Who To Test, When, And For What: Why Diagnostic Stewardship in Infectious Diseases Matters
New rapid molecular diagnostic technologies for infectious diseases provide faster diagnostic test results and if used correctly, will enable more rapid delivery of care to patients. This perspective piece outlines how we can more effectively utilize this new technology-with a focus on collaborative team approaches and tools clinicians and laboratorians can use to optimally affect patient care. Here, we also showcase a patient case outlining problems with the diagnostic process as it currently stands and pose potential strategies on how we can try to improve this process. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 2, 2020 Category: Pathology Authors: Sejal Morjaria, Kimberle C. Chapin Tags: Perspectives Source Type: research

Improved diagnosis of rare disease patients through systematic detection of runs of homozygosity
Autozygosity is associated with an increased risk of genetic rare disease (RD), thus being a relevant factor for clinical genetic studies. More than 2400 ES datasets were analysed and screened for autozygosity based on detection of>1Mbp runs of homozygosity (ROH). A model was built to predict if an individual is likely to be a consanguineous offspring (accuracy 98%) and “probability of consanguinity” ranges were established according to the total ROH size. Application of the model resulted in the re-classification of the consanguinity status of 12% of the patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 30, 2020 Category: Pathology Authors: Leslie Matalonga, Steven Laurie, Anastasios Papakonstantinou, Davide Piscia, Elisabetta Mereu, Gemma Bullich, Rachel Thompson, Rita Horvath, Luis P érez-Jurado, Olaf Riess, Ivo Gut, Gert-Jan van Ommen, Hanns Lochmüller, Sergi Beltran, RD-Connect GPAP an Source Type: research

Specific gyrA gene mutations correlate with high prevalence of discordant levofloxacin resistance in Mycobacterium tuberculosis isolates from Beijing, China
Although rapid, highly sensitive molecular diagnostics tests are useful for diagnosing fluoroquinolone (FQ)-resistant tuberculosis (TB), results of molecular testing versus conventional sequential phenotypic drug susceptibility testing (pDST) are frequently discordant. Here we determined the discordance rate of levofloxacin (LFX) resistance results obtained via MeltPro TB molecular testing versus pDST of clinical TB isolates collected in Beijing, China between January and December 2018. Isolates with discordant results were further subjected to LFX minimal inhibitory concentration (MIC) determinations and DNA sequence anal...
Source: Journal of Molecular Diagnostics - June 29, 2020 Category: Pathology Authors: Fengmin Huo, Yifeng Ma, Shanshan Li, Yi Xue, Yuanyuan Shang, Lingling Dong, Yunxu Li, Yu Pang Tags: Regular Article Source Type: research

Prognostic and Predictive Molecular Biomarkers in Chronic Lymphocytic Leukemia
Chronic lymphocytic leukemia (CLL) is a malignancy of B cells with a variable clinical course. Prognostication is important to place patients into different risk categories for guiding decisions on clinical management, to treat or not to treat. Although a number of clinical, cytogenetic and molecular parameters have been established, in the past decade, a tremendous understanding of molecular lesions has been obtained with the advent of high-throughput sequencing. Meanwhile, rapid advances in the understanding of the CLL oncogenic pathways have led to the development of small molecules targeting signal transducers, BTK and...
Source: Journal of Molecular Diagnostics - June 29, 2020 Category: Pathology Authors: Jimmy Lee, Y. Lynn Wang Tags: Review Source Type: research

A Role for Chromosomal Microarray Testing in the Workup of Male Infertility
Genetic analysis is a critical component in the male infertility workup. For male infertility due to oligo/azoospermia, standard guidelines recommend karyotype and Y-chromosome microdeletion analyses. A karyotype is used to identify structural and numerical chromosome abnormalities, while Y-chromosome microdeletions are commonly evaluated by multiplex PCR analysis due to their submicroscopic size. Since these assays often require different vacutainer tubes to be sent to different laboratories, ordering is prone to errors. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 29, 2020 Category: Pathology Authors: Kelsey J. McIntyre, Elissa Murphy, Lauren Mertens, Adrian M. Dubuc, Ruth A. Heim, Heather Mason-Suares Source Type: research

