Relative Sensitivity of Saliva and Upper Airway Swabs for Initial Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Ambulatory Patients
Saliva has been proposed as an alternative to upper airway swabs when testing for severe acute respiratory syndrome coronavirus 2. Although some studies have suggested higher viral loads and clinical sensitivity when testing saliva, studies have been relatively small and have given rise to contradictory results. To better understand the relative performance characteristics of saliva and upper airway samples, I performed a rapid systematic review (registered on PROSPERO as CRD42020205035), focusing on studies that included at least 20 subjects who provided diagnostic saliva and upper airway samples on the same day, which we...
Source: Journal of Molecular Diagnostics - December 31, 2020 Category: Pathology Authors: Timothy J. O'Leary Tags: Mini review Source Type: research

Relative Sensitivity of Saliva and Upper Airway Swabs for Initial Detection of SARS-CoV-2 in Ambulatory Patients: Rapid Review
Saliva has been proposed as an alternative to upper airway swabs when testing for SARS-CoV-2. Although some studies have suggested a higher viral loads and clinical sensitivity when testing saliva, studies have been relatively small and have given rise to contradictory results. To better understand the relative performance characteristics of saliva and upper airway samples, I performed a rapid systematic review (registered on PROSPERO as CRD42020205035), focusing on studies that included at least 20 subjects who provided diagnostic saliva and upper airway samples on the same day which were tested by nucleic acid amplificat...
Source: Journal of Molecular Diagnostics - December 31, 2020 Category: Pathology Authors: Timothy J. O ’Leary Source Type: research

Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors
DNA junctions (DNAJs) frequently impact clinically relevant genes in patient tumors and are important for diagnostic and therapeutic purposes. Although routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single-gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole-genome sequencing. Structural variance analysis from whole-genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 30, 2020 Category: Pathology Authors: Stephen Murphy, James Smadbeck, Bruce Eckloff, Yean Lee, Sarah Johnson, Giannoula Karagouga, Vishnu Serla, Anurag Sharma, Robert Sikkink, Jesse Voss, Faye Harris, Janet Schaefer Kline, Farhad Kosari, Andrew Feldman, Eric Wieben, Marie Christine Aubry, Ben Tags: Technical advance Source Type: research

Chromosomal Junction Detection from Whole Genome Sequencing on Formalin-fixed, Paraffin-embedded Tumors.
DNA junctions (DNAJs) frequently impact clinically relevant genes in patient tumors and are important for diagnostic and therapeutic purposes. While routinely screened through fluorescence in situ hybridization assays, such testing only allows the interrogation of single gene regions or known fusion partners. Comprehensive assessment of DNAJs present across the entire genome can only be determined from whole genome sequencing. Structural variance analysis (SVA) from whole genome paired-end sequencing data is, however, frequently restricted to copy number changes without DNAJ detection. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 30, 2020 Category: Pathology Authors: Stephen Murphy, James Smadbeck, Bruce Eckloff, Yean Lee, Sarah Johnson, Giannoula Karagouga, Vishnu Serla, Anurag Sharma, Robert Sikkink, Jesse Voss, Faye Harris, Janet Schaefer Kline, Farhad Kosari, Andrew Feldman, Eric Wieben, Marie Christine Aubry, Ben Tags: Technical Advance Source Type: research

Molecular Subtyping of Diffuse Large B-Cell Lymphoma Using a Novel Quantitative RT-PCR Assay
We report development of a quantitative RT-PCR –based lymphoma cell-of-origin (LCOO) assay to determine ABC, GCB, and unclassifiable subtypes in formalin-fixed, paraffin-embedded tissue (FFPET) DLBCL samples. We trained the LCOO classifier on two DLBCL cohorts with validation performed by using an analytical grade assay in an independent cohor t of 60 FFPET DLBCL samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 29, 2020 Category: Pathology Authors: Robert Ta, Chris Santini, Patricia Gou, Greg Lee, Yu Chuan Tai, Cathal O ’Brien, Marcel Fontecha, Cliona Grant, Larry Bacon, Stephen Finn, Elisabeth Vandenberghe, Fiona Quinn, Rajiv Dua, Richard Flavin Tags: Regular article Source Type: research

Assessment of a multiplex PCR for the simultaneous diagnosis of intestinal cryptosporidiosis and microsporidiosis: epidemiological report from a French prospective study.
The objectives of this study were to : i) assess a multiplex quantitative PCR assay targeting Cryptosporidium spp and the microsporidian Enterocytozoon bieneusi and Encephalitozoon spp; ii) give an update about the epidemiology of these pathogens. A prospective study was conducted from January 2017 to January 2019. Performances of the assay were assessed, and genotyping of all cryptosporidia and microsporidia isolates was performed. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 29, 2020 Category: Pathology Authors: Maxime Moniot, C éline Nourrisson, Charlotte Faure, Frédéric Delbac, Loïc Favennec, Frédéric Dalle, Cyril Garrouste, Philippe Poirier Tags: Regular Article Source Type: research

