Preemptive Pharmacogenomic Testing for Precision Medicine
Significant barriers, such as lack of professional guidelines, specialized training for interpretation of pharmacogenomics (PGx) data, and insufficient evidence to support clinical utility, prevent preemptive PGx testing from being widely clinically implemented. The current study, as a pilot project for the Right Drug, Right Dose, Right Time–Using Genomic Data to Individualize Treatment Protocol, was designed to evaluate the impact of preemptive PGx and to optimize the workflow in the clinic setting. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 3, 2016 Category: Pathology Authors: Yuan Ji, Jennifer M. Skierka, Joseph H. Blommel, Brenda E. Moore, Douglas L. VanCuyk, Jamie K. Bruflat, Lisa M. Peterson, Tamra L. Veldhuizen, Numrah Fadra, Sandra E. Peterson, Susan A. Lagerstedt, Laura J. Train, Linnea M. Baudhuin, Eric W. Klee, Matthew Tags: Regular Article Source Type: research

Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens
Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed, paraffin-embedded biopsy specimens has many unique challenges. Herein, we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers in diagnostic prostate needle core biopsy specimens. One-hundred fifty-eight samples from diagnostic needle core biopsy specimens (Bx) and radical prostatectomies (RPs) were collected from 33 patients at three hospitals; each patient provided up to six tumor and benign samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 2, 2016 Category: Pathology Authors: Beatrice S. Knudsen, Hyung L. Kim, Nicholas Erho, Heesun Shin, Mohammed Alshalalfa, Lucia L.C. Lam, Imelda Tenggara, Karen Chadwich, Theo Van Der Kwast, Neil Fleshner, Elai Davicioni, Peter R. Carroll, Matthew R. Cooperberg, June M. Chan, Jeffry P. Simko Tags: Regular Article Source Type: research

Detection and Quantification of Mosaic Mutations in Disease Genes by Next-Generation Sequencing
The identification of mosaicism is important in establishing a disease diagnosis, assessing recurrence risk, and genetic counseling. Next-generation sequencing (NGS) with deep sequence coverage enhances sensitivity and allows for accurate quantification of the level of mosaicism. NGS identifies low-level mosaicism that would be undetectable by conventional Sanger sequencing. A customized DNA probe library was used for capturing targeted genes, followed by deep NGS analysis. The mean coverage depth per base was approximately 800×. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 1, 2016 Category: Pathology Authors: Lan Qin, Jing Wang, Xia Tian, Hui Yu, Cavatina Truong, John J. Mitchell, Klaas J. Wierenga, William J. Craigen, Victor Wei Zhang, Lee-Jun C. Wong Tags: Regular Article Source Type: research

Eligibility Criteria and Genetic Testing Results from a High-Risk Cohort for Hereditary Breast and Ovarian Cancer Syndrome in Southeastern Ontario
Germline mutations in breast and ovarian cancer are rare, with approximately 5% to 10% and 13% being hereditary in origin, respectively. In 2001, the Ontario Ministry of Health and Long Term Care, in an effort to contain costs, defined criteria to determine an individual's eligibility for BRCA genetic screening. We studied a cohort of individuals that have undergone genetic testing at Kingston General Hospital between 2001 and late 2013. We focused on determining whether the 13 risk criteria, defined by an expert working group for the Ontario Ministry of Health and Long Term Care, have performed according to expectations i...
Source: Journal of Molecular Diagnostics - February 29, 2016 Category: Pathology Authors: Ricardo dos Santos Vidal, Andrea Hawrysh, Jagdeep S. Walia, Scott Davey, Harriet Feilotter Tags: Regular Article Source Type: research

Sensitivity Analysis of the MGMT-STP27 Model and Impact of Genetic and Epigenetic Context to Predict the Methylation Status in Gliomas and Other Tumors
The methylation status of the O6-methylguanine-DNA methyltransferase (MGMT) gene is an important predictive biomarker for benefit from alkylating agent therapy in glioblastoma. Our model MGMT-STP27 allows prediction of the methylation status of the MGMT promoter by using data from the HumanMethylationBeadChip (Illumina, HM-27K, and HM-450K) that is publically available for many cancer data sets. Here, we present investigations addressing the impact of the context of genetic and epigenetic alterations and tumor type on the classification and report on technical aspects, such as robustness of cutoff definition and preprocess...
Source: Journal of Molecular Diagnostics - February 26, 2016 Category: Pathology Authors: Pierre Bady, Mauro Delorenzi, Monika E. Hegi Source Type: research

