MPA, a Free, Accessible, and Efficient Pipeline for Single Nucleotide Variant Annotation and Prioritization for Next-Generation Sequencing Routine Molecular Diagnosis
Interpretation of next-generation sequencing data constitutes the main limitation in molecular genetics diagnosis. In diagnosis of myopathies and muscular dystrophies (MMD), another major issue is to efficiently predict pathogenicity of variants identified in large genes, especially TTN, since current in silico prediction tools show limitations to predict and rank the numerous variants of such genes. We propose a unique variant prioritization score called mobidic prioritization algorithm (MPA) based on curated interpretation for previously reported variants, biological assumptions, and splice and missense predictors to pri...
Source: Journal of Molecular Diagnostics - April 21, 2018 Category: Pathology Authors: Kevin Yauy, David Baux, Henri Pegeot, Charles Van Goethem, Charly Mathieu, Thomas Guignard, Raul Juntas Morales, Delphine Lacourt, Martin Krahn, Vilma-Lotta Lehtokari, Gisele Bonne, Sylvie Tuffery-Giraud, Michel Koenig, Mireille Coss ée Tags: Regular article Source Type: research

Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-Associated Endonuclease Cas9 –Mediated Homology-Independent Integration for Generating Quality Control Materials for Clinical Molecular Genetic Testing
Genome-edited human cell lines are important resources for producing quality control materials for clinical molecular genetic testing. Generating cell lines with defined mutations through homology-directed repair –based methods are inefficient and can lead to unwanted insertions and deletions in the target loci. Nonhomologous end joining in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease Cas9 (Cas9) system was harnessed to generate genome-engineered cell lines harboring target mutations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 18, 2018 Category: Pathology Authors: Guigao Lin, Kuo Zhang, Rongxue Peng, Yanxi Han, Jiehong Xie, Jinming Li Tags: Regular article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 18, 2018 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 18, 2018 Category: Pathology Source Type: research

A Highly Sensitive and Robust Method for Hepatitis B Virus Covalently Closed Circular DNA Detection in Single Cells and Serum
Despite implications of persistence of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in the development of hepatocellular carcinoma (HCC), little is known about serum cccDNA in HBV-infected diseases. We developed a cccDNA-selective droplet digital PCR (ddPCR) to assess cccDNA content and dynamics across different stages of HCC development. One hundred forty-seven serum samples and 35 formalin-fixed, paraffin-embedded tumor tissues were derived from patients with HCC or HBV hepatitis/cirrhosis. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 12, 2018 Category: Pathology Authors: Jing-Tao Huang, Ying Yang, Yi-Min Hu, Xing-Hui Liu, Mei-Yan Liao, Roy Morgan, Er-Feng Yuan, Xia Li, Song-Mei Liu Tags: Regular articles Source Type: research

Transferring a Quantitative Molecular Diagnostic Test to Multiple Real-Time Quantitative PCR Platforms
Quantitative gene expression assays are increasingly used for diagnosis and research, but are often restricted to specific instrumentation. We propose a robust technical and statistical framework that enables transferring of established real-time quantitative PCR assays across real-time quantitative PCR platforms without compromising analytical and clinical validity. The feasibility of our approach was tested on MammaTyper, an in  vitro diagnostic assay that quantifies breast cancer biomarkers and dichotomizes results according to cutoff points. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Claudia G ürtler, Mark Laible, Wolfgang Schwabe, Heike Steinhäuser, Xingmin Li, Shujin Liu, Kornelia Schlombs, Ugur Sahin Tags: Technical advance Source Type: research

Added Value of 50-Gene Panel Sequencing to Distinguish Multiple Primary Lung Cancers from Pulmonary Metastases
This study systematically investigated the value of routine morphologic and IHC characteristics, p53 protein expression, TP53 mutation analysis, and 50-gene panel sequencing (GPS) in 111 lesions from 50 patients with multiple lung lesions. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Paul Roepman, Alexandra ten Heuvel, Karen C. Scheidel, Tobias Sprong, Danielle A.M. Heideman, Cees A. Seldenrijk, Gerarda J.M. Herder, J. Alain Kummer Tags: Regular article Source Type: research

Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing
Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate allele...
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Chang Liu, Fangzhou Xiao, Jessica Hoisington-Lopez, Kathrin Lang, Philipp Quenzel, Brian Duffy, Robi David Mitra Tags: Regular article Source Type: research

How to Transfer a Quantitative Molecular Diagnostic Test to Multiple Real-Time Quantitative PCR Platforms
Quantitative gene expression assays are increasingly used for diagnosis and research, but are often restricted to specific instrumentation. We propose a robust technical and statistical framework that enables transferring of established real-time quantitative RT-PCR assays across real-time quantitative PCR platforms without compromising analytical and clinical validity. The feasibility of our approach on MammaTyper, an in  vitro diagnostic assay that quantifies breast cancer biomarkers and dichotomizes results according to cutoff points, was tested. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Claudia G ürtler, Mark Laible, Wolfgang Schwabe, Heike Steinhäuser, Xingmin Li, Shujin Liu, Kornelia Schlombs, Ugur Sahin Tags: Technical advance Source Type: research

Droplet Digital PCR Is a Robust Tool for Monitoring Minimal Residual Disease in Adult Philadelphia-Positive Acute Lymphoblastic Leukemia
The BCR-ABL1 p190 fusion transcript is the most frequent variant observed in Philadelphia-positive (Ph+) acute lymphoblastic leukemia (ALL). Qualitative-PCR and real-time quantitative PCR are the currently used methods to monitor minimal residual disease (MRD) in Ph+  ALL patients; for the latter, full standardization and an international quality validation are lacking. Here, we developed a droplet digital PCR (ddPCR) assay for MRD monitoring in p190+ ALL cases. The analytical performance was assessed by the limit-of-detection determination, showing a reliabil ity, sensitivity, and precision of the assay of up to...
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Nicoletta Coccaro, Luisa Anelli, Antonella Zagaria, Paola Casieri, Giuseppina Tota, Paola Orsini, Luciana Impera, Angela Minervini, Crescenzio F. Minervini, Cosimo Cumbo, Elisa Parciante, Paola Carluccio, Claudia Brunetti, Giorgina Specchia, Francesco Alb Tags: Regular article Source Type: research

External Quality Assessment Identifies Training Needs to Determine the Neoplastic Cell Content for Biomarker Testing
Neoplastic cell content determination is crucial for biomarker testing. It is known that interobserver variation exists, but largescale data are missing about variation in tumor delineation and cell content determination between pathologists. Results were obtained from the external quality assessment program for metastatic colorectal cancer from the European Society of Pathology (N  = 5776 observations). The study included three parts: current practices were surveyed, neoplastic cell content estimations and delineations were retrieved from stained slides, and clinical reports were analyzed. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Kelly Dufraing, Gert De Hertogh, V éronique Tack, Cleo Keppens, Elisabeth M.C. Dequeker, Han J.H. van Krieken Tags: Regular article Source Type: research

Added value of 50-gene panel sequencing to distinguish multiple primary lung cancers from pulmonary metastases - a systematic investigation
This study systematically investigated the value of routine morphological and immunohistochemical characteristics, p53 protein expression, TP53 mutation analysis, and 50-gene panel sequencing on 111 lesions from 50 patients with multiple lung lesions. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Paul Roepman, Alexandra ten Heuvel, Karen C. Scheidel, Tobias Sprong, Danielle A.M. Heideman, Cees A. Seldenrijk, Gerarda J.M. Herder, J. Alain Kummer Tags: Regular Article Source Type: research

Accurate typing of Human Leukocyte Antigen class I genes by Oxford nanopore sequencing
Oxford Nanopore Technologies ’ MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunological compatibility between organ don ors and recipients, but the platform’s high error rate makes it challenging to type alleles with accuracy. Here, we developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) ident...
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Chang Liu, Fangzhou Xiao, Jessica Hoisington-Lopez, Kathrin Lang, Philipp Quenzel, Brian Duffy, Robi David Mitra Tags: Regular Article Source Type: research

