Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 19, 2017 Category: Pathology Source Type: research

Targeted Next-Generation Sequencing of 51 Genes Involved in Primary Electrical Disease
Primary electrical disease (PED) is characterized by cardiac arrhythmias, which can lead to sudden cardiac death in the absence of detectable structural heart disease. PED encompasses a diversity of inherited syndromes, predominantly Brugada syndrome, early repolarization syndrome, long QT syndrome, short QT syndrome, arrhythmogenic right ventricular cardiomyopathy, and catecholaminergic polymorphic ventricular tachycardia. To overcome the diagnostic challenges imposed by the clinical and genetic heterogeneity of PED, we developed a targeted gene panel for next-generation sequencing of 51 PED genes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 21, 2017 Category: Pathology Authors: Dorien Proost, Johan Saenen, Geert Vandeweyer, Annelies Rotthier, Maaike Alaerts, Emeline M. Van Craenenbroeck, Joachim Van Crombruggen, Geert Mortier, Wim Wuyts, Christiaan Vrints, Jurgen Del Favero, Bart Loeys, Lut Van Laer Tags: Regular Article Source Type: research

Impact of Rapid Molecular Respiratory Virus Testing on Real-Time Decision Making in a Pediatric Emergency Department
Acute respiratory illnesses (ARIs) are usually viral [influenza, respiratory syncytial virus (RSV)] and account for 25% of emergency department (ED) peak-season visits. Laboratory respiratory PCR testing is accurate albeit slow for ED management, whereas rapid antigen testing is inaccurate. We determined the impact of bedside influenza/RSV PCR (molecular point-of-care test; mPOCT) on pediatric ARI management. This was a prospective cohort study of consecutive pediatric patients with ED-ordered respiratory PCR test, enrolled over 9 weeks during peak flu season. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 21, 2017 Category: Pathology Authors: Daniel T. Rogan, Mohit S. Kochar, Samuel Yang, James V. Quinn Tags: Regular Article Source Type: research

Guidelines for Validation of Next-Generation Sequencing –Based Oncology Panels
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference c...
Source: Journal of Molecular Diagnostics - March 21, 2017 Category: Pathology Authors: Lawrence J. Jennings, Maria E. Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M. Lubin, John Pfeifer, Robyn L. Temple-Smolkin, Karl V. Voelkerding, Marina N. Nikiforova Tags: Special Article Source Type: research

Current and Emerging Molecular Tests for Human Papillomavirus –Related Neoplasia in the Genomic Era
Laboratory tests have a key role in preventing human papillomavirus (HPV) –driven carcinomas and in guiding therapeutic interventions. An understanding of the virology, immunology, and carcinogenesis of HPV is essential for choosing appropriate diagnostic test modalities and developing new and even more effective cancer prevention strategies. HPV infects basal epithelia l cells on multiple surfaces and induces carcinoma primarily in the cervix and the oropharynx. HPV types are stratified as high risk or low risk based on their carcinogenic potential, driven largely by viral interference with cell cycle regulation and...
Source: Journal of Molecular Diagnostics - March 19, 2017 Category: Pathology Authors: Sixto M. Leal, Margaret L. Gulley Tags: Review Source Type: research

Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA
Chromosomal microarray (CMA) testing to detect copy number aberrations among individuals with multiple congenital anomalies and/or developmental delay is typically performed on peripheral blood DNA. However, the use of saliva DNA may be preferred for some patients, which prompted our validation study using six saliva DNA samples with a range of bacterial content (approximately 3% to 21%) and 20 paired blood and saliva specimens on the Agilent Technologies, Illumina, and Affymetrix CMA platforms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 16, 2017 Category: Pathology Authors: Jennifer Reiner, Lisa Karger, Ninette Cohen, Lakshmi Mehta, Lisa Edelmann, Stuart A. Scott Tags: Regular Article Source Type: research