The Pitfalls of Companion Diagnostics
We present two cases in which central laboratories inaccurately reported EGFR mutation status because of improper identification and isolation of tumor material and failure to accurately report assay limitations, resulting in enrollment denial. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 25, 2016 Category: Pathology Authors: Scott A. Turner, Jason D. Peterson, Jason R. Pettus, Francine B. de Abreu, Christopher I. Amos, Konstantin H. Dragnev, Gregory J. Tsongalis Tags: Technical Advance Source Type: research

Multicenter Evaluation of a Novel, Automated Rapid Detection System of BRAF Status in Formalin-Fixed, Paraffin-Embedded Tissues
The mutated BRAF oncogene represents a therapeutic target in malignant melanoma. Because BRAF mutations are also involved in the pathogenesis of other human malignancies, the use of specific BRAF inhibitors might also be extended to other diseases in the future. A prerequisite for the clinical application of BRAF inhibitors is the reliable detection of activating BRAF mutations in routine histopathological samples. In a multicenter approach, we evaluated a novel and fully automated PCR-based system (Idylla) capable of detecting BRAF V600 mutations in formalin-fixed, paraffin-embedded tissue within 90 minutes with high sens...
Source: Journal of Molecular Diagnostics - February 24, 2016 Category: Pathology Authors: Ana-Iris Schiefer, Laura Parlow, Lisa Gabler, Ildiko Mesteri, Oskar Koperek, Andreas von Deimling, Berthold Streubel, Matthias Preusser, Annika Lehmann, Udo Kellner, Patrick Pauwels, Suzan Lambin, Manfred Dietel, Michael Hummel, Frederick Klauschen, Peter Tags: Regular Article Source Type: research

Multicenter Evaluation of a Novel, Automated Rapid Detection System of Status in Formalin-Fixed, Paraffin-Embedded Tissues
The mutated BRAF oncogene represents a therapeutic target in malignant melanoma. Because BRAF mutations are also involved in the pathogenesis of other human malignancies, the use of specific BRAF inhibitors might also be extended to other diseases in the future. A prerequisite for the clinical application of BRAF inhibitors is the reliable detection of activating BRAF mutations in routine histopathological samples. In a multicenter approach, we evaluated a novel and fully automated PCR-based system (Idylla) capable of detecting BRAF V600 mutations in formalin-fixed, paraffin-embedded tissue within 90 minutes with high sens...
Source: Journal of Molecular Diagnostics - February 24, 2016 Category: Pathology Authors: Ana-Iris Schiefer, Laura Parlow, Lisa Gabler, Ildiko Mesteri, Oskar Koperek, Andreas von Deimling, Berthold Streubel, Matthias Preusser, Annika Lehmann, Udo Kellner, Patrick Pauwels, Suzan Lambin, Manfred Dietel, Michael Hummel, Frederick Klauschen, Peter Tags: Regular Article Source Type: research

The Application of Molecular Diagnostics to Stained Cytology Smears
Detection of mutational alterations is important for guiding treatment decisions of lung non–small-cell carcinomas and thyroid nodules with atypical cytologic findings. Inoperable lung tumors requiring further testing for staging and thyroid lesions often are diagnosed using only cytology material. Molecular diagnostic tests of these samples typically are performed on cell blocks; however, insufficient cellularity of cell blocks is a limitation for test performance. In addition, some of the fixatives used while preparing cell blocks often introduces artifacts for mutation detection. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 24, 2016 Category: Pathology Authors: Maja H. Oktay, Esther Adler, Laleh Hakima, Eli Grunblatt, Evan Pieri, Andrew Seymour, Samer Khader, Antonio Cajigas, Mark Suhrland, Sumanta Goswami Tags: Regular Article Source Type: research

Multicenter Evaluation of a Novel Automated Rapid Detection System of BRAF Status in Formalin-Fixed, Paraffin-Embedded Tissues
The mutated BRAF oncogene represents a therapeutic target in malignant melanoma. Because BRAF mutations are also involved in the pathogenesis of other human malignancies, the use of specific BRAF inhibitors might also be extended to other diseases in the future. A prerequisite for the clinical application of BRAF inhibitors is the reliable detection of activating BRAF mutations in routine histopathological samples. In a multicenter approach, we evaluated a novel and fully automated PCR-based system (Idylla) capable of detecting BRAF V600 mutations in formalin-fixed, paraffin-embedded tissue within 90 minutes with high sens...
Source: Journal of Molecular Diagnostics - February 24, 2016 Category: Pathology Authors: Ana-Iris Schiefer, Laura Parlow, Lisa Gabler, Ildiko Mesteri, Oskar Koperek, Andreas von Deimling, Berthold Streubel, Matthias Preusser, Annika Lehmann, Udo Kellner, Patrick Pauwels, Suzan Lambin, Manfred Dietel, Michael Hummel, Frederick Klauschen, Peter Tags: Regular article 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, 2015. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 11, 2016 Category: Pathology Tags: Reviewer acknowledgment Source Type: research