How to transfer a quantitative molecular diagnostic test to multiple qPCR platforms
Quantitative gene expression assays are increasingly used for diagnosis and research, but are often restricted to specific instrumentation. We propose a robust technical and statistical framework that enables transferring of established RT-qPCR assays across qPCR platforms without compromising analytical and clinical validity. The feasibility of our approach on MammaTyper ®, an in vitro diagnostic assay which quantifies breast cancer biomarkers and dichotomizes results according to cut-off points, was tested. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Claudia G ürtler, Mark Laible, Wolfgang Schwabe, Heike Steinhäuser, Xingmin Li, Shujin Liu, Kornelia Schlombs, Ugur Sahin Tags: Technical Advance Source Type: research

Droplet Digital Pcr Is A Robust Tool For Monitoring Minimal Residual Disease In Adult Philadelphia-Positive Acute Lymphoblastic Leukemia
The BCR-ABL1 p190 fusion transcript (m-bcr) is the most frequent variant observed in Philadelphia-positive (Ph+) acute lymphoblastic leukemia (ALL). Qualitative-PCR and real-time quantitative PCR are the currently used methods to monitor minimal residual disease (MRD) in Ph+ ALL patients; for the latter, full standardization and an international quality validation are lacking. Here, we developed a droplet digital PCR (ddPCR) assay for MRD monitoring in p190+ ALL cases. The analytical performance was assessed by the limit of detection determination, demonstrating a reliability, sensitivity, and precision of the assay of up ...
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Nicoletta Coccaro, Luisa Anelli, Antonella Zagaria, Paola Casieri, Giuseppina Tota, Paola Orsini, Luciana Impera, Angela Minervini, Crescenzio F. Minervini, Cosimo Cumbo, Elisa Parciante, Paola Carluccio, Claudia Brunetti, Giorgina Specchia, Francesco Alb Tags: Regular Article Source Type: research

External quality assessment identifies training needs to determine the neoplastic cell content for biomarker testing
Neoplastic cell content determination is crucial for biomarker testing. It is known that inter-observer variation exists, but large-scale data are missing about variation in tumor delineation and cell content determination between pathologists. Results were obtained from the external quality assessment program for metastatic colorectal cancer from the European Society of Pathology (N=5,776 observations). The study included three parts: current practices were surveyed, neoplastic cell content estimations and delineations were retrieved from stained slides, and clinical reports were analyzed. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 3, 2018 Category: Pathology Authors: Kelly Dufraing, Gert De Hertogh, V éronique Tack, Cleo Keppens, Elisabeth M.C. Dequeker, Han J.H. van Krieken Tags: Regular Article Source Type: research

Abstracts of the 1st AMP Europe Congress
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 1, 2018 Category: Pathology Source Type: research

Author Index
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 1, 2018 Category: Pathology Source Type: research

Hepatitis B Virus Covalently Closed Circular DNA –Selective Droplet Digital PCR
This commentary highlights the article by Huang et  al that reports a highly sensitive assay for detection of closed circular DNA of hepatitis B virus. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 20, 2018 Category: Pathology Authors: Fan Shen, Consolato Sergi, Hui-lung Sun Tags: Commentary Source Type: research

HBV cccDNA-selective droplet digital PCR: A sensitive and noninvasive method for HCC diagnosis?
Chronic hepatitis B virus (HBV) infection (CHB) continues to be a major health burden with approximately 240 million CHB patients worldwide and 680,000 CHB-related deaths yearly (1). Although HBV vaccination is available, unsafe contact and immunosuppression may trigger CHB-related complications. CHB can cause hepatocellular damage. Also, CHB is strongly associated with the development of liver cirrhosis and the onset of autonomous neoplastic clones of hepatocytes that eventually become carcinomas (2,3). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - March 20, 2018 Category: Pathology Authors: Fan Shen, Consolato Sergi, Hui-lung Sun Tags: Commentary Source Type: research

MYD88 Mutations and Sensitivity to Ibrutinib Therapy
This Correspondence relates to the article by Bobee et  al (Determination of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using a Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Classifier: A CALYM Study. J Mol Diagn 2017,19:892–904). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 24, 2018 Category: Pathology Authors: Y. Lynn Wang Tags: Correspondence Source Type: research