Development and evaluation of a 3D Printer-based DNA extraction method coupled to loop mediated isothermal amplification (LAMP) for point-of-care diagnosis of congenital Chagas disease in endemic regions
Vertical transmission of T. cruzi is the cause of congenital Chagas disease, a re-emerging infectious disease that affects endemic and non-endemic regions alike. An early diagnosis is crucial because its prompt treatment achieves a high cure rate, precluding evolution to symptomatic chronic Chagas disease. However, early diagnosis involves low sensitive parasitological assays, making necessary serological confirmation after nine months of life. Aiming at implementing early diagnostic strategies suitable for minimally equipped laboratories, a T. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 29, 2020 Category: Pathology Authors: Diana Patricia Wehrendt, Julio Alonso-Padilla, Bo Liu, Lizeth Rojas Panozo, Silvia Rivera Nina, Lilian Pinto, Daniel Lozano, Albert Picado, Marcelo Abril, Maria Jesus Pinazo, Joaquim Gascon, Faustino Torrico, Season Wong, Alejandro Gabriel Schijman Tags: Technical Advance Source Type: research

Molecular Subtyping of Diffuse Large B-Cell Lymphoma Using a Novel Quantitative Reverse Transcription-polymerase Chain Reaction Assay
We report development of a qRT-PCR-based Lymphoma cell-of-origin (LCOO) assay to determine ABC, GCB, and Unclassifiable (UC) subtypes in formalin-fixed, paraffin embedded tissue (FFPET) DLBCL samples. We trained the LCOO classifier on two DLBCL cohorts with validation done using an analytical grade assay in an independent cohort of 60 FFPET DLBCL samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 29, 2020 Category: Pathology Authors: Robert Ta, Chris Santini, Patricia Gou, Greg Lee, Yu Chuan Tai, Cathal O ’Brien, Marcel Fontecha, Cliona Grant, Larry Bacon, Stephen Finn, Elisabeth Vandenberghe, Fiona Quinn, Rajiv Dua, Richard Flavin Tags: Regular Article Source Type: research

A real-time quantitative PCR targeting the viral vector for the monitoring of patients treated with axicabtagene ciloleucel
Axicabtagene ciloleucel or axi-cel (CD19-CAR T-cells) has been recently approved for refractory/ relapsed diffuse large B cell lymphoma and primary mediastinal B-cell lymphoma. Proliferation of CAR T-cells after infusion and their persistence have been reported as important factors. Laboratory tools are needed for the monitoring of patients.We developed a vector-based, simple and accurate real-time qPCR to measure axi-cel vector copy number (VCN) in peripheral blood samples.Primers and probe targeting the 5 ’LTR region of the gammaretroviral vector (mouse stem cell virus or MSCV) were designed for amplification. (Sou...
Source: Journal of Molecular Diagnostics - December 29, 2020 Category: Pathology Authors: Agathe Baras, Laurence Bocket, David Beauvais, Christophe Hallaert, Pauline Varlet, Ibrahim Yakoub Agha, Didier Hober, Enagnon Kazali Alidjinou Source Type: research

Comparison of Seven Commercial Severe Acute Respiratory Syndrome Coronavirus 2 Nucleic Acid Detection Reagents with Pseudovirus as Quality Control Material
The ongoing pandemic of coronavirus disease 2019 threatens the whole world, which catalyzes a variety of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid test (NAT) kits. To monitor test quality and evaluate NAT kits, quality control materials that best simulate real clinical samples are needed in this study; the performance of SARS-CoV-2 cell culture supernatant, PCDH-based pseudovirus, and MS2-based pseudovirus as quality control materials was compared. As a result, PCDH-based pseudovirus was more similar in characteristics to SARS-CoV-2 particle, and was more suitable for evaluating SARS-CoV-2 N...
Source: Journal of Molecular Diagnostics - December 28, 2020 Category: Pathology Authors: Ying Yan, Le Chang, Wenxin Luo, Junyi Liu, Fei Guo, Lunan Wang Tags: Regular article Source Type: research

Comparison of seven commercial SARS-CoV-2 nucleic acid detection reagents with pseudovirus as quality control material
The ongoing pandemic of COVID-19 threats the whole world, which catalyzes a variety of SARS-CoV-2 nucleic acid test (NAT) kits. To monitor test quality and evaluate NAT kits, quality control materials that best simulate real clinical samples are needed in this study, the performance of SARS-CoV-2 cell culture supernatant, PCDH-based pseudovirus, and MS2-based pseudovirus as quality control materials was compared. As a result, PCDH-based pseudovirus was more similar in characteristics to SARS-CoV-2 particle, and was more suitable for evaluating SARS-CoV-2 NAT kits than MS2-based pseudovirus. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 28, 2020 Category: Pathology Authors: Ying Yan, Le Chang, Wenxin Luo, Junyi Liu, Fei Guo, Lunan Wang Tags: Regular Article Source Type: research