Development and Clinical Validation of a 90-Gene Expression Assay for Identifying Tumor Tissue Origin
In this study, we aim to develop a gene expression assay for tumor molecular classification and integrate it with clinicopathological evaluations to identify the tissue origin for cancer of uncertain primary (CUP). A 90-gene expression signature covering 21 tumor types was identified and validated with an overall accuracy of 89.8% (95% CI, 0.87-0.92) in 609 tumor samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 27, 2020 Category: Pathology Authors: Qing Ye, Qifeng Wang, Peng Qi, Jinying Chen, Yifeng Sun, Shichai Jin, Wanli Ren, Chengshu Chen, Mei Liu, Midie Xu, Gang Ji, Jun Yang, Ling Nie, Qinghua Xu, Deshuang Huang, Xiang Du, Xiaoyan Zhou Tags: Regular Article Source Type: research

Targeted informatics for optimal FLT3-ITD detection, characterization, and quantification across multiple NGS platforms.
In this study, data from multiple NGS platforms -- anchored multiplex PCR (AMP), amplicon (TSCA), and hybrid-capture (HC) – was analyzed through a custom algorithm including platform-specific measures of allelic ratio. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 27, 2020 Category: Pathology Authors: Harrison K. Tsai, Diane Brackett, David Szeto, Ryan Frazier, Allison MacLeay, Phani Davineni, Danielle Manning, Elizabeth Garcia, Neal I. Lindeman, Long P. Le, Jochen K. Lennerz, Chris J. Gibson, R. Coleman Lindsley, Annette S. Kim, Valentina Nardi Tags: Regular Article Source Type: research

High-throughput molecular cancer cell line characterization using digital multiplex ligation-dependent probe amplification for improved standardization of in vitro research
Tumour cell lines are widely used for cancer research, but challenges regarding quality control of cell line identity, cross-contamination and tumour somatic molecular stability remain, demanding novel approaches beyond conventional short tandem repeat profiling. We analyzed 21 commonly used multiple myeloma (MM) cell lines obtained from public repositories by digital multiplex ligation-dependent probe amplification (digitalMLPA) to characterise germline single nucleotide (SNP), insertion/deletion polymorphisms (indels) and somatic copy number aberrations (CNA). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 27, 2020 Category: Pathology Authors: Karen Menezes, Lilit Atanesyan, Amy L. Sherborne, Maryvonne Steenkamer, Ivo Clemens, Suvi Savola, Martin F. Kaiser Tags: Regular Article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 22, 2020 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 22, 2020 Category: Pathology Source Type: research

PARP inhibitors for Cancer: Essential Biologic, Diagnostic, and Therapeutic Concepts for Today ’s Practitioner
The PARPi Series Content Committee is a working group of the Association for Molecular Pathology (AMP) Training and Education Committee. The PARPi Series Content Committee members consisted of Diana Mandelker, Lynette Sholl (Chair) and Tracy Stockley. The 2020 Training and Education Committee consisted of Yassmine Akkari (Chair), Barbara Anderson, Nathanael Bailey (Chair-elect), Gerald Capraro, Alanna Church, Annie Garcia, Erin Graf, Lisa Haley, Sabah Kadri, Kristin Hunt Karner, Christian Kunder, Nathan Montgomery, Honey Reddi, Lauren Ritterhouse, Cinthya Zepeda-Mendoza, and Weiwei Zhang. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 20, 2020 Category: Pathology Authors: Lynette Sholl, Diana Mandelker, Tracy Stockley Tags: Other Source Type: research

Responding to the Challenges of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
Clinical molecular laboratory professionals are at the frontline of the response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, providing accurate, high-quality laboratory results to aid in diagnosis, treatment, and epidemiology. In this role, we have encountered numerous regulatory, reimbursement, supply-chain, logistical, and systems challenges that we have struggled to overcome to fulfill our calling to provide patient care. In this Perspective from the Association for Molecular Pathology Infectious Disease Subdivision Leadership team, we review how our members have  risen to these ch...
Source: Journal of Molecular Diagnostics - June 18, 2020 Category: Pathology Authors: Frederick S. Nolte, N. Esther Babady, Blake W. Buchan, Gerald A. Capraro, Erin H. Graf, Amy L. Leber, Erin McElvania, Joseph D.C. Yao Tags: Perspectives Source Type: research