Perspectives on the Affordability of Precision Medicine
This commentary highlights the article by Hsiao et  al, who explore the recent migration of Current Procedural Terminology codes for reimbursement of genomic tests. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 24, 2018 Category: Pathology Authors: Daniel H. Farkas Tags: Commentary Source Type: research

Authors ’ Reply
Authors' Reply to the Letter to the Editor by Y. Lynn Wang (MYD88 mutations and sensitivity to ibrutinib therapy). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 24, 2018 Category: Pathology Authors: Victor Bob ée, Philippe Ruminy, Vinciane Marchand, Pierre-Julien Viailly, Ahmad Abdel Sater, Liana Veresezan, Fanny Drieux, Caroline Bérard, Elodie Bohers, Sylvain Mareschal, Sydney Dubois, Jean-Philippe Jais, Karen Leroy, Martin Figeac, Jean-Michel Pic Tags: Correspondence 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,  2017. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 24, 2018 Category: Pathology Tags: Reviewer acknowledgment Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 24, 2018 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 24, 2018 Category: Pathology Source Type: research

Recommendations for Clinical CYP2C19 Genotyping Allele Selection
This document was developed by the Pharmacogenetics (PGx) Working Group of the Association for Molecular Pathology Clinical Practice Committee, whose aim is to recommend variants for inclusion in clinical pharmacogenetic testing panels. The goals of the Association for Molecular Pathology PGx Working Group are to define the key attributes of PGx alleles recommended for clinical testing and to define a minimum set of variants that should be included in clinical PGx genotyping assays. These recommendations include a minimum panel of variant alleles (tier 1) and an extended panel of variant alleles (tier 2) that will aid clin...
Source: Journal of Molecular Diagnostics - February 20, 2018 Category: Pathology Authors: Victoria M. Pratt, Andria L. Del Tredici, Houda Hachad, Yuan Ji, Lisa V. Kalman, Stuart A. Scott, Karen E. Weck Tags: Special article Source Type: research

Chimerism Analysis in the Pediatric Setting
Certain blood components and anticoagulants interfere with the PCR process and subsequent analysis. Here we demonstrate that reliable test results can be obtained for chimerism analysis despite omitting a DNA-extraction step and performing PCR and fragment analysis directly on bone marrow, whole blood, and individual cell fractions. For chimerism analysis, this is possible with the use of a robust, commercially available PCR mix containing a DNA polymerase capable of DNA amplification directly from the sample without the need for pretreatment. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 20, 2018 Category: Pathology Authors: Susanne Kricke, Lana Mhaldien, Rozendo Fernandes, Charizel Villanueva, Alistair Shaw, Paul Veys, Stuart Adams Tags: Regular article Source Type: research

An In-Depth Evaluation of the Validity and Logistics Surrounding the Testing of AR-V7 mRNA Expression in Circulating Tumor Cells
Recent reports have emphasized the clinical relevance of detecting the androgen receptor splice variant 7 (AR-V7) in circulating tumor cells (CTCs). Our aim was to set up a validated multicenter pipeline to measure AR-V7 by RT-qPCR in RNA isolated from CellSearch-enriched CTCs to provide an AR-V7 positive/negative score in a clinically acceptable time range. CellSearch-enirched CTCs from metastatic castration-resistant prostate cancer patients were characterized by RT-qPCR. After optimization it was prospectively tested whether it was possible to report the AR-V7 status within 11 days (PRELUDE study). (Source: Journal of M...
Source: Journal of Molecular Diagnostics - February 20, 2018 Category: Pathology Authors: Anieta M. Sieuwerts, Bianca Mostert, Michelle van der Vlugt-Daane, Jaco Kraan, Corine Beaufort, Mai Van, Wendy J.C. Prager, Bram De Laere, Nick Beije, Paul Hamberg, Hans M. Westgeest, Metin Tascilar, Luc Y. Dirix, Wendy Onstenk, Ronald de Wit, Martijn P. Tags: Regular article Source Type: research

Optimal reference gene selection for expression studies in human reticulocytes
This study aimed at selecting optimal reference genes for gene-expression analysis of reticulocytes and validating them in hereditary spherocytosis (HS) and β-thalassemia intermedia (βTI) patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 20, 2018 Category: Pathology Authors: Anu Aggarwal, Manu Jamwal, Ganesh Kumar V, Prashant Sharma, Man Updesh Singh Sachdeva, Deepak Bansal, Pankaj Malhotra, Reena Das Tags: Regular Article Source Type: research

