Title Page
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Source Type: research

Disclosure Statement
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Source Type: research

Abstracts
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Source Type: research

Author Index
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Source Type: research

A Zika Reference Panel for Molecular-Based Diagnostic Devices as a US Food and Drug Administration Response Tool to a Public Health Emergency
In 2015, Zika virus (ZIKV) appeared as an emerging pathogen, generating a global and urgent need for accurate diagnostic devices. During this public health crisis, several nucleic acid testing (NAT) –based Zika assays were submitted to the US Food and Drug Administration (FDA) for Emergency Use Authorization. The FDA’s Center for Devices and Radiological Health, in collaboration with the FDA's Center for Biologics Evaluation and Research, responded to this Zika emergency by developing and p roducing a reference panel (RP) for Zika RNA (Zika FDA-RP) suitable for performance assessment of ZIKV NAT-based in v...
Source: Journal of Molecular Diagnostics - October 14, 2019 Category: Pathology Authors: Mayra Garc ía, Rafaelle Fares-Gusmao, Kim Sapsford, Caren Chancey, Andriyan Grinev, Stephen Lovell, Uwe Scherf, Maria Rios Tags: Regular article Source Type: research

Establishment of Coamplification at Lower Denaturation Temperature PCR/Fluorescence Melting Curve Analysis for Quantitative Detection of Hepatitis B Virus DNA, Genotype, and Reverse Transcriptase Mutation and Its Application in Diagnosis of Chronic Hepatitis B
Dynamic and real-time hepatitis B virus (HBV) DNA, genotype, and reverse transcriptase mutation analysis plays an important role in diagnosing and monitoring chronic hepatitis B (CHB) and in assessing the therapeutic response. We established a highly sensitive coamplification at lower denaturation temperature PCR (COLD-PCR) coupled with probe-based fluorescence melting curve analysis (FMCA) for precision diagnosis of CHB patients. The imprecision with %CV and detection limit of HBV DNA detected by COLD-PCR/FMCA were 2.58% to 4.42% and 500 IU/mL, respectively. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 9, 2019 Category: Pathology Authors: Can Liu, Jinpiao Lin, Zhen Xun, Jinlan Huang, Er Huang, Tianbin Chen, Yujue He, Ni Lin, Bin Yang, Qishui Ou Tags: Regular article Source Type: research

Rchimerism
A quantitative chimerism test monitors engraftment of donor hematopoietic stem cells or relapse of leukemias or lymphomas in hematopoietic stem cell transplantation patients. The most common method used for chimerism testing is PCR amplification of short tandem repeat loci, followed by capillary gel electrophoresis. Manual data analysis is tedious and time consuming, as it involves the selection of informative loci and the repetition of quantifying chimerism percentage for multiple loci from multiple cell types. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 8, 2019 Category: Pathology Authors: Zohair Siddiqui, Juan Maldonado, Jeremy Grojean, Fei Ye, David Zhang, Janina Longtine, Tae-Hyuk Ahn, Huazhang Guo Tags: Technical advance Source Type: research

A New Next-Generation Sequencing Strategy for the Simultaneous Analysis of Mutations and Chromosomal Rearrangements at Dna Level in Acute Myeloid Leukemia Patients
Acute myeloid leukemias (AMLs) are currently genomically characterized by karyotype, fluorescence in situ hybridization (FISH), RQ-PCR, and DNA sequencing. Next-generation sequencing offers the promise of detecting all genomic lesions in a single run. However, technical limitations have hampered the detection of chromosomal rearrangements, so most studies are limited to somatic mutation assessment, or require the use of RNA-based strategies. To overcome these limitations, we designed a targeted-DNA capture next-generation sequencing approach associated with easy-to-perform public bioinformatic tools for one-step identifica...
Source: Journal of Molecular Diagnostics - October 8, 2019 Category: Pathology Authors: M. Isabel Prieto-Conde, Luis A. Corchete, Mar ía García-Álvarez, Cristina Jiménez, Alejandro Medina, Ana Balanzategui, Montserrat Hernández-Ruano, Rebeca Maldonado, M. Eugenia Sarasquete, Miguel Alcoceba, Noemí Puig, Verónica González-Calle, Ramó Tags: Regular Article Source Type: research

Methylation markers in prostate biopsies are prognosticators for late biochemical recurrence and therapy after surgery in prostate cancer patients
After diagnosis of prostate cancer is confirmed by a positive biopsy, the tumor may be surgically removed via radical prostatectomy (RP). However, many prostate cancer patients experience biochemical recurrence post-surgery and/or undergo salvage radiotherapy or hormone therapy. Timely treatment is required to prevent the spread of disease in these cases, and biopsy tissue may hold potential for disease prognostication before surgery is ever performed. We previously developed a prognostic multi-gene methylation panel in RP specimens, including APC, CRIP3, HOXD3, and TGFB2. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 8, 2019 Category: Pathology Authors: Andrea J. Savio, Shivani Kamdar, Renu Jeyapala, Ekaterina Olkhov-Mitsel, Carmelle Cuizon, Antonio Finelli, Alexandre R. Zlotta, Ants Toi, Neil E. Fleshner, Theodorus van der Kwast, Bharati Bapat Tags: Regular Article Source Type: research

Rchimerism: An R-Package for Automated Chimerism Data Analysis
A quantitative chimerism test monitors engraftment of donor hematopoietic stem cells or relapse of leukemias or lymphomas in hematopoietic stem cell transplantation patients. The most common method used for chimerism testing is PCR amplification of short tandem repeat loci followed by capillary gel electrophoresis. Manual data analysis is tedious and time consuming, as it involves the selection of informative loci and the repetition of quantifying chimerism percentage for multiple loci from multiple cell types. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 8, 2019 Category: Pathology Authors: Zohair Siddiqui, Juan Maldonado, Jeremy Grojean, Fei Ye, David Zhang, Janina Longtine, Tae-Hyuk Ahn, Huazhang Guo Tags: Technical Advance Source Type: research

Using R and Bioconductor in Clinical Genomics and Transcriptomics
Bioinformatics pipelines are essential in the analysis of genomic and transcriptomic data generated by next-generation sequencing. Recent guidelines emphasize the need for rigorous validation and assessment of robustness, reproducibility, and quality of NGS analytic pipelines intended for clinical use. Software tools written in the R statistical language and in particular the set of tools available in the Bioconductor repository are widely used in research bioinformatics, and these frameworks offer several advantages for use in clinical bioinformatics, including the breath of available tools, modular nature of software &ld...
Source: Journal of Molecular Diagnostics - October 8, 2019 Category: Pathology Authors: Jorge L. Sepulveda Tags: Review Source Type: research

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 22, 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 and Pan-Tumor Characterization of 1000 Microsatellite Instability –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-high (MSI-H) solid tumors. Herein, 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. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 21, 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

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 21, 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 20, 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 20, 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 20, 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 20, 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 19, 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 19, 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 19, 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 19, 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 19, 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 11, 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 8, 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 8, 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 7, 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 7, 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 1, 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 1, 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 1, 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 26, 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 26, 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 24, 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 24, 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 24, 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 24, 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 19, 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 19, 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 19, 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 19, 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 19, 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 19, 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