovering insights from high-throughput genomics datasets; however, it is vastly underutilized in routine workflows in clinical and translation settings. We have developed three open-source, browser-based, interactive genomics data visualization widgets that can be used as intuitive standalone applications or integrated with existing web-based laboratory information solutions. The widgets were developed in JavaScript using the D3.js library. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 2, 2019 Category: Pathology Authors: Thomas M. Pearce, Marina M. Nikiforova, Somak Roy Source Type: research

Comparison of in Situ and Extraction-Based Methods for the Detection of ROS1 Rearrangements in Solid Tumors
Clinical data confirmed that patients with ROS1 rearrangement are sensitive to specific inhibitors like crizotinib. Therefore, reliable detection of ROS1 rearrangements is essential. Several diagnostic techniques are currently available. However, previous studies were hampered by the low number of ROS1 positive samples. Here, 35 samples, including 32 ROS1 fluorescent in situ hybridization (FISH) fusion positive and three ROS1 FISH negative samples were evaluated by ROS1 CISH, ROS1 immunohistochemistry (IHC), an Agilent SureSelect XT HS custom panel, the Archer FusionPlex CTL panel, and a custom NanoString fusion panel. (So...
Source: Journal of Molecular Diagnostics - August 2, 2019 Category: Pathology Authors: Carina Heydt, Vanessa Ruesseler, Roberto Pappesch, Svenja Wagener, Anja Haak, Udo Siebolts, Richard Riedel, Sebastian Michels, Juergen Wolf, Anne M. Schultheis, Jan Rehker, Reinhard Buettner, Sabine Merkelbach-Bruse Source Type: research

Reliable Gene Expression Profiling from Small and Hematoxylin and Eosin –Stained Clinical Formalin-Fixed, Paraffin-Embedded Specimens Using the HTG EdgeSeq Platform
Clinical biomarker studies are often hindered by the scarcity or suboptimal quality of biological specimens. EdgeSeq, a transcriptomics analysis platform, combines quantitative nuclease protection assay technology with next-generation sequencing, using small amounts of starting material and delivering reproducible gene expression profiles from challenging material, such as formalin-fixed, paraffin-embedded (FFPE) tissue. To evaluate EdgeSeq for analysis of archives of stained FFPE tissue, EdgeSeq was performed on unstained, hematoxylin and eosin (H&E)-stained, and immunohistochemically-stained slides from patients with...
Source: Journal of Molecular Diagnostics - June 27, 2019 Category: Pathology Authors: Zhenhao Qi, Lisu Wang, Keyur Desai, John Cogswell, Mark Stern, Byron Lawson, Sid P. Kerkar, Patrik Vitazka Tags: Regular article Source Type: research

Development and Clinical Validation of a Large Fusion Gene Panel for Pediatric Cancers
We report the development and clinical validation of a large custom-designed RNA sequencing panel, CHOP Fusion panel, using anchored multiplex PCR technology. The panel interrogates 106 cancer genes known to be involved in nearly 600 different fusions reported in hematological malignancies and solid tumors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 27, 2019 Category: Pathology Authors: Fengqi Change, Fumin Lin, Kajia Cao, Lea F. Surrey, Richard Aplenc, Rochelle Bagatell, Adam C. Resnick, Mariarita Santi, Phillip B. Storm, Sarah K. Tasian, Angela J. Waanders, Stephen P. Hunger, Marilyn M. Li Tags: Regular Article Source Type: research

Optimization of Population Frequency Cutoffs for Filtering Common Germline Polymorphisms from Tumor-Only Next-Generation Sequencing Data
In this study, five population databases plus the Catalog of Somatic Mutations in Cancer were used to demonstrate the impact of changing the PF cutoff on assignment of variants as germline versus somatic. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 25, 2019 Category: Pathology Authors: Samantha N. McNulty, Bijal A. Parikh, Eric J. Duncavage, Jonathan W. Heusel, John D. Pfeifer Tags: Regular article Source Type: research