Germline and Tumor Sequencing as a Diagnostic Tool to Resolve Suspected Lynch Syndrome
People who develop mismatch repair (MMR) deficient cancer in the absence of a germline MMR gene pathogenic variant or somatic hypermethylation of the MLH1 gene promoter are classified as having suspected Lynch syndrome (SLS). Germline whole genome sequencing (WGS) and targeted and genome-wide tumor sequencing was applied to identify the underlying cause of tumor MMR-deficiency in SLS. Germline WGS was performed on 14 cancer-affected people with SLS, including two sets of first-degree relatives. Germline pathogenic variants, including complex structural rearrangements and non-coding variants, were assessed for the MMR genes...
Source: Journal of Molecular Diagnostics - December 28, 2020 Category: Pathology Authors: Bernard J. Pope, Mark Clendenning, Christophe Rosty, Khalid Mahmood, Peter Georgeson, Jihoon E. Joo, Romy Walker, Ryan A. Hutchinson, Harindra Jayasekara, Sharelle Joseland, Julia Como, Susan Preston, Amanda B. Spurdle, Finlay A. Macrae, Aung K. Win, John Tags: Regular Article Source Type: research

Rapid EGFR Mutation Detection Using the Idylla Platform
We describe our validation and experience using an in-house developed analysis pipeline, enhanced with a manual review algorithm. Results are compared with corresponding NGS results. In all, 1249 samples were studied. Validation demonstrated 98.57% (69/70) concordance with the reference methods. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 23, 2020 Category: Pathology Authors: Amir Momeni-Boroujeni, Paulo Salazar, Tao Zheng, Nana Mensah, Ivelise Rijo, Snjezana Dogan, JinYuan Yao, Christine Moung, Chad Vanderbilt, Jamal Benhamida, Jason Chang, William Travis, Natasha Rekhtman, Marc Ladanyi, Khedoudja Nafa, Maria E. Arcila Tags: Regular article Source Type: research

Rapid EGFR Mutation Detection Using the Idylla Platform: Single institution experience of 1200 cases analyzed by an in-house developed pipeline and comparison with concurrent next-generation sequencing results
We describe our validation and experience using an in-house developed analysis pipeline, enhanced with a manual review algorithm. Results are compared with corresponding NGS results.In all, 1,249 samples were studied. Validation demonstrated 98.57% (69/70) concordance with the reference methods. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 23, 2020 Category: Pathology Authors: Amir Momeni-Boroujeni, Paulo Salazar, Tao Zheng, Nana Mensah, Ivelise Rijo, Snjezana Dogan, JinYuan Yao, Christine Moung, Chad Vanderbilt, Jamal Benhamida, Jason Chang, William Travis, Natasha Rekhtman, Marc Ladanyi, Khedoudja Nafa, Maria E. Arcila Tags: Regular Article Source Type: research

A rapid and cost-effective gene expression assay for the diagnosis of well-differentiated and dedifferentiated liposarcomas
Histology does not reliably distinguish benign lipomas from atypical lipomatous tumor / well differentiated liposarcoma, nor dedifferentiated liposarcoma from other pleomorphic sarcomas, entities with different prognosis and management. Molecular confirmation of pathognomonic 12q13-15 amplifications leading to overexpression of MDM2 is a diagnostic gold standard. Currently the most commonly used assay for this purpose is Fluorescent In-Situ Hybridization (FISH), but this is labor-intensive. We assessed if newer NanoString-based technology could allow for more rapid and cost-efficient diagnosis of liposarcomas on standard f...
Source: Journal of Molecular Diagnostics - December 23, 2020 Category: Pathology Authors: Xiu Qing Wang, Xue Qi Wang, Anika Terra Ye Way Hsu, Angela Goytain, Tony Ling Tin Ng, Torsten Owen Nielsen Tags: Technical Advance Source Type: research

Multicenter Next-Generation Sequencing Studies Between Theory and Practice
In the age of personalized medicine, genetic testing by means of targeted sequencing has taken a key role. However, when comparing different sets of targeted sequencing data, these are often characterized by a considerable lack of harmonization. Laboratories follow their own best practices, analyzing their own target regions. The question on how to best integrate data from different sites remains unanswered. Studying the example of myelodysplastic syndrome (MDS), we analyzed 11 targeted sequencing sets, collected from six different centers (n = 831). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 22, 2020 Category: Pathology Authors: Sarah Sandmann, Aniek O. de Graaf, Magnus Tobiasson, Olivier Kosmider, Mar ía Abáigar, Emmanuelle Clappier, Anna Gallì, Bert A. van der Reijden, Luca Malcovati, Pierre Fenaux, María Díez-Campelo, Michaela Fontenay, Eva Hellström-Lindberg, Joop H. Ja Tags: Regular article Source Type: research