Detection of Aberrant TERT Promoter Methylation by Combined Bisulfite Restriction Enzyme Analysis for Cancer Diagnosis
Aberrant CpG dinucleotide methylation in a specific region of the telomerase reverse transcriptase (TERT) promoter is associated with increased TERT mRNA levels and malignancy in several cancer types. However, routine screening of this region to aid cancer diagnosis can be challenging because i) several established methylation assays may inaccurately report on hypermethylation of this particular region, ii) interpreting the results of methylation assays can sometimes be difficult for clinical laboratories, and iii) use of high-throughput methylation assays for a few patient samples can be cost prohibitive. (Source: Journal...
Source: Journal of Molecular Diagnostics - March 8, 2017 Category: Pathology Authors: Seungjae Lee, Sumit Borah, Armita Bahrami Tags: Technical Advance Source Type: research

Droplet Digital PCR Is a Reliable Tool for Monitoring Minimal Residual Disease in Acute Promyelocytic Leukemia
Nested PCR (nPCR) and real-time quantitative PCR (qPCR) are well-established methods for monitoring minimal residual disease (MRD) in acute promyelocytic leukemia (APL). Despite their remarkable sensitivity and specificity, both methods have inherent limitations, such as qualitative MRD evaluation and relative quantification. Herein, we used droplet digital PCR (ddPCR) to monitor MRD in 21 APL patients and compared its performance with nPCR and qPCR. After assessing the limit of detection (LOD) for each technique on serial dilutions of PML-RARA bcr1 and bcr3 transcripts, a total of 48 follow-up samples were analyzed and th...
Source: Journal of Molecular Diagnostics - March 4, 2017 Category: Pathology Authors: Claudia Brunetti, Luisa Anelli, Antonella Zagaria, Angela Minervini, Crescenzio F. Minervini, Paola Casieri, Nicoletta Coccaro, Cosimo Cumbo, Giuseppina Tota, Luciana Impera, Paola Orsini, Giorgina Specchia, Francesco Albano Tags: Regular Article Source Type: research

Abstracts of the 1st Global Congress on Molecular Pathology
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 1, 2017 Category: Pathology Source Type: research

Author Index
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 1, 2017 Category: Pathology Source Type: research

Correction
In the article entitled, “Next-Generation Assessment of Human Growth Factor Receptor 2 (ERBB2) Amplification Status Clinical Validation in the Context of a Hybrid Capture-Based, Comprehensive Solid Tumor Genomic Profiling Assay” (Volume 19, pages 244–254), which appeared in the March 2017 issue, the title contained er rors that were inadvertently introduced by the editorial office during the proof process. The correct title is “Next-Generation Assessment of Human Epithelial Growth Factor Receptor 2 (ERBB2) Amplification Status Clinical Validation in the Context of a Hybrid Capture-Based, C...
Source: Journal of Molecular Diagnostics - February 18, 2017 Category: Pathology Tags: Correction Source Type: research

Detection of Mycobacterium chelonae, Mycobacterium abscessus Group, and Mycobacterium fortuitum Complex by a Multiplex Real-Time PCR Directly from Clinical Samples Using the BD MAX System
A new multiplex PCR test was designed to detect Mycobacterium chelonae, Mycobacterium abscessus group, and Mycobacterium fortuitum complex on the BD MAX System. A total of 197 clinical samples previously submitted for mycobacterial culture were tested using the new protocol. Samples were first treated with proteinase K, and then each sample was inoculated into the BD MAX Sample Buffer Tube. Extraction and multiplex PCR were performed by the BD MAX System, using the BD MAX ExK TNA-3 extraction kit and BD TNA Master Mix, along with specific in-house designed primers and probes for each target. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Authors: Talita T. Rocchetti, Suzane Silbert, Alicia Gostnell, Carly Kubasek, Antonio C. Campos Pignatari, Raymond Widen Tags: Regular article Source Type: research

Guidelines for Colorectal Cancer Testing
This Editorial provides readers additional insight on the colorectal guideline appearing in this issue. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Authors: Barbara Zehnbauer, Robyn Temple-Smolkin, Federico A. Monzon Tags: Editorial Source Type: research