Pre-Analytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis
An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our increasing understanding of the biology and molecular signatures of individual tumor types has facilitated the identification of predictive biomarkers and has led to an increasing number of diagnostic tests to be performed, often as serial and distinct assays on limited tumor specimens. The biomarker diagnostics field has been revolutionized by next-generation sequencing (NGS), which provides a comprehensive overview of the genomic profile of a tumor. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 25, 2019 Category: Pathology Authors: Paolo A. Ascierto, Carlo Bifulco, Giuseppe Palmieri, Solange Peters, Nikoletta Sidiropoulos Tags: Review Source Type: research

Preanalytic Variables and Tissue Stewardship for Reliable Next-Generation Sequencing (NGS) Clinical Analysis
An enduring goal of personalized medicine in cancer is the ability to identify patients who are likely to respond to specific therapies. Our growing understanding of the biology and molecular signatures of individual tumor types has facilitated the identification of predictive biomarkers and has led to an increasing number of diagnostic tests to be performed, often as serial and distinct assays on limited tumor specimens. The biomarker diagnostics field has been revolutionized by next-generation sequencing (NGS), which provides a comprehensive overview of the genomic profile of a tumor. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 25, 2019 Category: Pathology Authors: Paolo A. Ascierto, Carlo Bifulco, Giuseppe Palmieri, Solange Peters, Nikoletta Sidiropoulos Tags: Review Source Type: research

Optimization of Population Frequency Cut-offs for Filtering Common Germline Polymorphisms from Tumor-Only Next-Generation Sequencing Data
In this study, five population databases plus the Catalog of Somatic Mutations in Cancer was employed to demonstrate the impact of changing the PF cut-off on assignment of variants as germline versus somatic. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 25, 2019 Category: Pathology Authors: Samantha N. McNulty, Bijal A. Parikh, Eric J. Duncavage, Jonathan W. Heusel, John D. Pfeifer Tags: Regular article Source Type: research

Expanding the Scope of The Journal of Molecular Diagnostics to the Informatics Subdivision of the Association for Molecular Pathology
This editorial describes the expanded scope of The Journal of Molecular Diagnostics, to include informatics-based articles. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 22, 2019 Category: Pathology Authors: Alexis B. Carter, Barbara Zehnbauer Tags: Editorial Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 22, 2019 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 22, 2019 Category: Pathology Source Type: research

PipeIT
The accurate identification of somatic mutations has become a pivotal component of tumor profiling and precision medicine. In molecular diagnostics laboratories, somatic mutation analyses on the Ion Torrent sequencing platform are typically performed on the Ion Reporter platform, which requires extensive manual review of the results and lacks optimized analysis workflows for custom targeted sequencing panels. Alternative solutions that involve custom bioinformatics pipelines involve the sequential execution of software tools with numerous parameters, leading to poor reproducibility and portability. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Andrea Garofoli, Viola Paradiso, Hesam Montazeri, Philip M. Jermann, Guglielmo Roma, Luigi Tornillo, Luigi M. Terracciano, Salvatore Piscuoglio, Charlotte K.Y. Ng Tags: Regular article Source Type: research

Optimized (Pre) Analytical Conditions and Workflow for Droplet Digital PCR Analysis of Cell-Free DNA from Patients with Suspected Lung Carcinoma
For patients with suspected lung carcinoma, the analysis of circulating tumor DNA, obtained by liquid biopsy, has the potential to support cancer diagnosis and guide targeted therapy. To ensure sensitive and reproducible detection of circulating tumor DNA in routine clinical practice, a standardized (pre) analytical workflow is required. Plasma was obtained from patients and healthy volunteers. Using the QIAmp Circulating Nucleic Acid Kit (Qiagen Valencia, CA), six different procedures for the isolation of cell-free DNA (cfDNA) were compared. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Remco de Kock, Birgit Deiman, Raisa Kraaijvanger, Volkher Scharnhorst Tags: Regular article Source Type: research