The Challenges of Applying Massively Parallel Sequencing to Newborn Screening for Cystic Fibrosis
This Commentary highlights the article by Lefterova et al that describes newborn screening of cystic fibrosis using massively parallel sequencing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 11, 2016 Category: Pathology Authors: Lawrence M. Silverman Tags: Commentary Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 11, 2016 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 11, 2016 Category: Pathology Source Type: research

Instructions for Authors
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 11, 2016 Category: Pathology Source Type: research

Scientific Integrity Policy
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 11, 2016 Category: Pathology Source Type: research

Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development
In this study, we measure the magnitude and pattern of differential methylation of this region across colon, lung, breast, stomach, and endometrial tumor samples using next-generation bisulfite amplicon sequencing. We found that all tumor types and subtypes are hypermethylated at this locus compared with normal tissue. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 5, 2016 Category: Pathology Authors: Gennady Margolin, Hanna M. Petrykowska, Nader Jameel, Daphne W. Bell, Alice C. Young, Laura Elnitski Tags: Regular article Source Type: research

A Suggested Molecular Pathology Curriculum for Residents
Molecular pathology is an essential element of pathology training. As more molecular tests have become available, there is an increasing need for pathology trainees to receive a strong foundation in molecular pathology. Appointed by the Training and Education Committee of the Association for Molecular Pathology, the Molecular Curriculum Task Force has developed a suggested curriculum in molecular pathology for residents. The foundations of molecular pathology are presented as a series of goals and objectives that residency programs can use to develop their educational programs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 5, 2016 Category: Pathology Authors: Dara L. Aisner, Anna Berry, D. Brian Dawson, Randall T. Hayden, Loren Joseph, Charles E. Hill Tags: Special article Source Type: research

Next-Generation Sequencing-Assisted DNA-Based Digital PCR for a Personalized Approach to the Detection and Quantification of Residual Disease in Chronic Myeloid Leukemia Patients
Recent studies indicate that 40% of chronic myeloid leukemia patients who achieve sustained undetectable BCR-ABL1 transcripts on tyrosine kinase inhibitor therapy remain disease-free after drug discontinuation. In contrast, 60% experience return of detectable disease and have to restart treatment, thus highlighting the need for an improved method of identifying patients with the lowest likelihood of relapse. Here we describe the validation of a personalized DNA-based digital PCR (dPCR) approach for quantifying very low levels of residual disease, which involves the rapid identification of t(9;22) fusion junctions using tar...
Source: Journal of Molecular Diagnostics - February 5, 2016 Category: Pathology Authors: Mary Alikian, Peter Ellery, Martin Forbes, Gareth Gerrard, Dalia Kasperaviciute, Alona Sosinsky, Michael Mueller, Alexandra S. Whale, Dragana Milojkovic, Jane Apperley, Jim F. Huggett, Letizia Foroni, Alistair G. Reid Tags: Regular Article Source Type: research

Robust Detection of DNA Hypermethylation of as a Pan-Cancer Locus with Modeling for Blood-Based Diagnostic Development
In this study, we measure the magnitude and pattern of differential methylation of this region across colon, lung, breast, stomach, and endometrial tumor samples using next-generation bisulfite amplicon sequencing. We found that all tumor types and subtypes are hypermethylated at this locus compared with normal tissue. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 5, 2016 Category: Pathology Authors: Gennady Margolin, Hanna M. Petrykowska, Nader Jameel, Daphne W. Bell, Alice C. Young, Laura Elnitski Tags: Regular Article Source Type: research

Next-Generation Molecular Testing of Newborn Dried Blood Spots for Cystic Fibrosis
Newborn screening for cystic fibrosis enables early detection and management of this debilitating genetic disease. Implementing comprehensive CFTR analysis using Sanger sequencing as a component of confirmatory testing of all screen-positive newborns has remained impractical due to relatively lengthy turnaround times and high cost. Here, we describe CFseq, a highly sensitive, specific, rapid ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 1, 2016 Category: Pathology Authors: Martina I. Lefterova, Peidong Shen, Justin I. Odegaard, Eula Fung, Tsoyu Chiang, Gang Peng, Ronald W. Davis, Wenyi Wang, Martin Kharrazi, Iris Schrijver, Curt Scharfe Tags: Regular Article Source Type: research