Reviewer Acknowledgment
The Editors gratefully acknowledge the generous assistance of the following reviewers who served The Journal of Molecular Diagnostics between January 1 and December 31,  2016. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Tags: Reviewer acknowledgment Source Type: research

Correction
In the article entitled, “The Clinical Implications of Inconsistently Methylated Results from Glioblastoma MGMT Testing by Replicate Methylation-Specific PCR” (Volume 18, pages 864–871 of the November 2016 issue of The Journal of Molecular Diagnostics; http://dx.doi.org/10.1016/j.jmoldx.2016.06.009), the authors infor med the editorial office of the following errors; on page 865, author N.L. is noted as the corresponding author and should be noted as the senior author. On page 867, “iii) year of diagnosis, age, and MGMT methylation status” should have been deleted from the following paragraph:...
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Tags: Correction Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Source Type: research

Instructions to Authors
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Source Type: research

Scientific Integrity Policy
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 10, 2017 Category: Pathology Source Type: research

Precision Medicine Requires Precision Laboratories
This commentary highlights the validation study by Lih et  al that supports the use of precision medicine for improved clinical trials. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 24, 2017 Category: Pathology Authors: Mangalathu S. Rajeevan, Tengguo Li, Elizabeth R. Unger Tags: Commentary Source Type: research

Application of Nuclear Magnetic Resonance to Detect Toxigenic Clostridium difficile from Stool Specimens
We evaluated the performance of an early prototype core molecular mirroring nuclear magnetic resonance detection platform (Mentor-100) to detect toxigenic Clostridium difficile from stool. This technology uses customized nanoparticles bound to target specific oligonucleotide probes that form binaries in the presence of nucleic acid from the target microorganism. Liquid patient stool specimens were seeded with C. difficile or other Clostridium species to determine the analytical sensitivity and specificity. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 9, 2017 Category: Pathology Authors: Paul Yang, Sara Hash, Katherine Park, Charlene Wong, Loganathan Doraisamy, Jonas Petterson, Cathy A. Petti, Pamela M. Ward, Seung H. Lee, Suresh Menon, Rosemary C. She Tags: Technical Advance Source Type: research

Targeted Next-Generation Sequencing in Molecular Subtyping of Lower-Grade Diffuse Gliomas
The 2007 World Health Organization Classification of Tumours of the Central Nervous System classifies lower-grade gliomas [LGGs (grades II to III diffuse gliomas)] morphologically as astrocytomas or oligodendrogliomas, and tumors with unclear ambiguous morphology as oligoastrocytomas. The World Health Organization's newly released (2016) classification incorporates molecular data. A single, targeted next-generation sequencing (NGS) panel was used for detecting single-nucleotide variation and copy number variation in 50 LGG cases originally classified using the 2007 criteria, including 36 oligoastrocytomas, 11 oligodendrogl...
Source: Journal of Molecular Diagnostics - December 31, 2016 Category: Pathology Authors: Jamal H. Carter, Samantha N. McNulty, Patrick J. Cimino, Catherine E. Cottrell, Jonathan W. Heusel, Katinka A. Vigh-Conrad, Eric J. Duncavage Tags: Regular Article Source Type: research

Development and Validation of a Preanalytic Procedure for Performing the cobas HPV Test in SurePath Preservative Fluid
The formation of chemical cross-links between nucleic acids and proteins in formalin-containing media presents challenges for human papillomavirus (HPV) testing of cervical samples collected in SurePath Preservative Fluid. A preanalytic process involving addition of a nucleophilic buffer and heating the sample to 120 °C was developed to reverse the effects of cross-linking and improve nucleic acid accessibility for the cobas HPV Test in SurePath. Cycle threshold (CT) values for cobas HPV detection were evaluated over time and various temperatures, and mean CT differences between pretreated and both untreated Su rePath ...
Source: Journal of Molecular Diagnostics - December 30, 2016 Category: Pathology Authors: Mark D. Krevolin, David Hardy, Jim Pane, Shagufta Aslam, Catherine M. Behrens Tags: Regular Article Source Type: research