Multicenter next-generation sequencing studies between theory and practice: harmonization of data analysis using real world myelodysplastic syndrome data
In the age of personalized medicine, genetic testing by means of targeted sequencing has taken a key role. However, when comparing different sets of targeted sequencing data these are often characterized by a considerable lack of harmonization. Laboratories follow their own best practices, analyzing their own target regions. The question on how to best integrate data from different sites remains unanswered.Studying the example of myelodysplastic syndromes (MDS), we analyzed 11 targeted sequencing sets, collected from 6 different centers (n=831). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 22, 2020 Category: Pathology Authors: Sarah Sandmann, Aniek O. de Graaf, Magnus Tobiasson, Olivier Kosmider, Mar ía Abáigar, Emmanuelle Clappier, Anna Gallì, Bert A. van der Reijden, Luca Malcovati, Pierre Fenaux, María Díez-Campelo, Michaela Fontenay, Eva Hellström-Lindberg, Joop H. Ja Tags: Regular Article Source Type: research

Patient-Specific Minimal Residual Disease Primers Amplify with Uniformly High Efficiency
The widespread use of PCR to quantify MRD has been hampered by the apparently wide variation in amplification efficiency (AE) of PCR primers. A new method to measure AE was developed based on the Ct results of PCR amplification of single copies of a target molecule placed by limiting dilution into wells of a microplate. The mean one copy Ct of a population of primers or of a reference primer was calibrated against the AE determined by the standard method of regression analysis. The AE of a test primer could then be determined by relating its one copy Ct value to the calibrated mean one copy Ct value. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 21, 2020 Category: Pathology Authors: Susan Latham, Elizabeth Hughes, Bradley Budgen, Paul Bartley, Alexander A. Morley Tags: Regular Article Source Type: research

A Transparent Approach to Calculate Detection Rate and Residual Risk for Carrier Screening
Carrier screening involves detection of carrier status for genes associated with recessive conditions. A negative carrier screening test result bears a nonzero residual risk (RR) for the individual to have an affected child. The RR depends on the prevalence of specific conditions and the detection rate (DR) of the test itself. Herein, we provide a detailed approach for calculating DR and RR. DR was calculated on the basis of the sum of disease allele frequencies (DAFs) of pathogenic variants found in published literature. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2020 Category: Pathology Authors: Marco L. Leung, Sallie McAdoo, Deborah Watson, Kallyn Stumm, Margaret Harr, Xiang Wang, Christine H. Chung, Fernanda Mafra, Addie I. Nesbitt, Hakon Hakonarson, Avni Santani Tags: Regular article Source Type: research

Diagnostics in the Time of Coronavirus Disease 2019 (COVID-19)
Welcome to a new year and congratulations on surviving 2020. The demands for disease identification during this pandemic have brought an unprecedented focus on clinical laboratory diagnostic testing. Despite early shared data about the viral sequence, the rapid pace of changing knowledge about coronavirus disease 2019 (COVID-19) prevalence, transmission, symptoms, pathology, test implementation, and potential treatment options increased awareness around the globe of the value of professional communication and collaborations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2020 Category: Pathology Authors: Barbara Zehnbauer Tags: Editorial Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2020 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2020 Category: Pathology Source Type: research

Instructions to Authors
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2020 Category: Pathology Source Type: research

Scientific Integrity Policy
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2020 Category: Pathology Source Type: research

Variant Benchmark Tool
Next-generation sequencing is increasingly being adopted as a valuable method for the detection of somatic variants in clinical oncology. However, it is still challenging to reach a satisfactory level of robustness and standardization in clinical practice when using the currently available bioinformatics pipelines to detect variants from raw sequencing data. Moreover, appropriate reference data sets are lacking for clinical bioinformatics pipeline development, validation, and proficiency testing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 17, 2020 Category: Pathology Authors: Ziyang Li, Shuangsang Fang, Rui Zhang, Lijia Yu, Jiawei Zhang, Dechao Bu, Liang Sun, Yi Zhao, Jinming Li Tags: Technical advance Source Type: research

VarBen: Generating in silico Reference Datasets for Clinical Next-Generation Sequencing Bioinformatics Pipeline Evaluation
Next-generation sequencing (NGS) is increasingly being adopted as a valuable method for the detection of somatic variants in clinical oncology. However, it is still challenging to reach a satisfactory level of robustness and standardization in clinical practice when using the currently available bioinformatics pipelines to detect variants from raw sequencing data. Moreover, appropriate reference datasets are lacking for clinical bioinformatics pipeline development, validation and proficiency testing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 17, 2020 Category: Pathology Authors: Ziyang Li, Shuangsang Fang, Rui Zhang, Lijia Yu, Jiawei Zhang, Dechao Bu, Liang Sun, Yi Zhao, Jinming Li Tags: Technical Advance Source Type: research