Responding to the Challenges of SARS-CoV-2: Perspectives from the Association for Molecular Pathology (AMP) Infectious Disease Subdivision Leadership
Clinical molecular laboratory professionals are at the frontline of the response to the SARS-CoV-2 pandemic, providing accurate, high-quality laboratory results to aid in diagnosis, treatment, and epidemiology. In this role, we have encountered numerous regulatory, reimbursement, supply-chain, logistical, and systems challenges that we have struggled to overcome in order to fulfill our calling to provide patient care. In this Perspective from the Association for Molecular Pathology Infectious Disease Subdivision Leadership team we review how our members have risen to these challenges, provide recommendations for managing t...
Source: Journal of Molecular Diagnostics - June 18, 2020 Category: Pathology Authors: Frederick S. Nolte, N. Esther Babady, Blake W. Buchan, Gerald A. Capraro, Erin H. Graf, Amy L. Leber, Erin McElvania, Joseph D.C. Yao Tags: Perspectives Source Type: research

Comparative Evaluation of five Assays for Detection of Carbapenemases with a Proposed Scheme for Their Precise Application
The escalating problem of the dissemination of carbapenemase-producing bacteria (CPB) has gained worldwide attention. The prompt diagnosis of CPB and precise identification of carbapenemases are imperative to enable specific antibiotic therapy and control the spread of these bacteria. The present study was designed to assess the performance of five important assays for the detection of carbapenemases. The mCIM, CARBA-5, Xpert Carba-R, BD MAX Check-Points CPO, and GeneFields CPE assays were evaluated with an international collection of 159 bacterial isolates, including 93 CPB and 66 non-CPB isolates. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 15, 2020 Category: Pathology Authors: Hazim O. Khalifa, Takashi Okanda, Amer Ali Abd El-Hafeez, Amera Abd El Latif, Ahmed G.K. Habib, Hisakazu Yano, Yasuyuki Kato, Tetsuya Matsumoto Tags: Regular Article Source Type: research

Clinical service delivery of non-invasive prenatal diagnosis (NIPD) by relative haplotype dosage (RHDO) for single gene disorders
We have developed and implemented into routine clinical practice a relative haplotype dosage (RHDO) based method for non-invasive prenatal diagnosis (NIPD) of multiple single gene disorders: spinal muscular atrophy (SMA), Duchenne and Becker muscular dystrophies (DMD/BMD) and cystic fibrosis (CF). This review describes our experience of the first 152 pregnancies to have NIPD by RHDO as part of a routine clinical service. We have demonstrated that it is possible to provide a result within a clinically useful timeframe (mean 11 calendar days) with a very low failure rate (4%), none being due to a technical failure. (Source: ...
Source: Journal of Molecular Diagnostics - June 15, 2020 Category: Pathology Authors: Elizabeth Young, Benjamin Bowns, Amy Gerrish, Michael Parks, Samantha Court, Samuel Clokie, Chipo Mashayamombe-Wolfgarten, Julie Hewitt, Denise Williams, Trevor Cole, Stephanie Allen Tags: Regular Article Source Type: research

Identification of Three Circular RNA Cargoes in Serum Exosomes as Diagnostic Biomarkers of Non –Small-Cell Lung Cancer in the Chinese Population
The recent discovery of circular RNAs (circRNAs) in serum exosomes suggests a novel and potentially useful tool for noninvasive cancer diagnosis. However, there are currently no substantial studies addressing this topic. RNA-sequencing analysis was performed between three pairs of non –small-cell lung cancer (NSCLC) patients and controls. The diagnostic values of exosomal circRNAs were assessed in a training set, validation set 1, and validation set 2. A total of 46 abnormally expressional circRNAs were identified. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 11, 2020 Category: Pathology Authors: Jianfeng Xian, Wenpeng Su, Li Liu, Boqi Rao, Mingzhu Lin, Yinyi Feng, Fuman Qiu, Jinbin Chen, Qiang Zhou, Zhuxiang Zhao, Jiachun Lu, Lei Yang Tags: Regular article Source Type: research

One-Step duplex droplet digital PCR for WT1 overexpression
With the improvement of treatment methods in acute hematology malignancies, the development of sensitive tools for minimal residual disease (MRD) assessment has become a priority. The monitoring of WT1 expression level by Quantitative Polymerase Chain Reaction has been a standard for MRD evaluation in Acute Myeloid Leukemia (AML) and, since 2009, has been optimized through a European LeukemiaNet (ELN) effort in an established protocol with well-defined clinical endpoints. Building on the work of the ELN, we report the development of a novel, One-Step duplex WT1/ABL1 droplet digital assay for WT1 overexpression detection. (...
Source: Journal of Molecular Diagnostics - June 11, 2020 Category: Pathology Authors: Laurent Dewispelaere, Leonore Bleret, Tom Van Acker, Cindy Van Branteghem, Pascale Cochaux, Pierre Heimann, Hakim El Housni Tags: Technical Advance Source Type: research