High-Throughput Screening for CYP21A1P-TNXA/TNXB Chimeric Genes Responsible for Ehlers-Danlos Syndrome in Patients with Congenital Adrenal Hyperplasia
Many patients with congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency have CAH-X syndrome, a connective tissue dysplasia consistent with hypermobility-type Ehlers-Danlos syndrome due to a contiguous gene deletion involving the adjacent CYP21A2 and TNXB genes. CAH-X syndrome is caused by carrying CYP21A1P-TNXA/TNXB chimeric genes (CAH-X CH-1 and CH-2) on one or more alleles. Genetic analysis is cumbersome due to pseudogene interference. We developed a PCR-based CAH-X high-throughput screening method to assess the copy numbers of TNXB exons 35 and 40; this method is amenable to either real-time quantitativ...
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Qizong Lao, Brittany Brookner, Deborah P. Merke Tags: Regular article Source Type: research

PipeIT: A Singularity Container for Molecular Diagnostic Somatic Variant Calling on the Ion Torrent Next-Generation Sequencing Platform
The accurate identification of somatic mutations has become a pivotal component of tumor profiling and precision medicine. In molecular diagnostics laboratories, somatic mutation analyses on the Ion Torrent sequencing platform are typically performed on the Ion Reporter platform, which requires extensive manual review of the results and lacks optimized analysis workflows for custom targeted sequencing panels. Alternative solutions that involve custom bioinformatics pipelines involve the sequential execution of software tools with numerous parameters, leading to poor reproducibility and portability. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Andrea Garofoli, Viola Paradiso, Hesam Montazeri, Philip M. Jermann, Guglielmo Roma, Luigi Tornillo, Luigi M. Terracciano, Salvatore Piscuoglio, Charlotte K.Y. Ng Tags: Regular article Source Type: research

PipeIT: Singularity Container for Molecular Diagnostic Somatic Variant Calling on Ion Torrent NGS Platform
The accurate identification of somatic mutations has become a pivotal component of tumor profiling and precision medicine. In molecular diagnostics laboratories, somatic mutation analyses on the Ion Torrent sequencing platform are typically performed on the Ion Reporter platform, which requires extensive manual review of the results and lacks optimized analysis workflows for custom targeted sequencing panels. Alternative solutions involving custom bioinformatics pipelines involve the sequential execution of software tools with numerous parameters, leading to poor reproducibility and portability. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Andrea Garofoli, Viola Paradiso, Hesam Montazeri, Philip M. Jermann, Guglielmo Roma, Luigi Tornillo, Luigi M. Terracciano, Salvatore Piscuoglio, Charlotte K.Y. Ng Tags: Regular Article Source Type: research

Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids
Next-generation sequencing –based 16S rRNA gene metagenomic sequencing (16S MG) technology has tremendous potential for improving diagnosis of bacterial infections given its quantitative capability and culture-independent approach. We validated and utilized a quantitative 16S MG assay to identify and quantify bacterial spec ies in clinical samples from a wide spectrum of infections including meningitis, septic arthritis, brain abscess, intra-abdominal abscess, soft tissue abscess, and pneumonia. Twenty clinical samples were tested and 16S MG identified a total of 34 species, compared to 22 species and three descripti...
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Karissa Culbreath, Suzanne Melanson, James Gale, Justin Baker, Fan Li, Oystein Saebo, Oyvind Kommedal, Deisy Contreras, Omai B. Garner, Shangxin Yang Tags: Regular article Source Type: research