Deciphering Elevated Microsatellite Alterations at Selected Tetra/Pentanucleotide Repeats, Microsatellite Instability, and Loss of Heterozygosity in Colorectal Cancers
Elevated microsatellite alterations at selected tetranucleotide repeats are common in colorectal cancers (CRCs). Its association with classic mono/dinucleotide microsatellite instability (MSI) is unknown. We assessed the stability of 13 tetranucleotide and three pentanucleotide repeat markers on both tumor and normal tissue from a cohort of 22 MSI-high (MSI-H) and 107 microsatellite stable (MSS) CRCs. When present, instability was observed at tetra/pentanucleotide repeats and defined as elevated microsatellite alterations at selected tetra/pentanucleotide repeats-high (EMASTP-H) ( ≥ 30% instability), EMASTP-low ( (Sourc...
Source: Journal of Molecular Diagnostics - February 20, 2018 Category: Pathology Authors: Yang Wang, Cindy L. Vnencak-Jones, Justin M. Cates, Chanjuan Shi Tags: Regular Article Source Type: research

Recommendations for Clinical CYP2C19 Genotyping Allele Selection: A Report of the Association for Molecular Pathology
This document was developed by the Pharmacogenetics (PGx) Working Group of the Association for Molecular Pathology (AMP) Clinical Practice Committee, whose aim is to recommend variants for inclusion in clinical pharmacogenetic testing panels. The goals of the AMP PGx Working Group are to define the key attributes of PGx alleles recommended for clinical testing, and to define a minimum set of variants that should be included in clinical PGx genotyping assays. These recommendations include a minimum panel of variant alleles (Tier 1) and an extended panel of variant alleles (Tier 2) that will aid clinical laboratories when de...
Source: Journal of Molecular Diagnostics - February 20, 2018 Category: Pathology Authors: Victoria M. Pratt, Andria L. Del Tredici, Houda Hachad, Yuan Ji, Lisa V. Kalman, Stuart A. Scott, Karen E. Weck Tags: Special Article Source Type: research

Chimerism analysis in the pediatric setting – Direct PCR from bone marrow, whole-blood, and cell fractions
Certain blood components and anticoagulants interfere with the PCR process and subsequent analysis. Here we demonstrate that reliable test results can be obtained for chimerism analysis despite omitting a DNA extraction step and performing PCR and fragment analysis directly on bone marrow, whole-blood, and individual cell fractions. For chimerism analysis, this is possible with the use of a robust commercially available PCR mix containing a DNA polymerase capable of DNA amplification directly from the sample without the need for pre-treatment. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 20, 2018 Category: Pathology Authors: Susanne Kricke, Lana Mhaldien, Rozendo Fernandes, Charizel Villanueva, Alistair Shaw, Paul Veys, Stuart Adams Tags: Regular Article Source Type: research

Reference Size Matching, Whole-Genome Amplification, and Fluorescent Labeling as a Method for Chromosomal Microarray Analysis of Clinically Actionable Copy Number Alterations in Formalin-Fixed, Paraffin-Embedded Tumor Tissue
Cancer genome copy number alterations (CNAs) assist clinicians in selecting targeted therapeutics. Solid tumor CNAs are most commonly evaluated in formalin-fixed, paraffin-embedded (FFPE) tissue by fluorescence in situ hybridization. Although fluorescence in situ hybridization is a sensitive and specific assay for interrogating preselected genomic regions, it provides no information about coexisting clinically significant copy number changes. Chromosomal microarray analysis is an alternative DNA-based method for interrogating genome-wide CNAs in solid tumors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 19, 2018 Category: Pathology Authors: Shelly R. Gunn, Shailin Govender, Cynthe L. Sims, Aditi Khurana, Samuel Koo, Jayne Scoggin, Mathew W. Moore, Philip D. Cotter Tags: Technical advance Source Type: research