The Effect of Nucleic Acid Extraction Platforms and Sample Storage on the Integrity of Viral RNA for Use in Whole Genome Sequencing
This study examined the fitness of one manual and four automated RNA extraction platforms commonly used in diagnostic laboratories for use in metagenomic sequencing, how the practice of storing sample material in Qiagen buffer AVL before extraction affected the integrity of viral RNA and its suitability for use in amplicon-based WGS methods, and how the addition of Triton X-100 to buffer AVL affected the capability of the extraction platforms and the integrity of viral RNA in stored samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 30, 2016 Category: Pathology Authors: Kuiama Lewandowski, Andrew Bell, Rory Miles, Simon Carne, David Wooldridge, Carmen Manso, Nicola Hennessy, Daniel Bailey, Steven T. Pullan, Saheer Gharbia, Richard Vipond Tags: Regular Article Source Type: research

Next-Generation Assessment of Human Epidermal Growth Factor Receptor 2 (ERBB2) Amplification Status
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to treatment selection. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 24, 2016 Category: Pathology Authors: Dara S. Ross, Ahmet Zehir, Donavan T. Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F. Hechtman, Yelena Y. Janjigian, Britta Weigelt, Pedram Razavi, David M. Hyman, Jos é Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila Tags: Regular article Source Type: research

Next-Generation Assessment of Human Epithelial Growth Factor Receptor 2 (ERBB2) Amplification Status
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to treatment selection. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 24, 2016 Category: Pathology Authors: Dara S. Ross, Ahmet Zehir, Donavan T. Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F. Hechtman, Yelena Y. Janjigian, Britta Weigelt, Pedram Razavi, David M. Hyman, Jos é Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila Tags: Regular article Source Type: research

Next-Generation Assessment of Human Growth Factor Receptor 2 (ERBB2) Amplification Status
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to treatment selection. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 24, 2016 Category: Pathology Authors: Dara S. Ross, Ahmet Zehir, Donavan T. Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F. Hechtman, Yelena Y. Janjigian, Britta Weigelt, Pedram Razavi, David M. Hyman, Jos é Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila Tags: Regular article Source Type: research

Next-Generation Assessment of ERBB2 Amplification Status
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to treatment selection. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 24, 2016 Category: Pathology Authors: Dara S. Ross, Ahmet Zehir, Donavan T. Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F. Hechtman, Yelena Y. Janjigian, Britta Weigelt, Pedram Razavi, David M. Hyman, Jos é Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila Tags: Regular Article Source Type: research

Next-Generation Assessment of ERBB2 (Human  Epidermal Growth Factor Receptor 2) Amplification Status
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to patients' treatment plans. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 24, 2016 Category: Pathology Authors: Dara S. Ross, Ahmet Zehir, Donavan T. Cheng, Ryma Benayed, Khedoudja Nafa, Jaclyn F. Hechtman, Yelena Y. Janjigian, Britta Weigelt, Pedram Razavi, David M. Hyman, Jos é Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila Tags: Regular Article Source Type: research

Clinical Genomic Profiling of a Diverse Array of Oncology Specimens at a Large Academic Cancer Center
Large cancer panels are being increasingly used in the practice of precision medicine to generate genomic profiles of tumors with the goal of identifying targetable variants and guiding eligibility for clinical trials. To facilitate identification of mutations in a broad range of solid and hematological malignancies, a 467-gene oncology panel (Columbia Combined Cancer Panel) was developed in collaboration with pathologists and oncologists and is currently available and in use for clinical diagnostics. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 23, 2016 Category: Pathology Authors: Anthony N. Sireci, Vimla S. Aggarwal, Andrew T. Turk, Tatyana Gindin, Mahesh M. Mansukhani, Susan J. Hsiao Tags: Regular Article Source Type: research