Identification of three circular RNA cargoes in serum exosomes as diagnostic biomarkers of non-small-cell lung cancer in the Chinese population
The recent discovery of circular RNAs (circRNAs) in serum exosomes has suggested a novel and potentially useful tool for cancer non-invasive diagnosis. However, there is yet, no substantial studies addressing this topic. RNA-seq analysis was performed between three pairs of non-small-cell lung cancer (NSCLC) patients and controls. The diagnostic values of exosomal circRNAs were assessed in a training set, validation set 1 and validation set 2. A total of 46 abnormally expressional circRNAs were identified. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 11, 2020 Category: Pathology Authors: Jianfeng Xian, Wenpeng Su, Li Liu, Boqi Rao, Mingzhu Lin, Yinyi Feng, Fuman Qiu, Jinbin Chen, Qiang Zhou, Zhuxiang Zhao, Jiachun Lu, Lei Yang Tags: Regular Article Source Type: research

Molecular Pathology Economics 101: An Overview of Molecular Diagnostics Coding, Coverage, and Reimbursement
Widespread indications for use of molecular diagnostics in various aspects of clinical medicine have driven proliferation of testing. The rapid adoption and continuous technological evolution of molecular diagnostics have often strained the development and maintenance of a functional underlying framework of coding, coverage, and reimbursement policies, thereby presenting challenges to various stakeholders, including molecular professionals, payers, and patients. A multidisciplinary working group convened by the Association for Molecular Pathology Economic Affairs Committee was tasked to describe the complex landscape of mo...
Source: Journal of Molecular Diagnostics - June 2, 2020 Category: Pathology Authors: Anthony N. Sireci, Jay L. Patel, Loren Joseph, Matthew C. Hiemenz, Oana C. Rosca, Samuel K. Caughron, Sarah A. Thibault-Sennett, Tara L. Burke, Dara L. Aisner Tags: Special article Source Type: research

Molecular Pathology Economics 101: an Overview of Molecular Diagnostics Coding, Coverage and Reimbursement
Widespread indications for use of molecular diagnostics in various aspects of clinical medicine have driven proliferation of testing. The rapid adoption and continuous technological evolution of molecular diagnostics have often strained the development and maintenance of a functional underlying framework of coding, coverage, and reimbursement policies, thereby presenting challenges to various stakeholders including molecular professionals, payers, and patients. A multidisciplinary working group convened by the Association for Molecular Pathology Economic Affairs Committee was tasked to describe the complex landscape of mol...
Source: Journal of Molecular Diagnostics - June 2, 2020 Category: Pathology Authors: Anthony N. Sireci, Jay L. Patel, Loren Joseph, Matthew C. Hiemenz, Oana C. Rosca, Samuel K. Caughron, Sarah A. Thibault-Sennett, Tara L. Burke, Dara L. Aisner Tags: Special Article Source Type: research

Assessment of Pre-Analytical Sample Handling Conditions for Comprehensive Liquid Biopsy Analysis
Liquid biopsies as a minimally invasive approach have the potential to revolutionize molecular diagnostics. Yet, although protocols for sample handling and the isolation of circulating tumor DNA (ctDNA) are numerous, comprehensive guidelines for diagnostics and research considering all aspects of real-life multicenter clinical studies are currently not available. These include limitations in sample volume, transport, and blood collection tubes. Our study aimed at testing the impact of commonly used (EDTA and heparin) and specialized blood collection tubes and storage conditions on the yield and purity of cell-free DNA for ...
Source: Journal of Molecular Diagnostics - June 1, 2020 Category: Pathology Authors: Teresa Gerber, Sabine Taschner-Mandl, Lisa Saloberger-Sindh öringer, Niko Popitsch, Ellen Heitzer, Volker Witt, René Geyeregger, Caroline Hutter, Raphaela Schwentner, Inge M. Ambros, Peter F. Ambros Tags: Regular article Source Type: research