Clinical Validation and Implementation of a Targeted Next-Generation Sequencing Assay to Detect Somatic Variants in Non–Small Cell Lung, Melanoma, and Gastrointestinal Malignancies
We tested and clinically validated a targeted next-generation sequencing (NGS) mutation panel using 80 formalin-fixed, paraffin-embedded (FFPE) tumor samples. Forty non-small cell lung carcinoma, 30 melanoma, and 30 gastrointestinal (12 colonic, 10 gastric, and 8 pancreatic adenocarcinoma) FFPE samples were selected from laboratory archives. After appropriate specimen and nucleic acid quality control, 80 NGS libraries were prepared using the Illumina TruSight tumor (TST) kit and sequenced on the Illumina MiSeq. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 19, 2016 Category: Pathology Authors: Kevin E. Fisher, Linsheng Zhang, Jason Wang, Geoffrey H. Smith, Scott Newman, Thomas M. Schneider, Rathi N. Pillai, Ragini R. Kudchadkar, Taofeek K. Owonikoko, Suresh S. Ramalingam, David H. Lawson, Keith A. Delman, Bassel F. El-Rayes, Malania M. Wilson, Source Type: research

Analytical Validation of a Personalized Medicine APOL1 Genotyping Assay for Nondiabetic Chronic Kidney Disease Risk Assessment
The incidence of chronic kidney disease (CKD) varies by ancestry, with African Americans (AA) having a threefold to fourfold higher rate than whites. Notably, two APOL1 alleles, termed G1 [c.(1072A>G; 1200T>G)] and G2 (c.1212_1217del6), are strongly associated with higher rates of nondiabetic CKD and an increased risk for hypertensive end-stage renal disease. This has prompted the opportunity to implement APOL1 testing to identify at-risk patients and modify other risk factors to reduce the progression of CKD to end-stage renal disease. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 7, 2016 Category: Pathology Authors: Jinglan Zhang, Anastasia Fedick, Stephanie Wasserman, Geping Zhao, Lisa Edelmann, Erwin P. Bottinger, Ruth Kornreich, Stuart A. Scott Tags: Regular article Source Type: research

Analytical Validation of a Personalized Medicine Genotyping Assay for Nondiabetic Chronic Kidney Disease Risk Assessment
The incidence of chronic kidney disease (CKD) varies by ancestry, with African Americans (AA) having a threefold to fourfold higher rate than whites. Notably, two APOL1 alleles, termed G1 [c.(1072A>G; 1200T>G)] and G2 (c.1212_1217del6), are strongly associated with higher rates of nondiabetic CKD and an increased risk for hypertensive end-stage renal disease. This has prompted the opportunity to implement APOL1 testing to identify at-risk patients and modify other risk factors to reduce the progression of CKD to end-stage renal disease. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 7, 2016 Category: Pathology Authors: Jinglan Zhang, Anastasia Fedick, Stephanie Wasserman, Geping Zhao, Lisa Edelmann, Erwin P. Bottinger, Ruth Kornreich, Stuart A. Scott Tags: Regular Article Source Type: research

Quantitative Detection and Resolution of BRAF V600 Status in Colorectal Cancer Using Droplet Digital PCR and a Novel Wild-Type Negative Assay
We report a diagnostic technology that leverages the unique capabilities of droplet digital PCR to achieve not only accurate and sensitive detection of BRAFV600E but also all known somatic point mutations within the BRAF V600 codon. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 4, 2016 Category: Pathology Authors: Roza Bidshahri, Dean Attali, Kareem Fakhfakh, Kelly McNeil, Aly Karsan, Jennifer R. Won, Robert Wolber, Jennifer Bryan, Curtis Hughesman, Charles Haynes Tags: Regular article Source Type: research

Quantitative Detection and Resolution of V600 Status in Colorectal Cancer Using Droplet Digital PCR and a Novel Wild-Type Negative Assay
We report a diagnostic technology that leverages the unique capabilities of droplet digital PCR to achieve not only accurate and sensitive detection of BRAFV600E but also all known somatic point mutations within the BRAF V600 codon. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 4, 2016 Category: Pathology Authors: Roza Bidshahri, Dean Attali, Kareem Fakhfakh, Kelly McNeil, Aly Karsan, Jennifer R. Won, Robert Wolber, Jennifer Bryan, Curtis Hughesman, Charles Haynes Tags: Regular Article Source Type: research

Identification of Combinatorial Genomic Abnormalities Associated with Prostate Cancer Early Recurrence
Multiple biomarkers are needed to distinguish aggressive from indolent prostate cancer. We tested the prognostic utility of a three-marker fluorescent in situ hybridization panel (TMPRSS2/ERG rearrangements, AR gain, and PTEN deletion) in a retrospective cohort (n = 210; median follow-up, 5.7 years). PTEN deletion was associated with an increased risk of biochemical recurrence (BcR; hazard ratio, 3.58; 95% CI, 1.39–9.22; P  (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 2, 2016 Category: Pathology Authors: Xiaoyu Qu, Claudio Jeldres, Lena Glaskova, Cynthia Friedman, Sarah Schroeder, Peter S. Nelson, Christopher Porter, Min Fang Tags: Regular Article Source Type: research