A Targeted High-Throughput Next-Generation Sequencing Panel for Clinical Screening of Mutations, Gene Amplifications, and Fusions in Solid Tumors
Clinical next-generation sequencing (NGS) assay choice requires careful consideration of panel size, inclusion of appropriate markers, ability to detect multiple genomic aberration types, compatibility with low quality and quantity of nucleic acids, and work flow feasibility. Herein, in a high-volume clinical molecular diagnostic laboratory, we have validated a targeted high-multiplex PCR-based NGS panel (OncoMine Comprehensive Assay) coupled with high-throughput sequencing using Ion Proton sequencer for routine screening of solid tumors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 22, 2016 Category: Pathology Authors: Rajyalakshmi Luthra, Keyur P. Patel, Mark J. Routbort, Russell R. Broaddus, Jonathan Yau, Crystal Simien, Wei Chen, David Z. Hatfield, L. Jeffrey Medeiros, Rajesh R. Singh Tags: Regular Article Source Type: research

Accurate Quantification of T Cells by Measuring Loss of Germline T-Cell Receptor Loci with Generic Single Duplex Droplet Digital PCR Assays
Quantifying T cells accurately in a variety of tissues of benign, inflammatory, or malignant origin can be of great importance in a variety of clinical applications. Flow cytometry and immunohistochemistry are considered to be gold-standard methods for T-cell quantification. However, these methods require fresh, frozen, or fixated cells and tissue of a certain quality. In addition, conventional and droplet digital PCR (ddPCR), whether followed by deep sequencing techniques, have been used to elucidate T-cell content by focusing on rearranged T-cell receptor (TCR) genes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 22, 2016 Category: Pathology Authors: Willem H. Zoutman, Rogier J. Nell, Mieke Versluis, Debby van Steenderen, Rajshri N. Lalai, Jacoba J. Out-Luiting, Mark J. de Lange, Maarten H. Vermeer, Anton W. Langerak, Pieter A. van der Velden Tags: Technical Advance Source Type: research

An mRNA Gene Expression –Based Signature to Identify FGFR1-Amplified Estrogen Receptor–Positive Breast Tumors
Fibroblast growth factor receptor 1 (FGFR1) amplification drives poor prognosis and is an emerging therapeutic target. We sought to construct a multigene mRNA expression signature to efficiently identify FGFR1-amplified estrogen receptor –positive (ER+) breast tumors. Five independent breast tumor series were analyzed. Genes discriminative for FGFR1 amplification were screened transcriptome-wide by receiver operating characteristic analyses. The METABRIC series was leveraged to construct/evaluate four approaches to signature compo sition. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 16, 2016 Category: Pathology Authors: Jingqin Luo, Shuzhen Liu, Samuel Leung, Alejandro A. Gru, Yu Tao, Jeremy Hoog, Julie Ho, Sherri R. Davies, D. Craig Allred, Andrea L. Salavaggione, Jacqueline Snider, Elaine R. Mardis, Torsten O. Nielsen, Matthew J. Ellis Tags: Regular article Source Type: research

Diagnostic Quality Assurance Pilot
This Editorial highlights a model demonstrating laboratory test performance with a companion diagnostic assay. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 16, 2016 Category: Pathology Authors: Barbara Zehnbauer, Catherine Lofton-Day, John Pfeifer, Elizabeth Shaughnessy, Lindee Goh Tags: Editorial Source Type: research

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer
Widespread clinical laboratory implementation of next-generation sequencing –based cancer testing has highlighted the importance and potential benefits of standardizing the interpretation and reporting of molecular results among laboratories. A multidisciplinary working group tasked to assess the current status of next-generation sequencing–based cancer testing and esta blish standardized consensus classification, annotation, interpretation, and reporting conventions for somatic sequence variants was convened by the Association for Molecular Pathology with liaison representation from the American College of Med...
Source: Journal of Molecular Diagnostics - December 16, 2016 Category: Pathology Authors: Marilyn M. Li, Michael Datto, Eric J. Duncavage, Shashikant Kulkarni, Neal I. Lindeman, Somak Roy, Apostolia M. Tsimberidou, Cindy L. Vnencak-Jones, Daynna J. Wolff, Anas Younes, Marina N. Nikiforova Tags: Special article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 16, 2016 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 16, 2016 Category: Pathology Source Type: research