Optimized (pre) Analytic Conditions and Workflow for ddPCR Analysis of cfDNA from Patients Suspected of Lung Carcinoma
For patients suspected of lung carcinoma, the analysis of circulating tumor DNA, obtained by liquid biopsy, has the potential to support cancer diagnosis and guide targeted therapy. To ensure sensitive and reproducible detection of circulating tumor DNA in daily routine practice, a standardized (pre) analytical workflow is required. Plasma was obtained from patients and healthy volunteers. Using the Qiagen Circulating Nucleic Acid kit, six different procedures for the isolation of cell-free DNA (cfDNA) were compared. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Remco de Kock, Birgit Deiman, Raisa Kraaijvanger, Volkher Scharnhorst Tags: Regular Article Source Type: research

High-Throughput Screening for CYP21A1P-TNXA/TNXB Chimeric Genes Responsible for Ehlers Danlos Syndrome in Patients with Congenital Adrenal Hyperplasia
Many patients with congenital adrenal hyperplasia (CAH) due to 21 hydroxylase deficiency have CAH-X syndrome, a connective tissue dysplasia consistent with hypermobility type Ehlers Danlos syndrome due to a contiguous gene deletion involving the adjacent CYP21A2 and TNXB genes. CAH-X syndrome is caused by carrying CYP21A1P-TNXA/TNXB chimeric genes (CAH-X CH-1 and CH-2) on one or more alleles. Genetic analysis is cumbersome due to pseudogene interference. We developed a PCR-based CAH-X high-throughput screening method to assess the copy numbers of TNXB exons 35 and 40 that is amenable to either quantitative PCR or droplet d...
Source: Journal of Molecular Diagnostics - June 20, 2019 Category: Pathology Authors: Qizong Lao, Brittany Brookner, Deborah P. Merke Tags: Regular Article Source Type: research

Detection of Single-Nucleotide Polymorphism Markers of Antimalarial Drug Resistance Directly from Whole Blood
Monitoring of antimalarial resistance is important to prevent its further spread, but the available options for assessing resistance are less than ideal for field settings. Although molecular detection is perhaps the most efficient method, it is also the most complex because it requires DNA extraction and PCR instrumentation. To develop a more deployable approach, we designed new probes, which, when used in combination with an inhibitor-tolerant Taq polymerase, enable single-nucleotide polymorphism genotyping directly from whole blood. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 13, 2019 Category: Pathology Authors: Mindy Leelawong, Nicholas M. Adams, William E. Gabella, David W. Wright, Frederick R. Haselton Tags: Regular article Source Type: research

Multi-Gene Panel Testing of 23,179 Individuals for Hereditary Cancer Risk Identifies Pathogenic Variant Carriers Missed by Current Genetic Testing  Guidelines
Recent advancements in next-generation sequencing have greatly expanded the use of multi-gene panel testing for hereditary cancer risk. Although genetic testing helps guide clinical diagnosis and management, testing recommendations are based on personal and family history of cancer and ethnicity, and many carriers are being missed. Herein, we report the results from 23,179 individuals who were referred for 30-gene next-generation sequencing panel testing for hereditary cancer risk, independent of current testing guidelines —38.7% of individuals would not have met National Comprehensive Cancer Network criteria for gen...
Source: Journal of Molecular Diagnostics - June 11, 2019 Category: Pathology Authors: Cynthia L. Neben, Anjali D. Zimmer, Will Stedden, Jeroen van den Akker, Robert O'Connor, Raymond C. Chan, Elaine Chen, Zheng Tan, Annette Leon, Jack Ji, Scott Topper, Alicia Y. Zhou Tags: Regular articles Source Type: research

Proof of Concept for a Portable Platform for Molecular Diagnosis of Tropical Diseases
Although molecular diagnostics is well established in clinical laboratories, its full potential has not been extended to field settings. Typically, diagnostic real-time quantitative PCR (qPCR) reagents require temperature-controlled transportation and storage. Furthermore, thermocyclers are bulky and fragile, requiring good infrastructure for optimal operation. These major hurdles strongly limit use of molecular-based tests in low-resource scenarios. Herein, Trypanosoma cruzi or Plasmodium spp. DNA were detected with qPCR using commercial equipment (ABI7500 instrument) and a prototype platform comprising a portable device ...
Source: Journal of Molecular Diagnostics - June 4, 2019 Category: Pathology Authors: Rita C.P. Rampazzo, Ana C. Graziani, Keren K. Leite, Jhully A. Surdi, Cheysa A. Biondo, Maykon L.N. Costa, Thiago Jacomasso, Marco Cereda, Marco De Fazio, Marco A. Bianchessi, Otac ílio C. Moreira, Constança Britto, Joana D.N. Costa, Viviane M. Góes, A Tags: Regular article Source Type: research