Multiplex Preamplification of Serum DNA to Facilitate Reliable Detection of Extremely Rare Cancer Mutations in Circulating DNA by Digital PCR
Tumor-specific mutations can be identified in circulating, cell-free DNA in plasma or serum and may serve as a clinically relevant alternative to biopsy. Detection of tumor-specific mutations in the plasma, however, is technically challenging. First, mutant allele fractions are typically low in a large background of wild-type circulating, cell-free DNA. Second, the amount of circulating, cell-free DNA acquired from plasma is also low. Even when using digital PCR (dPCR), rare mutation detection is challenging because there is not enough circulating, cell-free DNA to run technical replicates and assay or instrument noise doe...
Source: Journal of Molecular Diagnostics - January 2, 2016 Category: Pathology Authors: Jennifer B. Jackson, Daniel S. Choi, James D. Luketich, Arjun Pennathur, Anders Ståhlberg, Tony E. Godfrey Source Type: research

Assessment of Targeted Next-Generation Sequencing as a Tool for the Diagnosis of Charcot-Marie-Tooth Disease and Hereditary Motor Neuropathy
Charcot-Marie-Tooth disease is characterized by broad genetic heterogeneity with>50 known disease-associated genes. Mutations in some of these genes can cause a pure motor form of hereditary motor neuropathy, the genetics of which are poorly characterized. We designed a panel comprising 56 genes associated with Charcot-Marie-Tooth disease/hereditary motor neuropathy. We validated this diagnostic tool by first testing 11 patients with pathological mutations. A cohort of 33 affected subjects was selected for this study. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 2, 2016 Category: Pathology Authors: Vincenzo Lupo, Francisco García-García, Paula Sancho, Cristina Tello, Mar García-Romero, Liliana Villarreal, Antonia Alberti, Rafael Sivera, Joaquín Dopazo, Samuel I. Pascual-Pascual, Celedonio Márquez-Infante, Carlos Casasnovas, Teresa Sevilla, Carm Tags: Regular Article Source Type: research

Three Rounds of External Quality Assessment in France to Evaluate the Performance of 28 Platforms for Multiparametric Molecular Testing in Metastatic Colorectal and Non-Small Cell Lung Cancer
Personalized medicine has gained increasing importance in clinical oncology, and several clinically important biomarkers are implemented in routine practice. In an effort to guarantee high quality of molecular testing in France, three subsequent external quality assessment rounds were organized at the initiative of the National Cancer Institute between 2012 and 2014. The schemes included clinically relevant biomarkers for metastatic colorectal (KRAS, NRAS, BRAF, PIK3CA, microsatellite instability) and non-small cell lung cancer (EGFR, KRAS, BRAF, PIK3CA, ERBB2), and they represent the first multigene/multicancer studies th...
Source: Journal of Molecular Diagnostics - January 2, 2016 Category: Pathology Authors: Elisabeth M.C. Dequeker, Cleo Keppens, Caroline Egele, Sofie Delen, Aude Lamy, Antoinette Lemoine, Jean-Christophe Sabourin, Catherine Andrieu, Marjolijn Ligtenberg, Dominique Fetique, Bastiaan Tops, Clotilde Descarpentries, Hélène Blons, Yves Denoux, C Tags: Regular Article Source Type: research

A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing
We describe a next-generation sequencing approach that uses a multiplex PCR-based amplicon panel to interrogate fusion transcripts that involve 19 driver genes and 94 partners implicated in solid tumors. The panel also includes control assays that evaluate the 3′/5′ expression ratios of 12 oncogenic kinases, which might be used to infer gene fusion events when the partner is unknown or not included on the panel. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 30, 2015 Category: Pathology Authors: Carol Beadling, Abigail I. Wald, Andrea Warrick, Tanaya L. Neff, Shan Zhong, Yuri E. Nikiforov, Christopher L. Corless, Marina N. Nikiforova Tags: Technical Advance Source Type: research

External Quality Assessment for Detection of Fetal Trisomy 21, 18, and 13 by Massively Parallel Sequencing in Clinical Laboratories
An external quality assessment for detection of trisomy 21, 18, and 13 by massively parallel sequencing was implemented by the National Center for Clinical Laboratories of People's Republic of China in 2014. Simulated samples were prepared by mixing fragmented abnormal DNA with plasma from non-pregnant women. The external quality assessment panel, comprising 5 samples from pregnant healthy women, 2 samples with sex chromosome aneuploidies, and 13 samples with different concentrations of fetal fractions positive for trisomy 21, 18, and 13, was then distributed to participating laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 30, 2015 Category: Pathology Authors: Rui Zhang, Hongyun Zhang, Yulong Li, Yanxi Han, Jiehong Xie, Jinming Li Source Type: research