PITX2 DNA Methylation as Biomarker for Individualized Risk Assessment of Prostate Cancer in Core Biopsies
Hypermethylation of the paired-like homeodomain transcription factor 2 (PITX2) gene is a strong predictor of the risk of biochemical recurrence in patients with prostate cancer (PCa) after radical prostatectomy. We investigate whether PITX2 methylation is feasible for individualized risk assessment in prostate core biopsies before surgery. A quantitative, methylation-specific real-time PCR was used to measure PITX2 in three cohorts: i) matched samples of neoplastic and nonneoplastic tissue from 24 patients with PCa, ii) a well-characterized cohort of 300 patients with PCa after radical prostatectomy, and iii) core biopsy s...
Source: Journal of Molecular Diagnostics - December 8, 2016 Category: Pathology Authors: Barbara Uhl, Heidrun Gevensleben, Yuri Tolkach, Verena Sailer, Michael Majores, Maria Jung, Sebastian Meller, Johannes Stein, J örg Ellinger, Dimo Dietrich, Glen Kristiansen Tags: Regular article Source Type: research

Analytical Validation of Androgen Receptor Splice Variant 7 Detection in a Clinical Laboratory Improvement Amendments (CLIA) Laboratory Setting
Patients with castration-resistant prostate cancer (CRPC) often are treated with drugs that target the androgen receptor (AR) ligand-binding domain. Constitutively active AR splice variant 7 (AR-V7) lacks the ligand-binding domain and, if detected in circulating tumor cells, may be associated with resistance to these agents. We validated an AR-V7 assay in a Clinical Laboratory Improvement Amendments (CLIA) –certified laboratory. Circulating tumor cells were isolated, and mRNA was reverse-transcribed into cDNA. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 2, 2016 Category: Pathology Authors: Parvez M. Lokhandwala, Stacy L. Riel, Lisa Haley, Changxue Lu, Yan Chen, John Silberstein, Yezi Zhu, Gang Zheng, Ming-Tseh Lin, Christopher D. Gocke, Alan W. Partin, Emmanuel S. Antonarakis, Jun Luo, James R. Eshleman Tags: Regular article Source Type: research

Application of Single-Molecule Amplification and Resequencing Technology for Broad Surveillance of Plasma Mutations in Patients with Advanced Lung Adenocarcinoma
Liquid biopsy to access the circulating tumor DNA is a promising surrogate for invasive tumor genotyping. We designed a multiplex assay based on circulating single-molecule amplification and resequencing technology (cSMART) to simultaneously detect and quantitate hot spot EGFR, KRAS, BRAF, ERBB2, and ALK plasma DNA variants in 103 patients with advanced lung adenocarcinoma. In validation studies using an analytical mutation standard, the sensitivity of the assay for EGFR mutation detection was at least 0.1% and specificity was 100%. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 18, 2016 Category: Pathology Authors: Zheng Wang, Gang Cheng, Xiaohong Han, Xinlin Mu, Yuhui Zhang, Di Cui, Chang Liu, Li Zhang, Zaiwen Fan, Lingyun Ma, Li Yang, Jing Di, David S. Cram, Yuankai Shi, Dongge Liu Tags: Regular Article Source Type: research

A Comparison of Cell-Free DNA Isolation Kits
In this study, we compared the isolation efficiency of the QIAamp circulating nucleic acid kit (QIA) with four other cfDNA isolation kits: the PME free-circulating DNA Extraction Kit (PME), the Maxwell RSC ccfDNA Plasma Kit (RSC), the EpiQuick Circulating Cell-Free DNA Isolation Kit (EQ), and two consecutive versions of the NEXTprep-Mag cfDNA Isolation Kit (NpMV1/2). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2016 Category: Pathology Authors: Laure Sorber, Karen Zwaenepoel, Vanessa Deschoolmeester, Geert Roeyen, Filip Lardon, Christian Rolfo, Patrick Pauwels Tags: Regular Article Source Type: research