Evaluation of Two Commercial Real-Time PCR Kits for Aspergillus DNA Detection in Bronchoalveolar Lavage Fluid in Patients with Invasive Pulmonary Aspergillosis
Invasive pulmonary aspergillosis (IPA) is a common complication of immunosuppression. Rapid diagnosis using molecular techniques is essential to improve patient survival. PCR techniques are promising in enhancing Aspergillus detection in blood and respiratory samples. We evaluate for the first time the performances of two commercial real-time PCR kits, the A. fumigatus Bio-Evolution and the MycoGENIE A. fumigatus for the detection of A. fumigatus DNA in bronchoalveolar lavage (BAL) from patients with and without IPA. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 19, 2018 Category: Pathology Authors: Julie Denis, Faezeh Forouzanfar, Raoul Herbrecht, Elise Toussaint, Romain Kessler, Marcela Sabou, Ermanno Candolfi, Val érie Letsher-Bru Tags: Regular article Source Type: research

Reference size-matching, whole-genome amplification, and fluorescent labeling as a method for chromosomal microarray analysis of clinically actionable copy number alterations in formalin-fixed, paraffin-embedded tumor tissue
Cancer genome copy number alterations (CNAs) assist clinicians in selecting targeted therapeutics. Solid tumor CNAs are most commonly evaluated in formalin-fixed, paraffin-embedded (FFPE) tissue by fluorescence in situ hybridization. Although fluorescence in situ hybridization is a sensitive and specific assay for interrogating pre-selected genomic regions, it provides no information about co-existing clinically significant copy number changes. Chromosomal microarray analysis is an alternative DNA-based method for interrogating genome-wide CNAs in solid tumors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 19, 2018 Category: Pathology Authors: Shelly R. Gunn, Shailin Govender, Cynthe L. Sims, Aditi Khurana, Samuel Koo, Jayne Scoggin, Mathew W. Moore, Philip D. Cotter Tags: Technical Advance Source Type: research

Evaluation of two commercial Real-Time PCR kits, A. fumigatus ® Bio-Evolution and MycoGENIE® A. fumigatus for Aspergillus DNA detection in Bronchoalveolar Lavage Fluid in patients with invasive pulmonary aspergillosis
Invasive pulmonary aspergillosis (IPA) is a common complication of immunosuppression. Rapid diagnosis using molecular techniques is essential to improve patient survival. PCR techniques are promising in enhancing Aspergillus detection in blood and respiratory samples. Here, we evaluate for the first time the performances of two commercial Real-Time PCR kits, the A. fumigatus ® Bio-Evolution and the MycoGENIE® A. fumigatus for the detection of A. fumigatus DNA in broncho-alveolar lavage (BAL) from patients with and without IPA. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 19, 2018 Category: Pathology Authors: Julie Denis, Faezeh Forouzanfar, Raoul Herbrecht, Elise Toussaint, Romain Kessler, Marcela Sabou, Ermanno Candolfi, Val érie Letsher-Bru Tags: Regular Article Source Type: research

Targeted Next-Generation Sequencing Is a Sensitive Tool for Differential Diagnosis of Myelodysplastic Syndromes in Bone Marrow Trephines
Myelodysplastic syndromes are hematological neoplasias in which immunohistological examination of bone-marrow trephines is important for a definite diagnosis. Unequivocal distinction from reactive bone-marrow changes is, however, sometimes difficult. As neoplastic clones in myelodysplastic syndrome carry mutations in recurrent genes, mutation detection by targeted next-generation sequencing may be a useful support for differential diagnosis. To elucidate the accuracy of this approach in the clinical diagnostic setting, we analyzed single and consecutive bone-marrow trephines processed for immunohistological examination fro...
Source: Journal of Molecular Diagnostics - February 19, 2018 Category: Pathology Authors: Andreas Br äuninger, Wolfgang Blau, Kristin Kunze, Ann-Kathrin Desch, Alexander Brobeil, Mehmet Kemal Tur, Benjamin Etschmann, Ulrich Günther, Dieter Körholz, Georg Schliesser, Andreas Käbisch, Michael Kiehl, Mathias Rummel, Stefan Gattenlöhner Tags: Regular article Source Type: research