Electric Field –Induced Release and Measurement (EFIRM)
Electric field –induced release and measurement (EFIRM) is a novel, plate-based, liquid biopsy platform capable of detecting circulating tumor DNA containing EGFR mutations directly from saliva and plasma in both early- and late-stage patients with non–small-cell lung cancer. We investigated the properties of the target molecule for EFIRM and determined that the platform preferentially detects single-stranded DNA molecules. We then investigated the properties of the EFIRM assay and determined the linearity, linear range, precision, and limit of detection for six different EGFR variants (the four most com mon g....
Source: Journal of Molecular Diagnostics - June 1, 2020 Category: Pathology Authors: Michael Tu, Jordan Cheng, Yi-Lin Chen, Wen-Chien Jea, Wan-Li Chen, Chien-Jung Chen, Chung-Liang Ho, Wei-Lun Huang, Chien-Chung Lin, Wu-Chou Su, Qianlin Ye, Josh Deignan, Wayne Grody, Feng Li, David Chia, Fang Wei, Wei Liao, David T.W. Wong, Charles M. Str Tags: Regular article Source Type: research

Application of Whole-Exome Sequencing in Detecting Copy Number Variants in Patients with Developmental Delay and/or Multiple Congenital Malformations
Overcoming challenges for the unambiguous detection of copy number variations is essential to broaden our understanding of the role of genomic variants in the clinical phenotype. With the improvement of software and databases, whole-exome sequencing quickly can become an excellent strategy in the routine diagnosis of patients with a developmental delay and/or multiple congenital malformations. However, even after a detailed analysis of pathogenic single-nucleotide variants and indels in known disease genes, using whole-exome sequencing, some patients with suspected syndromic conditions are left without a conclusive diagnos...
Source: Journal of Molecular Diagnostics - June 1, 2020 Category: Pathology Authors: Évelin A. Zanardo, Fabíola P. Monteiro, Samar N. Chehimi, Yanca G. Oliveira, Alexandre T. Dias, Larissa A. Costa, Luiza L. Ramos, Gil M. Novo-Filho, Marília M. Montenegro, Amom M. Nascimento, João P. Kitajima, Fernando Kok, Leslie D. Kulikowski Tags: Regular article Source Type: research

Economics of Coding, Coverage, and Reimbursement for Molecular Diagnostics
For many years the members of the Association for Molecular Pathology ’s (AMP) Economic Affairs Committee (EAC) have been advocating on behalf of their colleagues and laboratory professionals for a fairer and more transparent representation of appropriate billing practices and reimbursement policies for molecular pathology laboratory services. The EAC has routinely shared its expertise and insights in workshops and presentations at the AMP annual meeting and via AMP webinars. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 1, 2020 Category: Pathology Authors: Barbara A. Zehnbauer Tags: Editorial Source Type: research

Electric Field Induced Release and Measurement (EFIRM): Characterization and Technical Validation of a Novel Liquid Biopsy Platform in Plasma and Saliva
Electric Field Induced Release and Measurement (EFIRM) is a novel, plate based, liquid biopsy platform capable of detecting circulating tumor DNA containing EGFR mutations directly from saliva and plasma in both early and late stage patients with non-small cell lung cancer (NSCLC). We investigated the properties of the target molecule for EFIRM and determined that the platform preferentially detects single stranded DNA molecules. We then investigated the properties of the EFIRM assay and determined the linearity, linear range, precision, and limit of detection, for 6 different EGFR variants (the 4 most common g. (Source: J...
Source: Journal of Molecular Diagnostics - June 1, 2020 Category: Pathology Authors: Michael Tu, Jordan Cheng, Yi-Lin Chen, Wen-Chien Jea, Wan-Li Chen, Chien-Jung Chen, Chung-Liang Ho, Wei-Lun Huang, Chien-Chung Lin, Wu-Chou Su, Qianlin Ye, Josh Deignan, Wayne Grody, Feng Li, David Chia, Fang Wei, Wei Liao, David T.W. Wong, Charles M. Str Tags: Regular Article Source Type: research