In Silico Proficiency Testing for Clinical Next-Generation Sequencing
Quality assurance for clinical next-generation sequencing (NGS) –based assays is difficult given the complex methods and the range of sequence variants such assays can detect. As the number and range of mutations detected by clinical NGS assays has increased, it is difficult to apply standard analyte-specific proficiency testing (PT). Most current proficiency testing challenges for NGS are methods-based PT surveys that use DNA from reference samples engineered to harbor specific mutations that test both sequence generation and bioinformatics analysis. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 15, 2016 Category: Pathology Authors: Eric J. Duncavage, Haley J. Abel, John D. Pfeifer Tags: Mini-Review Source Type: research

Detection of Mismatch Repair Deficiency and Microsatellite Instability in Colorectal Adenocarcinoma by Targeted Next Generation Sequencing
Mismatch repair protein deficiency (MMR-D) and high microsatellite instability (MSI-H) are features of Lynch syndrome –associated colorectal carcinomas and have implications in clinical management. We evaluate the ability of a targeted next-generation sequencing panel to detect MMR-D and MSI-H based on mutational phenotype. Using a criterion of>40 total mutations per megabase or>5 single-base insertion or deletion mutations in repeats per megabase, sequencing achieves 92% sensitivity and 100% specificity for MMR-D by immunohistochemistry in a training cohort of 149 colorectal carcinomas and 91% sensitivity...
Source: Journal of Molecular Diagnostics - November 15, 2016 Category: Pathology Authors: Jonathan A. Nowak, Matthew B. Yurgelun, Jacqueline L. Bruce, Vanesa Rojas-Rudilla, Dimity L. Hall, Priyanka Shivdasani, Elizabeth P. Garcia, Agoston T. Agoston, Amitabh Srivastava, Shuji Ogino, Frank C. Kuo, Neal I. Lindeman, Fei Dong Tags: Regular Article Source Type: research

Applications of DNA-Based Liquid Biopsy for Central Nervous System Neoplasms
The management of central nervous system malignancies remains reliant on histopathological analysis and neuroimaging, despite their complex genetic profile. The intratumoral heterogeneity displayed by these tumors necessitates a more sophisticated method of tumor analysis and monitoring, with the ability to assess tumors over space and time. Circulating biomarkers, including circulating tumor cells, circulating tumor DNA, and extracellular vesicles, hold promise as a type of real-time liquid biopsy able to provide dynamic information not only regarding tumor burden to monitor disease progression and treatment response, but...
Source: Journal of Molecular Diagnostics - November 15, 2016 Category: Pathology Authors: Joanna Wang, Chetan Bettegowda Tags: Review Source Type: research

Validation of a Gene Expression Test for Mesothelioma Prognosis in Formalin-Fixed Paraffin-Embedded Tissues
A molecular test performed using fresh-frozen tissue was proposed for use in the prognosis of patients with pleural mesothelioma. The accuracy of the test and its properties was assessed under Clinical Laboratory Improvement Amendments –approved guidelines using FFPE tissue from an independent multicenter patient cohort. Concordance studies were performed using matched frozen and FFPE mesothelioma samples. The prognostic value of the test was evaluated in an independent validation cohort of 73 mesothelioma patients who underwent surgical resection. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 15, 2016 Category: Pathology Authors: Assunta De Rienzo, Robert W. Cook, Jeff Wilkinson, Corinne E. Gustafson, Waqas Amin, Clare E. Johnson, Kristen M. Oelschlager, Derek J. Maetzold, John F. Stone, Michael D. Feldman, Michael J. Becich, Beow Y. Yeap, William G. Richards, Raphael Bueno Tags: Regular Article Source Type: research

Detection of CALR and MPL Mutations in Low Allelic Burden JAK2 V617F Essential Thrombocythemia
Myeloproliferative neoplasms are clonal hematopoietic stem cell disorders characterized by aberrant proliferation and an increased tendency toward leukemic transformation. The genes JAK2, MPL, and CALR are frequently altered in these syndromes, and their mutations are often a strong argument for diagnosis. We analyzed the mutational profiles of these three genes in a cohort of 164 suspected myeloproliferative neoplasms. JAK2 V617F mutation was detected by real-time PCR, whereas high-resolution melting analysis followed by Sanger sequencing were used for searching for mutations in JAK2 exon 12, CALR, and MPL. (Source: Journ...
Source: Journal of Molecular Diagnostics - November 14, 2016 Category: Pathology Authors: Fabrice Usseglio, Nathalie Beaufils, Anne Calleja, Sophie Raynaud, Jean Gabert Tags: Regular Article Source Type: research