MammaPrint and BluePrint Molecular Diagnostics using targeted RNA Next-Generation Sequencing technology
Next-generation DNA sequencing (NGS) is rapidly becoming an indispensable tool for genome-directed cancer diagnostics, but next-generation RNA sequencing (RNA-seq) is currently not standardly used in clinical diagnostics for expression assessment. However, multi-gene RNA diagnostic assays are used increasingly in the routine diagnosis of early stage breast cancer. Two of the most widely used tests are currently available only as a central laboratory service, which limits their clinical use. We evaluated the use of RNA-seq as a de-centralized methodology to perform such tests. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 4, 2019 Category: Pathology Authors: Lorenza Mittempergher, Leonie JMJ. Delahaye, Anke Witteveen, Jacob B. Spangler, Fariet Hassenmahomed, Sammy Mee, Soufiane Mahmoudi, Jiang Chen, Simon Bao, Mireille HJ. Snel, Sandra Leidelmeijer, Naomi Besseling, Anne Bergstrom Lucas, Carlos Pab ón-Peña, Tags: Regular Article Source Type: research

Proof of concept for a portable platform for molecular diagnosis of tropical diseases: On-chip ready-to-use qPCR for detection of Trypanosoma cruzi or Plasmodium spp
Although molecular diagnostics is well established in clinical laboratories, its full potential has not been extended to field settings. Typically, diagnostic qPCR reagents require temperature-controlled transportation and storage. Furthermore, thermocyclers are bulky and fragile, requiring good infrastructure for optimal operation. These major hurdles strongly limit the use of molecular-based tests in low-resource scenarios. Here, qPCR was used for detection of Trypanosoma cruzi or Plasmodium spp. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 4, 2019 Category: Pathology Authors: Rita C.P. Rampazzo, Ana C. Graziani, Keren K. Leite, Jhully A. Surdi, Cheysa A. Biondo, Maykon L.N. Costa, Thiago Jacomasso, Marco Cereda, Marco De Fazio, Marco A. Bianchessi, Otac ílio C. Moreira, Constança Britto, Joana D.N. Costa, Viviane M. Góes, A Tags: Regular Article Source Type: research

Resolving MiSeq-generated ambiguities in HLA-DPB1 typing by using the Oxford Nanopore technology
The technical limitations of current next-generation sequencing technologies, combined with an ever-increasing number of human leukocyte antigen (HLA) alleles, forms the basis for the additional ambiguities we encounter in our clinical practice at an increasing rate. HLA-DPB1 characterization, particularly, generates a significant percent of ambiguities (25.5%) posing a challenge for accurate and unambiguous HLA-DPB1 genotyping. Phasing of exonic heterozygous positions between exon 2 and all other downstream exons has been the major cause of ambiguities. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 4, 2019 Category: Pathology Authors: Jamie L. Duke, Timothy L. Mosbruger, Deborah Ferriola, Nilesh Chitnis, Taishan Hu, Nikolaos Tairis, David J. Margolis, Dimitri S. Monos Tags: Regular Article Source Type: research