Rapid Implementation of Severe Acute Respiratory Syndrome Coronavirus 2 Emergency Use Authorization RT-PCR Testing and Experience at an Academic Medical Institution
We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time RT-PCR test offered in the NewYork-Presbyterian Hospital system following the Emergency Use Authorization issued by the US Food and Drug Administration. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2020 Category: Pathology Authors: Priya Velu, Arryn Craney, Phyllis Ruggiero, John Sipley, Lin Cong, Erika M. Hissong, Massimo Loda, Lars F. Westblade, Melissa Cushing, Hanna Rennert Tags: Regular article Source Type: research

Performance Characteristics of Severe Acute Respiratory Syndrome Coronavirus 2 PCR Tests in a Single Health System
The current pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in the approval of numerous molecular diagnostic assays with various performance and technical capacities. There are limited data comparing performance among assays. We conducted a retrospective analysis of>10,000 test results among three widely used RT-PCR assays for coronavirus disease 2019 (CDC, Simplexa Direct, and TaqPath) to assess performance characteristics. We also retested remnant weakly positive specimens to assess analytical sensitivity. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2020 Category: Pathology Authors: Travis K. Price, Brian C. Bowland, Sukantha Chandrasekaran, Omai B. Garner, Shangxin Yang Tags: Regular article Source Type: research

A Pan-Cancer Study of Somatic TERT Promoter Mutations and Amplification in 30,773 Tumors Profiled By Clinical Genomic Sequencing
Promoter mutations involving the TERT gene have been identified in multiple cancer types. Other TERT alterations remain poorly characterized.Sequencing data from 30,773 tumors analyzed by a hybridization capture next-generation sequencing assay (MSK- IMPACT) was analyzed for the presence of TERT alterations. Promoter rearrangements (500 bases upstream of the transcriptional start site), hypermethylation (n=57) and gene expression (n=155) was evaluated for a subset of cases.We identified mutually exclusive and recurrent promoter mutations at 3 hotspots upstream of the transcriptional start site in 11.3% of cases (-124: 74%;...
Source: Journal of Molecular Diagnostics - December 4, 2020 Category: Pathology Authors: Sounak Gupta, Chad Vanderbilt, Yun-Te Lin, Jamal K. Benhamida, Achim A. Jungbluth, Satshil Rana, Amir M. Boroujeni, Jason C. Chang, Tiffany Mcfarlane, Paulo Salazar, Kerry Mullaney, Sumit Middha, Ahmet Zehir, Anuradha Gopalan, Tejus A. Bale, Ian Ganly, Ma Source Type: research

Rapid implementation of SARS-CoV-2 emergency use authorization RT-PCR testing and experience at an academic medical institution
We present a detailed overview of the clinical validation and implementation of the first laboratory-developed real-time reverse-transcription-PCR (rRT-PCR) test offered in the NewYork-Presbyterian Hospital (NYPH) system following the emergency use authorization (EUA) issued by the US Food and Drug Administration. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2020 Category: Pathology Authors: Priya Velu, Arryn Craney, Phyllis Ruggiero, John Sipley, Lin Cong, Erika M. Hissong, Massimo Loda, Lars F. Westblade, Melissa Cushing, Hanna Rennert Source Type: research

Performance Characteristics of SARS-CoV-2 PCR Tests in A Single Health System: Analysis of over 10,000 Results from Three Different Assays
The current pandemic of SARS-CoV-2 has resulted in the approval of numerous molecular diagnostic assays with various performance and technical capacities. There are limited data comparing performance among assays. We conducted a retrospective analysis of>10,000 test results among three widely used RT-PCR assays for COVID-19 (CDC, Simplexa Direct, and TaqPath) to assess performance characteristics. We also re-tested remnant weakly positive specimens to assess analytical sensitivity. All assays had strong linear correlation and little bias among cycle threshold (Ct) values for PCR targets. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2020 Category: Pathology Authors: Travis K. Price, Brian C. Bowland, Sukantha Chandrasekaran, Omai B. Garner, Shangxin Yang Source Type: research

Development and Validation of an RNA Sequencing Assay for Gene Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tumors
RNA sequencing (RNA-seq) is a well-validated tool for detecting gene fusions in fresh frozen tumors, whereas it is much more challenging to use it with formalin-fixed paraffin-embedded (FFPE) tumor samples. We evaluated the performance of RNA-seq to detect gene fusions in clinical FFPE tumor samples. Our assay identified all 15 spiked-in NTRK fusions from RNA reference material and 6 known fusions from 5 cancer cell lines. Limit of detection for the assay was assessed with a series of dilutions of RNA from the cell line H2228. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 30, 2020 Category: Pathology Authors: Hao Peng, Rong Huang, Kui Wang, Cuiyun Wang, Bin Li, Youbing Guo, Meng Li, Dadong Zhang, Hua Dong, Hao Chen, Caifu Chen, Qing Xu, Fugen Li, Lei Tian, Jianbing Wu Source Type: research