Pitfalls of Multiple Ligation-Dependent Probe Amplifications in Detecting DMD Exon Deletions or Duplications
Multiple ligation-dependent probe amplifications (MLPAs) are a key technology for the molecular diagnosis of Duchenne/Becker muscular dystrophy, which is mainly caused by large gene arrangements. However, little is known about the false-positive rates of MLPA for this disease. Here, we review MLPA analysis results from 398 patients suspected to have Duchenne/Becker muscular dystrophy. MLPA assay was used for screening the entire coding region. If these amplifications produced normal results, direct sequencing was performed to search for sequence variations and to determine single-exon deletions, duplications, or indetermin...
Source: Journal of Molecular Diagnostics - December 29, 2015 Category: Pathology Authors: Man Jin Kim, Sung Im Cho, Jong-Hee Chae, Byung Chan Lim, Jee-Soo Lee, Seung Jun Lee, Soo Hyun Seo, Hyunwoong Park, Anna Cho, So Yeon Kim, Ji Yeon Kim, Sung Sup Park, Moon-Woo Seong Tags: Regular article Source Type: research

Pitfalls of Multiple Ligation-Dependent Probe Amplifications in Detecting Exon Deletions or Duplications
Multiple ligation-dependent probe amplifications (MLPAs) are a key technology for the molecular diagnosis of Duchenne/Becker muscular dystrophy, which is mainly caused by large gene arrangements. However, little is known about the false-positive rates of MLPA for this disease. Here, we review MLPA analysis results from 398 patients suspected to have Duchenne/Becker muscular dystrophy. MLPA assay was used for screening the entire coding region. If these amplifications produced normal results, direct sequencing was performed to search for sequence variations and to determine single-exon deletions, duplications, or indetermin...
Source: Journal of Molecular Diagnostics - December 29, 2015 Category: Pathology Authors: Man Jin Kim, Sung Im Cho, Jong-Hee Chae, Byung Chan Lim, Jee-Soo Lee, Seung Jun Lee, Soo Hyun Seo, Hyunwoong Park, Anna Cho, So Yeon Kim, Ji Yeon Kim, Sung Sup Park, Moon-Woo Seong Source Type: research

The Spectrum of Variants in Nonwhite Cystic Fibrosis Patients
Despite the implementation of cystic fibrosis (CF) newborn screening programs across the United States, the identification of CFTR gene variants in nonwhite populations compared with whites remains suboptimal. Our objective was to establish the spectrum of CFTR variants and their frequencies in CF patients in the United States with African, Native American, Asian, East Indian, or Middle Eastern backgrounds. By using direct DNA sequencing, we identified two CFTR variants in 89 of 140 affected nonwhite individuals with uncharacterized genotypes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2015 Category: Pathology Authors: Iris Schrijver, Lynn Pique, Steve Graham, Michelle Pearl, Athena Cherry, Martin Kharrazi Tags: Regular article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2015 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2015 Category: Pathology Source Type: research

Precision Diagnosis Is a Team Sport
This Editorial discusses the importance of engagement between clinicians and laboratorians in improving diagnosis and reducing diagnostic error. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 16, 2015 Category: Pathology Authors: Barbara A. Zehnbauer, Timothy G. Buchman Tags: Editorial Source Type: research

Cystic Fibrosis
Cystic fibrosis (CF) is an autosomal recessive disease with significant associated morbidity and mortality. It is now appreciated that the broad phenotypic CF spectrum is not explained by obvious genotype-phenotype correlations, suggesting that CF transmembrane conductance regulator (CFTR)–related disease may be because of multiple additive effects. These contributing effects include complex CFTR alleles, modifier genes, mutations in alternative genes that produce CF-like phenotypes, epigenetic factors, and environmental influences. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 26, 2015 Category: Pathology Authors: Marie-Luise Brennan, Iris Schrijver Tags: Review Source Type: research

Detection of Circulating in Patients with Papillary Thyroid Carcinoma
BRAFV600E is a common mutation in papillary thyroid carcinoma (PTC) correlated with aggressive features. Our objective was to assess the feasibility and accuracy of a novel RNA-based blood assay to identify individuals with a high-risk tumor mutation in patients with PTC. Patients with benign or malignant thyroid disorders were included between September 2013 and July 2014 before either thyroidectomy (n = 62) or treatment of recurrent or metastatic PTC (n = 8). RNA was isolated from peripheral blood lymphocytes and reverse transcribed and followed by two rounds of nested PCR amplification with a restric...
Source: Journal of Molecular Diagnostics - November 26, 2015 Category: Pathology Authors: Carrie C. Lubitz, Sareh Parangi, Tammy M. Holm, M. Jordana Bernasconi, Aislyn P. Schalck, Hyunsuk Suh, Konstantinos P. Economopoulos, Viswanath Gunda, Samuel E. Donovan, Peter M. Sadow, Lori J. Wirth, Ryan J. Sullivan, David J. Panka Tags: Regular Article Source Type: research