Genome Mining –Based Identification of Identical Multirepeat Sequences in Plasmodium falciparum Genome for Highly Sensitive Real-Time Quantitative PCR Assay and Its Application in Malaria Diagnosis
Malaria continues to impact global health, and developing ultrasensitive methods capable of detecting submicroscopic parasitemia —a challenge that persists in low transmission areas, asymptomatic carriers, and patients showing recrudescence—is vital to achieving malaria eradication. Nucleic acid amplification techniques offer improved analytical sensitivity but are limited by the number of copies of the amplification targ ets. Herein, we perform a novel genome mining approach to identify a pair of identical multirepeat sequences (IMRSs) that constitute 170 and 123 copies in the Plasmodium falciparum genome and ...
Source: Journal of Molecular Diagnostics - May 31, 2019 Category: Pathology Authors: Lolabattu S. Raju, Shwetha Kamath, Manjunatha C. Shetty, Sanghamitra Satpathi, Akshaya K. Mohanty, Susanta K. Ghosh, Nikunja Kolluri, Catherine M. Klapperich, Mario Cabodi, Govindarajan Padmanaban, Viswanathan A. Nagaraj Tags: Regular article Source Type: research

The Optimal Sequencing Depth of Tumor Biopsies for Identifying Clonal Cell Populations
The tumor content of a biopsy and the average depth of coverage are two essential aspects when performing DNA sequencing using next-generation sequencing technologies. The heterogeneous nature of cancer necessitates the identification of distinct clonal cell populations to better understand and treat cancer. Deep sequencing enables researchers to identify these populations, but no consensus on an optimal depth exists for identifying clonal populations. Data from eight deep sequenced oral squamous cell carcinoma biopsies obtained from three stage IV patients, with various degrees of tumor content, were used to randomly down...
Source: Journal of Molecular Diagnostics - May 31, 2019 Category: Pathology Authors: Siavosh Tabatabaeifar, Martin Jakob Larsen, Mads Thomassen, Stine Rosenkilde Larsen, Torben Arvid Kruse, Jens Ahm S ørensen Tags: Regular Article Source Type: research

Genome Mining –Based Identification of Identical Multi-Repeat Sequences (IMRS) in Plasmodium falciparum Genome for Highly Sensitive qPCR Assay and its Application in Malaria Diagnosis
Malaria continues to impact global health, and developing ultra-sensitive methods capable of detecting submicroscopic parasitemia —a challenge that persists in low transmission areas, asymptomatic carriers, and patients showing recrudescence—is vital to achieving malaria eradication. Nucleic acid amplification techniques offer improved analytical sensitivity, but limited by the number of copies of the amplification targets . Here, we perform a novel genome mining approach to identify a pair of identical multi-repeat sequences (IMRS) that constitute 170 and 123 copies in Plasmodium falciparum (Pf) genome, and ex...
Source: Journal of Molecular Diagnostics - May 31, 2019 Category: Pathology Authors: Lolabattu Srinivasa Raju, Shwetha Kamath, Manjunatha Chandana Shetty, Sanghamitra Satpathi, Akshaya Kumar Mohanty, Susanta Kumar Ghosh, Nikunja Kolluri, Catherine M. Klapperich, Mario Cabodi, Govindarajan Padmanaban, Viswanathan Arun Nagaraj Tags: Regular Article Source Type: research

A Rapid Allele-Specific Assay for HLA-A*32:01 to Identify Patients at Risk for Vancomycin-Induced Drug Reaction with Eosinophilia and Systemic Symptoms
Human leukocyte antigen (HLA) alleles have been implicated as risk factors for immune-mediated adverse drug reactions. We recently reported a strong association between HLA-A*32:01 and vancomycin-induced drug reaction with eosinophilia and systemic symptoms (DRESS). Identification of individuals with the risk allele prior to or shortly after the initiation of vancomycin therapy is of great clinical importance to prevent morbidity and mortality, improve drug safety and antibiotic treatment options. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 31, 2019 Category: Pathology Authors: Francois X. Rwandamuriye, Abha Chopra, Katherine C. Konvinse, Linda Choo, Jason A. Trubiano, Christian M. Shaffer, Mark Watson, Simon A. Mallal, Elizabeth J. Phillips Tags: Regular article Source Type: research