Classification and Regression Trees for Bacterial Vaginosis Diagnosis in Pregnant Women Based on High-Throughput Quantitative PCR
Bacterial vaginosis (BV) diagnosis in pregnancy is based on the Nugent score, which consists of semiquantitation of bacterial morphotypes. Limited data exist concerning molecular-based diagnosis in asymptomatic pregnant women. Using high-throughput quantitative PCR, 34 microorganisms were screened in asymptomatic pregnant women and compared with the Nugent score. Three hundred four vaginal samples had a Nugent score (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 28, 2020 Category: Pathology Authors: Aurore Loquet, R émi Le Guern, Teddy Grandjean, Claire Duployez, Marvin Bauduin, Eric Kipnis, Gilles Brabant, Damien Subtil, Rodrigue Dessein Tags: Regular article Source Type: research

Classification and regression-trees for bacterial vaginosis diagnosis in pregnant women based on high-throughput quantitative PCR
Bacterial vaginosis (BV) diagnosis in pregnancy is based on the Nugent score, which consists of semi-quantitation of bacterial morphotypes after Gram coloration. There are limited data concerning molecular method-based diagnosis in asymptomatic pregnant women. Using high-throughput quantitative PCR (qPCR), 34 microorganisms were screened in asymptomatic pregnant women compared to the Nugent score. Three hundred and four vaginal samples had a Nugent score (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 28, 2020 Category: Pathology Authors: Aurore LOQUET, R émi LE. GUERN, Teddy GRANDJEAN, Claire DUPLOYEZ, Marvin BAUDUIN, Eric KIPNIS, Gilles BRABANT, Damien SUBTIL, Rodrigue DESSEIN Source Type: research

An integrative DNA sequencing and methylation panel to assess mismatch repair deficiency
Clinical testing for mismatch repair (MMR) deficiency often entails serial testing of tumour and constitutional DNA using multiple assays. To minimize cost and specimen requirements of MMR testing, we developed an integrated targeted sequencing protocol (termed MultiMMR) that tests for promoter methylation, mutations, copy number alterations, copy neutral loss-of-heterozygosity, and microsatellite instability from a single aliquot of DNA. We performed hybrid capture of DNA sequencing libraries constructed with methylated adapters on 142 samples (60 tumours and 82 constitutional samples) from 82 patients with MMR-associated...
Source: Journal of Molecular Diagnostics - November 28, 2020 Category: Pathology Authors: Leslie E. Oldfield, Tiantian Li, Alicia Tone, Melyssa Aronson, Melissa Edwards, Spring Holter, Rene Quevedo, Emily Van de Laar, Jordan Lerner-Ellis, Aaron Pollett, Blaise Clarke, Uri Tabori, Steven Gallinger, Sarah E. Ferguson, Trevor J. Pugh Source Type: research

Comparison of 12 Molecular Detection Assays for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the mainstay for accurate diagnosis of the infection, but the diagnostic performances of available assays have not been defined. We compared 12 molecular diagnostic assays, including 8 commercial kits using 155 respiratory samples (65 nasopharyngeal swabs, 45 oropharyngeal swabs, and 45 sputum) collected at 2 Japanese hospitals. Sixty-eight samples were positive for more than one assay and one genetic locus and were defined as true positive samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 28, 2020 Category: Pathology Authors: Yasufumi Matsumura, Tsunehiro Shimizu, Taro Noguchi, Satoshi Nakano, Masaki Yamamoto, Miki Nagao Tags: Regular Article Source Type: research

SnackVar
In this study, SnackVar, a novel graphical user interface –based software for Sanger sequencing, was developed. All types of variants, including heterozygous insertion/deletion variants, can be identified by SnackVar with minimal user effort. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 23, 2020 Category: Pathology Authors: Young-Gon Kim, Man Jin Kim, Jee-Soo Lee, Jung Ae Lee, Ji Yun Song, Sung Im Cho, Sung-Sup Park, Moon-Woo Seong Tags: Technical advance Source Type: research

Minimal Residual Disease Monitoring Using a 3 ′ALK Universal Probe Assay in ALK-Positive Anaplastic Large-Cell Lymphoma
In ALK-positive anaplastic large-cell lymphomas, positive qualitative PCR for NPM1-ALK in peripheral blood and/or bone marrow at diagnosis and during treatment are associated with a higher risk of treatment failure. Real-time quantitative PCR allows identification of very high risk patients. However, this latter technique initially designed for patients with lymphomas carrying the most frequent NPM1-ALK translocation necessitates calibration curves, limiting interlaboratory reproducibility. We designed an ALK universal quantitative PCR based on 3 ′ALK transcript amplification to allow the detection of all ALK fusion ...
Source: Journal of Molecular Diagnostics - November 23, 2020 Category: Pathology Authors: Cathy Quelen, David Grand, Emeline Sarot, Laurence Brugi ères, David Sibon, Anne Pradines, Camille Laurent, Pierre Brousset, Laurence Lamant Tags: Technical advance Source Type: research