Deamination Effects in Formalin-Fixed, Paraffin-Embedded Tissue Samples in the Era of Precision Medicine
Deamination of nucleotides causes C:G>T:A changes in formalin-fixed, paraffin-embedded (FFPE) tissue samples and produces false positives during next-generation sequencing (NGS). Uracil DNA glycosylase (UDG) helps eliminate this issue, but the effect of UDG in different tissue preparation conditions has not been rigorously studied. To investigate whether UDG can reduce false-positive single-nucleotide variant (SNV) calls, we used tumor and normal tissues from gastric adenocarcinoma patients prepared using different fixation times and pH conditions. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 10, 2016 Category: Pathology Authors: Seokhwi Kim, Charny Park, Yongick Ji, Deok G. Kim, Hyunsik Bae, Michael van Vrancken, Duk-Hwan Kim, Kyoung-Mee Kim Tags: Regular Article Source Type: research

Methodologic Considerations in the Application of Next-Generation Sequencing of Human TRB Repertoires for Clinical Use
Next-generation sequencing (NGS) of immune receptors has become a standard tool to assess minimal residual disease (MRD) in patients treated for lymphoid malignancy, and it is being used to study the T-cell repertoire in many clinical settings. To better understanding the potential clinical utility and limitations of this application outside of MRD, we developed a BIOMED-2 primer –based NGS method and characterized its performance in controls and patients with graft-versus-host disease (GVHD) after allogeneic hematopoietic transplant. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 1, 2016 Category: Pathology Authors: Liwen Xu, Xiaoqing You, PingPing Zheng, Bing M. Zhang, Puja K. Gupta, Philip Lavori, Everett Meyer, James L. Zehnder Tags: Regular Article Source Type: research

FOXL2 402C > G Mutation Can Be Identified in the Circulating Tumor DNA of Patients with Adult-Type Granulosa Cell Tumor
Adult granulosa cell tumors (AGCTs) of the ovary are molecularly characterized by the pathognomonic FOXL2 402C>G (C134W) mutation. To improve diagnostics and follow-up, we developed a specific digital droplet PCR (ddPCR) assay to detect the FOXL2 mutation in the circulating tumor DNA (ctDNA) of AGCT patients. Optimization of the ddPCR assay was performed using a TaqMan primer/probe with the RainDance RainDrop digital PCR system. The ddPCR assay was performed on circulating cell-free DNA extracted from 120 serial plasma samples collected prospectively from 35 AGCT patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 31, 2016 Category: Pathology Authors: Anniina F ärkkilä, Melissa K. McConechy, Winnie Yang, Aline Talhouk, Ying Ng, Amy Lum, Ryan D. Morin, Kevin Bushell, Annika Riska, Jessica N. McAlpine, C. Blake Gilks, Leila Unkila-Kallio, Mikko Anttonen, David G. Huntsman Tags: Regular article Source Type: research

Differences in Microsatellite Instability Profiles between Endometrioid and Colorectal Cancers
Colorectal (CRCs) and endometrioid (EMCs) cancers in patients with Lynch syndrome exhibit microsatellite instability (MSI) detected by PCR or IHC. While both assays are equally sensitive for CRCs, some suggest that MSI has a higher false-negative rate than does IHC in EMCs. We assessed the MSI profiles of 91 EMC and 311 CRC specimens using five mononucleotide repeat markers: BAT25, BAT26, NR21, NR24, and MONO27. EMCs with high MSI (MSI-H) showed a mean left shift of 3 nucleotides (nt), which was significantly different from 6 nt in CRCs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 31, 2016 Category: Pathology Authors: Yang Wang, Chanjuan Shi, Rosana Eisenberg, Cindy L. Vnencak-Jones Tags: Regular Article Source Type: research