Development and Validation of a Fully Automated Platform for Extended Blood Group Genotyping
Thirty-five blood group systems, containing>300 antigens, are listed by the International Society of Blood Transfusion. Most of these antigens result from a single nucleotide polymorphism. Blood group typing is conventionally performed by serology. However, this technique has some limitations and cannot respond to the growing demand of blood products typed for a large number of antigens. The knowledge of the molecular basis of these red blood cell systems allowed the implementation of molecular biology methods in immunohematology laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 24, 2015 Category: Pathology Authors: Stephanie Andree Boccoz, Gaelle C. Le Goff, Celine A. Mandon, Benjamin P. Corgier, Loïc J. Blum, Christophe Andre Marquette Tags: Regular Article Source Type: research

Characterization of 137 Genomic DNA Reference Materials for 28 Pharmacogenetic Genes
Pharmacogenetic testing is increasingly available from clinical laboratories. However, only a limited number of quality control and other reference materials are currently available to support clinical testing. To address this need, the Centers for Disease Control and Prevention–based Genetic Testing Reference Material Coordination Program, in collaboration with members of the pharmacogenetic testing community and the Coriell Cell Repositories, has characterized 137 genomic DNA samples for 28 genes commonly genotyped by pharmacogenetic testing assays (CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, C...
Source: Journal of Molecular Diagnostics - November 24, 2015 Category: Pathology Authors: Victoria M. Pratt, Robin E. Everts, Praful Aggarwal, Brittany N. Beyer, Ulrich Broeckel, Ruth Epstein-Baak, Paul Hujsak, Ruth Kornreich, Jun Liao, Rachel Lorier, Stuart A. Scott, Chingying Huang Smith, Lorraine H. Toji, Amy Turner, Lisa V. Kalman Tags: Regular Article Source Type: research

Multiplexed High Resolution Melting Assay for Versatile Sample Tracking in a Diagnostic and Research Setting
Modern experimental procedures in molecular genetics, such as next-generation sequencing experiments, require that samples are taken along a whole series of wet- and dry-laboratory steps. It generally is accepted that by increasing the complexity and number of steps in the experimental pipeline, the risk of sample swaps increases. It therefore is recommended to confirm the identity of each individual sample at the end of any pipeline. Here, we present a versatile assay to determine the identity of samples rapidly and efficiently by genotyping 21 single-nucleotide polymorphisms (SNPs) using multiplex high resolution melting...
Source: Journal of Molecular Diagnostics - November 21, 2015 Category: Pathology Authors: Céline Helsmoortel, R. Frank Kooy, Geert Vandeweyer Tags: Regular article Source Type: research

Multiplexed High-Resolution Melting Assay for Versatile Sample Tracking in a Diagnostic and Research Setting
Modern experimental procedures in molecular genetics, such as next-generation sequencing experiments, require that samples are taken along a whole series of wet- and dry-laboratory steps. It generally is accepted that by increasing the complexity and number of steps in the experimental pipeline, the risk of sample swaps increases. It therefore is recommended to confirm the identity of each individual sample at the end of any pipeline. Here, we present a versatile assay to determine the identity of samples rapidly and efficiently by genotyping 21 single-nucleotide polymorphisms (SNPs) using multiplex high-resolution melting...
Source: Journal of Molecular Diagnostics - November 21, 2015 Category: Pathology Authors: Céline Helsmoortel, R. Frank Kooy, Geert Vandeweyer Tags: Regular Article Source Type: research

Hepatitis C Virus RNA Real-Time Quantitative RT-PCR Method Based on a New Primer Design Strategy
Viral nucleic acids are unstable when improperly collected, handled, and stored, resulting in decreased sensitivity of currently available commercial quantitative nucleic acid testing kits. Using known unstable hepatitis C virus RNA, we developed a real-time quantitative RT-PCR method based on a new primer design strategy to reduce the impact of nucleic acid instability on nucleic acid testing. The performance of the method was evaluated for linearity, limit of detection, precision, specificity, and agreement with commercial hepatitis C virus assays. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 20, 2015 Category: Pathology Authors: Lida Chen, Wenli Li, Kuo Zhang, Rui Zhang, Tian Lu, Mingju Hao, Tingting Jia, Yu Sun, Guigao Lin, Lunan Wang, Jinming Li Tags: Regular Article Source Type: research