Assessment of pre-analytical sample handling conditions for comprehensive liquid biopsy analyses
Liquid biopsies as minimally invasive approach have the potential to revolutionize molecular diagnostics. Yet while protocols for sample handling and the isolation of circulating tumor DNA (ctDNA) are numerous, comprehensive guidelines for diagnostics and research considering all aspects of real-life multi-center clinical studies are currently not available. These include limitations in sample volume, transport, and blood collection tubes.Our study aimed at testing the impact of commonly used (EDTA, heparin) and specialized blood collection tubes and storage conditions on the yield and purity of cell-free DNA (cfDNA) for t...
Source: Journal of Molecular Diagnostics - June 1, 2020 Category: Pathology Authors: Teresa Gerber, Sabine Taschner-Mandl, Lisa Saloberger-Sindh öringer, Niko Popitsch, Ellen Heitzer, Volker Witt, René Geyeregger, Caroline Hutter, Raphaela Schwentner, Inge M. Ambros, Peter F. Ambros Tags: Regular Article Source Type: research

Application of whole exome sequencing in detecting copy number variants in patients with developmental delay and/or multiple congenital malformations
Overcoming the challenges for the unambiguous detection of copy number variations is essential to broaden our understanding of the role of genomic variants in the clinical phenotype, in that sense, with the improvement of software and databases the whole exome sequencing can quickly become an excellent strategy in the routine diagnosis of patients with developmental delay and/or multiple congenital malformations. However, even after a detailed analysis of pathogenic single nucleotide variants and indels in known disease genes, using whole exome sequencing, some patients with suspected syndromic conditions are left without ...
Source: Journal of Molecular Diagnostics - June 1, 2020 Category: Pathology Authors: Évelin A. Zanardo, Fabíola P. Monteiro, Samar N. Chehimi, Yanca G. Oliveira, Alexandre T. Dias, Larissa A. Costa, Luiza L. Ramos, Gil M. Novo-Filho, Marília M. Montenegro, Amom M. Nascimento, João P. Kitajima, Fernando Kok, Leslie D. Kulikowski Tags: Regular Article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 30, 2020 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 30, 2020 Category: Pathology Source Type: research

A Nested Asymmetric PCR Melting Curve Assay for One-Step Genotyping of Nondeletional α-Thalassemia Mutations
In this study, a strategy of nested asymmetric PCR melting curve analysis was designed to tackle these factors and ensure sensitivity and accuracy. H erein, a novel one-step assay for genotyping of nondeletional α-thalassemia mutations, including hemoglobin (Hb) Westmead (HBA2: c.369C>G), Hb Quong Sze (HBA2: c.377T>C), Hb Constant Spring (HBA2: c.427T>C), CD30 (HBA2: c.91-93delGAG), and CD31 (HBA2: c.95G>A) in a single closed tube, was established and evaluated. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 29, 2020 Category: Pathology Authors: Jiachun Qin, Mingli Xu, Qiang Zhang, Xiaojun Wen, Sheng He, Yong Zhou, Haiping Liu, Wanjun Zhou Tags: Regular article Source Type: research

Long-Molecule Sequencing
Currently, carrier testing for thalassemia requires the application of different molecular tests to provide an accurate genotype. As an alternative method, long-molecule sequencing (LMS) was evaluated on the PacBio Sequel platform for genotyping carriers of α-thalassemia or β-thalassemia. Multiplex long PCR was used to generate representative amplicons for the α (HBA1/2) and β (HBB) gene loci. Following LMS, circular consensus sequencing reads were aligned to the hg19 reference genome and variants called using FreeBayes software. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 28, 2020 Category: Pathology Authors: Liangpu Xu, Aiping Mao, Hui Liu, Baoheng Gui, Kwong Wai Choy, Hailong Huang, Qian Yu, Xiaojie Zhang, Meihuan Chen, Na Lin, Lingji Chen, Jin Han, Yan Wang, Min Zhang, Xiaoyu Li, Deqin He, Yuan Lin, Jianguang Zhang, David S. Cram, Hua Cao Tags: Regular article Source Type: research

Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridizatio...
Source: Journal of Molecular Diagnostics - May 28, 2020 Category: Pathology Authors: Rajesh R. Singh Tags: Review Source Type: research

Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges, Advances and Applications
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Owing to their capability for high throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies such as Sanger sequencing and Pyrosequencing, expression arrays, real-time polymerase chain reaction and fluorescence in...
Source: Journal of Molecular Diagnostics - May 28, 2020 Category: Pathology Authors: Rajesh R. Singh Source Type: research