Validation of a customized bioinformatics pipeline for a clinical next-generation sequencing test targeting solid tumor –associated variants
We present the validation of an open source tumor amplicon pipeline (OTA-pipeline) for clinical next-generation sequencing targeting solid tumor –associated variants. Raw data generated from 557 TruSight Tumor 26 samples as well as in silico data were analyzed by the OTA-pipeline and legacy pipeline and compared. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 19, 2018 Category: Pathology Authors: Thomas Schneider, Geoffrey H. Smith, Michael R. Rossi, Charles E. Hill, Linsheng Zhang Tags: Regular Article Source Type: research

Spinocerebellar Ataxia Tethering PCR
Spinocerebellar ataxia (SCA) types 1, 2, 3, 6, and 7, associated with a (CAG)n repeat expansion in coding sequences, are the most prevalent autosomal dominant ataxias worldwide (approximately 60% of the cases). In addition, the phenotype of SCA2 expansions has been now extended to Parkinson disease and amyotrophic lateral sclerosis. Their diagnosis is currently based on a PCR to identify small expanded alleles, followed by a second-level test whenever a false normal homozygous or a CAT interruption in SCA1 needs to be verified. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 17, 2018 Category: Pathology Authors: Claudia Cagnoli, Alessandro Brussino, Cecilia Mancini, Marina Ferrone, Laura Orsi, Paola Salmin, Patrizia Pappi, Elisa Giorgio, Elisa Pozzi, Simona Cavalieri, Eleonora Di Gregorio, Marta Ferrero, Alessandro Filla, Giuseppe De Michele, Cinzia Gellera, Cate Tags: Regular article Source Type: research

Rapid, Loop-Mediated Isothermal Amplification Detection of Celiac Disease Risk Alleles
Human leukocyte antigen (HLA) genotyping has become a useful investigation in the diagnostic work-up of celiac disease (CD), with utility in risk stratification and screening. However, broad application of this technology has been hindered by the cost and time burden of conventional laboratory-based assays. We have developed and validated CD –loop-mediated isothermal amplification (CD-LAMP), a LAMP assay, which enables rapid identification of the signature CD risk genotypes, HLA-DQ2.5, HLA-DQ8, HLA-DQ2.2, and HLA-DQA1*05. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 17, 2018 Category: Pathology Authors: Michael Erlichster, Jason A. Tye-Din, Michael D. Varney, Efstratios Skafidas, Patrick Kwan Tags: Regular article Source Type: research

SCA Tethering-PCR: A Rapid Genetic Test for the Diagnosis of SCA1 –3, 6, and 7 by PCR and Capillary Electrophoresis
Spinocerebellar ataxias (SCA) type 1, 2, 3, 6, and 7, associated with a (CAG)n repeat expansion in coding sequences, are the most prevalent autosomal dominant ataxias worldwide (approximately 60% of the cases). In addition, the phenotype of SCA2 expansions has been now extended to Parkinson's disease and amyotrophic lateral sclerosis. Their diagnosis is presently based on a PCR to identify small expanded alleles, followed by a second-level test whenever the suspect of false normal homozygous, or a CAT interruption in SCA1 needs to be verified. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 17, 2018 Category: Pathology Authors: Claudia Cagnoli, Alessandro Brussino, Cecilia Mancini, Marina Ferrone, Laura Orsi, Paola Salmin, Patrizia Pappi, Elisa Giorgio, Elisa Pozzi, Simona Cavalieri, Eleonora Di Gregorio, Marta Ferrero, Alessandro Filla, Giuseppe De Michele, Cinzia Gellera, Cate Tags: Regular article Source Type: research

Rapid, Loop-Mediated Isothermal Amplification Detection of Coeliac Disease Risk Alleles
Human leukocyte antigen (HLA) genotyping has become a useful investigation in the diagnostic work-up of coeliac disease (CD), with utility in risk stratification and screening. However, broad application of this technology has been hindered by the cost and time burden of conventional laboratory-based assays. We have developed and validated CD –loop-mediated isothermal amplification (CD-LAMP), a LAMP assay, which enables rapid identification of the signature CD risk genotypes, HLA-DQ2.5, HLA-DQ8, HLA-DQ2.2, and HLA-DQA1*05. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 17, 2018 Category: Pathology Authors: Michael Erlichster, Jason A. Tye-Din, Michael D. Varney, Efstratios Skafidas, Patrick Kwan Tags: Regular article Source Type: research

Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management
Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 8, 2018 Category: Pathology Authors: Stacy S. Hung, Barbara Meissner, Elizabeth A. Chavez, Susana Ben-Neriah, Daisuke Ennishi, Martin R. Jones, Hennady P. Shulha, Fong Chun Chan, Merrill Boyle, Robert Kridel, Randy D. Gascoyne, Andrew J. Mungall, Marco A. Marra, David W. Scott, Joseph M. Con Tags: Regular articles Source Type: research

Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors
In 2013, an evidence-based guideline was published by the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology to set standards for the molecular analysis of lung cancers to guide treatment decisions with targeted inhibitors. New evidence has prompted an evaluation of additional laboratory technologies, targetable genes, patient populations, and tumor types for testing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 23, 2018 Category: Pathology Authors: Neal I. Lindeman, Philip T. Cagle, Dara L. Aisner, Maria E. Arcila, Mary Beth Beasley, Eric Bernicker, Carol Colasacco, Sanja Dacic, Fred R. Hirsch, Keith Kerr, David J. Kwiatkowski, Marc Ladanyi, Jan A. Nowak, Lynette Sholl, Robyn Temple-Smolkin, Benjam Tags: Special Article Source Type: research

Next-Generation Sequencing for Lymphomas
This commentary highlights the article by Hung et  al that details the design and implementation of a 32-gene next-generation sequencing panel for lymphomas and compares hybrid-capture with amplicon-based next-generation sequencing approaches. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 19, 2018 Category: Pathology Authors: Robert S. Ohgami, Andreas Rosenwald, Adam Bagg Tags: Commentary Source Type: research

Keeping Practice Recommendations in Step with Advancing Knowledge
This editorial comments on the updated molecular testing guideline for lung cancer patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 19, 2018 Category: Pathology Authors: Barbara Zehnbauer Tags: Editorial Source Type: research

Next-Generation Sequencing for Lymphomas: Perfecting a Pipeline for Personalized Pathobiologic and Prognostic Predictions
This commentary highlights the article by Hung et al that details the design and implementation of a 32-gene next-generation sequencing (NGS) panel for lymphomas, and compares hybrid-capture versus amplicon-based NGS approaches. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 19, 2018 Category: Pathology Authors: Robert S. Ohgami, Andreas Rosenwald, Adam Bagg Tags: Commentary Source Type: research

Evaluation of a pan-Leishmania Spliced-Leader RNA Detection Method in Human Blood and Experimentally-Infected Syrian Golden Hamsters
This study compared the limits of detection of various real-time PCR assays in hamsters infected with Leishmania infantum, in spiked human blood and in clinical blood samples from visceral leishmaniasis patients. The SL-RNA assay showed an excellent analytical sensitivity in tissues (0.005 and 0.002 parasites per mg liver and spleen, respectively) and was not prone to false-positive reactions. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 17, 2018 Category: Pathology Authors: Eline Eberhardt, Magali Van den Kerkhof, Dimitri Bult é, Dorien Mabille, Lieselotte Van Bockstal, Séverine Monnerat, Fabiana Alves, Jane Mbui, Peter Delputte, Paul Cos, Sarah Hendrickx, Louis Maes, Guy Caljon Tags: Regular article Source Type: research

SNPitty
Exploration and visualization of next-generation sequencing data are crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions of interest coupled with dynamic heuristic filtering of genetic aberrations is, however, lacking. Therefore, the authors developed the web application SNPitty that allows interactive visualization and interrogation of variant call format files by using B-allele frequencies of single-nucleotide polymorphisms and single-nucleotide variants, coverage metrics, and copy numbers analysis results. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 2, 2018 Category: Pathology Authors: Job van Riet, Niels M.G. Krol, Peggy N. Atmodimedjo, Erwin Brosens, Wilfred. F.J. van IJcken, Maurice P.H.M. Jansen, John W.M. Martens, Leendert H. Looijenga, Guido Jenster, Hendrikus J. Dubbink, Winand N.M. Dinjens, Harmen J.G. van de Werken Tags: Technical advance Source Type: research