Characterization of Deletions of the and Loci by Array Comparative Genomic Hybridization
Thalassemia is among the most common genetic diseases worldwide. α-Thalassemia is usually caused by deletion of one or more of the duplicated HBA genes on chromosome 16. In contrast, most β-thalassemia results from point mutations that decrease or eliminate expression of the HBB gene on chromosome 11. Deletions within the HBB locus result in thalassemia or hereditary persistence of fetal Hb. Although routine diagnostic testing cannot distinguish thalassemia deletions from point mutations, deletional hereditary persistence of fetal Hb is notable for having an elevated HbF level with a normal mean corpuscular volu...
Source: Journal of Molecular Diagnostics - November 20, 2015 Category: Pathology Authors: Daniel E. Sabath, M.A. Bender, Vijay G. Sankaran, Esther Vamos, Alex Kentsis, Hye-Son Yi, Harvey A. Greisman Tags: Regular Article Source Type: research

Analytical Validation and Application of a Targeted Next-Generation Sequencing Mutation-Detection Assay for Use in Treatment Assignment in the NCI-MPACT Trial
Robust and analytically validated assays are essential for clinical studies. We outline an analytical validation study of a targeted next-generation sequencing mutation-detection assay used for patient selection in the National Cancer Institute Molecular Profiling–Based Assignment of Cancer Therapy (NCI-MPACT) trial (NCT01827384). Using DNA samples from normal or tumor cell lines and xenografts with known variants, we assessed the sensitivity, specificity, and reproducibility of the NCI-MPACT assay in five variant types: single-nucleotide variants (SNVs), SNVs at homopolymeric (HP) regions (≥3 identical bases), sm...
Source: Journal of Molecular Diagnostics - November 19, 2015 Category: Pathology Authors: Chih-Jian Lih, David J. Sims, Robin D. Harrington, Eric C. Polley, Yingdong Zhao, Michele G. Mehaffey, Thomas D. Forbes, Biswajit Das, William D. Walsh, Vivekananda Datta, Kneshay N. Harper, Courtney H. Bouk, Lawrence V. Rubinstein, Richard M. Simon, Barb Tags: Regular Article Source Type: research

High-Resolution Genomic Profiling of Disseminated Tumor Cells in Prostate Cancer
Circulating and disseminated tumor cells are of great interest because they provide a minimally invasive window for assessing aspects of cancer biology, including tumor heterogeneity, a means to discover biomarkers of disease behavior, and a way to identify and prioritize therapeutic targets in the emerging era of precision oncology. However, the rarity of circulating and disseminated tumor cells poses a substantial challenge to the consistent success in analyzing their molecular features, including genomic aberrations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 19, 2015 Category: Pathology Authors: Yu Wu, Jamie R. Schoenborn, Colm Morrissey, Jing Xia, Sandy Larson, Lisha G. Brown, Xiaoyu Qu, Paul H. Lange, Peter S. Nelson, Robert L. Vessella, Min Fang Source Type: research

Varying Mutational Alterations in Multiple Primary Melanomas
In melanoma, the mitogen-activated protein (MAP) kinase pathway plays a crucial oncogenic role. Recent studies identified additional genetic alterations, eg, TERT-promoter mutations. Up to 8% of melanoma patients present with multiple primary melanomas (MPMs). The pathogenesis is not fully understood, and data on the genetic diversity of MPMs are limited. To identify putative diagnostic and therapeutic consequences, we assessed the mutational status of the BRAF and NRAS genes and TERT promoter in patients with MPMs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 19, 2015 Category: Pathology Authors: Friederike Egberts, Ann-Sophie Bohne, Sandra Krüger, Jürgen Hedderich, Rainer Rompel, Jochen Haag, Christoph Röcken, Axel Hauschild Tags: Regular Article Source Type: research

Quantification of the Mutant Allelic Burden by Digital PCR
With the recent discovery of CALR mutations,>80% of patients with myeloproliferative neoplasms carry a phenotype-driving mutation. For JAK2 V617F, the most frequent mutation in myeloproliferative neoplasms, accurate determination of mutational loads is of interest at diagnosis, for phenotypic and prognostic purposes, and during follow-up for minimal residual disease assessment. We developed a digital PCR technique that allowed the accurate determination of CALR allelic burdens for the main mutations (types 1 and 2). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2015 Category: Pathology Authors: Olivier Mansier, Marina Migeon, Arnaud Saint-Lézer, Chloé James, Emmanuelle Verger, Marie Robin, Gérard Socié, Audrey Bidet, François-Xavier Mahon, Bruno Cassinat, Eric Lippert Tags: Regular Article Source Type: research