SnackVar: An Open-Source Software for Sanger Sequencing Analysis Optimized for Clinical Use
In this study, SnackVar, a novel graphical user interface-based software for Sanger sequencing, was developed. All types of variants, including heterozygous indel variants, can be identified by SnackVar with minimal user effort. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 23, 2020 Category: Pathology Authors: Young-gon Kim, Man Jin Kim, Jee-Soo Lee, Jung Ae Lee, Ji Yun Song, Sung Im Cho, Sung-Sup Park, Moon-Woo Seong Tags: Technical Advance Source Type: research

Minimal residual disease monitoring using a 3 ’ALK universal probe assay in ALK-positive anaplastic large cell lymphoma: ddPCR, an attractive alternative method to real-time quantitative PCR
In ALK-positive anaplastic large cell lymphomas, positive qualitative PCR for NPM1-ALK in peripheral blood and/or bone marrow at diagnosis and during treatment are associated with a higher risk of treatment failure. Real-time quantitative PCR allows identification of very high risk patients. However, this latter technique initially designed for patients with lymphomas carrying the most frequent NPM1-ALK translocation necessitates calibration curves, limiting inter-laboratory reproducibility. We designed an ALK universal quantitative PCR based on 3 ’ALK transcript amplification to allow the detection of all ALK fusion...
Source: Journal of Molecular Diagnostics - November 23, 2020 Category: Pathology Authors: Cathy Quelen, David Grand, Emeline Sarot, Laurence Brugi ères, David Sibon, Anne Pradines, Camille Laurent, Pierre Brousset, Laurence Lamant Tags: Technical Advance Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2020 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2020 Category: Pathology Source Type: research

Performance of Severe Acute Respiratory Syndrome Coronavirus 2 Real-Time RT-PCR Tests on Oral Rinses and Saliva Samples
In this study, the use of oral rinses (ORs) and posterior oropharyngeal saliva as an alternative to swab collection methods from symptomatic and asymptomatic health care workers for the detection of SARS-CoV-2 RNA by RT-PCR was evaluated. For saliva samples, the overall agreement with oropharyngeal swabs was 93% ( Ƙ = 0.84), with a sensitivity of 96.7% (95% CI, 83.3%–99.8%). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2020 Category: Pathology Authors: N. Esther Babady, Tracy McMillen, Krupa Jani, Agnes Viale, Elizabeth V. Robilotti, Anoshe Aslam, Maureen Diver, Desiree Sokoli, Greg Mason, Monika K. Shah, Deborah Korenstein, Mini Kamboj Tags: Regular article Source Type: research

Routine evaluation of minimal residual disease in myeloma using next-generation sequencing clonality testing – feasibility, challenges and direct comparison with high sensitivity flow cytometry
The 2016 International Myeloma Working Group consensus recommendations emphasize the importance of high sensitivity methods for minimal residual disease (MRD) detection, treatment response assessment and prognostication. Next generation sequencing (NGS) of IGH gene rearrangements is highly specific and sensitive, but its description in routine clinical practice and performance comparison with high sensitivity flow cytometry (hsFC) remain limited. In this large single institution study including 438 samples from 251 patients, we describe our use of NGS targeting the IGH and IGK genes for clonal characterization and monitori...
Source: Journal of Molecular Diagnostics - November 17, 2020 Category: Pathology Authors: Caleb Ho, Mustafa Syed, Mikhail Roshal, Kseniya Petrova-Drus, Christine Moung, JinJuan Yao, Andres E. Quesada, Jamal Benhamida, Chad Vanderbilt, Ying Liu, Menglei Zhu, Wayne Yu, Lidia Maciag, Meiyi Wang, Yuanyuan Ma, Qi Gao, Even H. Rustad, Malin Hultcran Source Type: research

Performance of SARS-CoV-2 Real-time RT-PCR Tests on Oral Rinses and Saliva Samples
In this study, the use of oral rinses and posterior oropharyngeal saliva as an alternative to swab collection methods from symptomatic and asymptomatic healthcare workers for the detection of SARS-CoV-2 RNA by RT-PCR was evaluated. For saliva samples, the overall agreement with oropharyngeal swabs (OPS) was 93% ( Ƙ=0.84) with a sensitivity of 96.7% (95%CI:83.3-99.8%). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2020 Category: Pathology Authors: N. Esther Babady, Tracy McMillen, Krupa Jani, Agnes Viale, Elizabeth V. Robilotti, Anoshe Aslam, Maureen Diver, Desiree Sokoli, Greg Mason, Monika K. Shah, Deborah Korenstein, Mini Kamboj Source Type: research

A Next-Generation Sequencing Test for Severe Congenital Neutropenia
Severe congenital neutropenia (SCN) is a collection of diverse disorders characterized by a chronically low absolute neutrophil count in the peripheral blood, increased susceptibility to infection, and a significant predisposition to the development of myeloid malignancies. SCN can be acquired or inherited. Inherited forms have been linked to variants in a group of diverse genes involved in the neutrophil-differentiation process. Variants that promote resistance to treatment have also been identified. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 16, 2020 Category: Pathology Authors: Samantha N. McNulty, Michael J. Evenson, Meaghan Riley, Jennifer M. Yoest, Meagan M. Corliss, Jonathan W. Heusel, Eric J. Duncavage, John D. Pfeifer Tags: Regular article Source Type: research

A Next-Generation Sequencing Test for Severe Congenital Neutropenia: Utility in a Broader Clinicopathologic Spectrum of Disease
Severe congenital neutropenia (SCN) is a diverse collection of disorders characterized by chronically low absolute neutrophil counts in the peripheral blood, increased susceptibility to infection, and a significant predisposition to the development of myeloid malignancies. SCN can be acquired or inherited. Inherited forms have been linked to variants in a diverse group of genes involved in the neutrophil differentiation process. Variants that promote resistance to treatment have also been identified. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 16, 2020 Category: Pathology Authors: Samantha N. McNulty, Michael J. Evenson, Meaghan Riley, Jennifer M. Yoest, Meagan M. Corliss, Jonathan W. Heusel, Eric J. Duncavage, John D. Pfeifer Source Type: research

Multicenter Evaluation of Xpert Carba-R Assay for detection and identification of the carbapenemase genes in rectal swabs and clinical isolates
Quick detection of carbapenemase-producing organisms is clinically desirable for hospital infection control and antibiotic stewardship. In this multicenter study, Xpert Carba-R assay was evaluated for detection the five carbapenemase genes (blaKPC, blaNDM, blaIMP, blaOXA-48 and blaVIM) in 2,404 non-duplicate rectal swabs of admitted inpatients and 521 Gram-negative isolates from four tertiary hospitals in China, compared to the reference growth-based method with DNA sequence analysis of colonies. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 15, 2020 Category: Pathology Authors: Xi Jin, Haomin Zhang, Shi Wu, Xiaohua Qin, Peiyao Jia, Fred C. Tenover, Yi-Wei Tang, Min Li, Fupin Hu, Qiwen Yang, Yunsong Yu Tags: Regular Article Source Type: research

Characterization of Reference Materials for Spinal Muscular Atrophy Genetic Testing
Spinal muscular atrophy (SMA) is an autosomal recessive disorder predominately caused by bi-allelic loss of the SMN1 gene. Increased copies of SMN2, a low functioning nearly identical paralog, is associated with a less severe phenotype. SMA was recently recommended for inclusion in newborn screening. Clinical laboratories must accurately measure SMN1 and SMN2 copy number to identify SMA patients and carriers, and to identify individuals likely to benefit from therapeutic interventions. Having publicly available and appropriately characterized reference materials with various combinations of SMN1 and SMN2 copy number varian...
Source: Journal of Molecular Diagnostics - November 13, 2020 Category: Pathology Authors: Thomas W. Prior, Pinar Bayrak-Toydemir, Ty C. Lynnes, Rong Mao, James D. Metcalf, Kasinathan Muralidharan, Aiko Iwata-Otsubo, Ha T. Pham, Victoria M. Pratt, Shumaila Qureshi, Deborah Requesens, Junqing Shen, Francesco Vetrini, Lisa Kalman Tags: Regular article Source Type: research

Characterization of Reference Materials for Spinal Muscular Atrophy Genetic Testing: A GeT-RM Collaborative Project
Spinal muscular atrophy (SMA) is an autosomal recessive disorder predominately caused by bi-allelic loss of the SMN1 gene. Increased copies of SMN2, a low functioning nearly identical paralog, is associated with a less severe phenotype. SMA was recently recommended for inclusion in newborn screening. Clinical laboratories must accurately measure SMN1 and SMN2 copy number to identify SMA patients, carriers, and to identify individuals likely to benefit from therapeutic interventions. Having publicly available and appropriately characterized reference materials with various combinations of SMN1 and SMN2 copy number variants ...
Source: Journal of Molecular Diagnostics - November 13, 2020 Category: Pathology Authors: Thomas W. Prior, Pinar Bayrak-Toydemir, Ty C. Lynnes, Rong Mao, James D. Metcalf, Kasinathan Muralidharan, Aiko Iwata-Otsubo, Ha T. Pham, Victoria M. Pratt, Shumaila Qureshi, Deborah Requesens, Junqing Shen, Francesco Vetrini, Lisa Kalman Tags: Regular Article Source Type: research