Long molecule sequencing: a new approach for identification of clinically significant DNA variants in alpha and beta thalassemia carriers
Currently, carrier testing for thalassemia requires the application of different molecular tests to provide an accurate genotype. As an alternative methodology, we evaluated long molecule sequencing (LMS) on the PacBio Sequel platform for genotyping carriers of alpha ( α) or beta (β) thalassemia. Multiplex long PCR was used to generate representative amplicons for the α (HBA1/2) and β (HBB) gene loci. Following LMS, circular consensus sequencing reads were aligned to the hg19 reference genome and variants called using Free-Bayes software. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 28, 2020 Category: Pathology Authors: Liangpu Xu, Aiping Mao, Hui Liu, Baoheng Gui, Kwong Wai Choy, Hailong Huang, Qian Yu, Xiaojie Zhang, Meihuan Chen, Na Lin, Lingji Chen, Jin Han, Yan Wang, Min Zhang, Xiaoyu Li, Deqin He, Yuan Lin, Jianguang Zhang, David S. Cram, Hua Cao Source Type: research

An Isothermal Method for Sensitive Detection of Mycobacterium tuberculosis Complex Using Clustered Regularly Interspaced Short Palindromic Repeats/Cas12a Cis and Trans Cleavage
Tuberculosis is one of the most serious infectious diseases, resulting in death worldwide. Traditional detection methods are not enough to meet the clinical requirements of rapid diagnosis, high specificity, and high sensitivity. Fast, sensitive, and accurate detection of Mycobacterium tuberculosis (MTB) is urgently needed to treat and control tuberculosis disease. Clustered regularly interspaced short palindromic repeats (CRISPR) –associated proteins (Cas12a) exhibit strong nonspecific degradation ability of exogenous single-strand nucleic acids (trans cleavage) after specific recognition of target sequence. (Source...
Source: Journal of Molecular Diagnostics - May 26, 2020 Category: Pathology Authors: Haipo Xu, Xiaolong Zhang, Zhixiong Cai, Xiuqing Dong, Geng Chen, Zhenli Li, Liman Qiu, Lei He, Bin Liang, Xiaolong Liu, Jingfeng Liu Tags: Regular article Source Type: research

An isothermal method for sensitive detection of Mycobacterium tuberculosis complex using CRISPR/Cas12a cis- and trans-cleavage
Tuberculosis is one of the most serious infectious diseases resulting in lethal death worldwide. Traditional detection methods are still not enough to meet the clinical requirements of rapid diagnosis, high specificity and sensitivity. Fast, sensitive and accurate detection of mycobacterium tuberculosis (MTB) is an urgent need for the treatment and control of tuberculosis disease. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-associated proteins (Cas12a) exhibits strong nonspecific degradation ability of exogenous single-strand nucleic acids (trans-cleavage) after specific recognition of target sequenc...
Source: Journal of Molecular Diagnostics - May 26, 2020 Category: Pathology Authors: Haipo Xu, Xiaolong Zhang, Zhixiong Cai, Xiuqing Dong, Geng Chen, Zhenli Li, Liman Qiu, Lei He, Bin Liang, Xiaolong Liu, Jingfeng Liu Tags: Regular Article Source Type: research

Diagnostic Accuracy of Presurgical Staphylococcus aureus PCR Assay Compared with Culture and Post-PCR Implementation Surgical Site Infection Rates
Nasal colonization with Staphylococcus aureus is a well-referenced risk factor for postoperative surgical site infections (SSIs). Our health care system that performs>40,000 surgeries per year assessed both the diagnostic accuracy of the BD MAX StaphSR assay (MAX StaphSR), a PCR-based test that detects and differentiates S. aureus and methicillin-resistant S. aureus (MRSA), compared with our standard of care culture and the subsequent clinical impact on SSIs 1 year after implementation. In addition, residual specimens were tested by broth-enriched culture. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 22, 2020 Category: Pathology Authors: Giannoula S. Tansarli, Lindsay LeBlanc, Dianne B. Auld, Kimberle C. Chapin Tags: Regular article Source Type: research

Diagnostic accuracy of pre-surgical Staphylococcus aureus PCR assay compared to culture and post-PCR implementation surgical site infection rates
Nasal colonization with S. aureus is a well referenced risk factor for post-operative surgical site infections (SSIs). Our healthcare system that performs>40,000 surgeries per year assessed both the diagnostic accuracy of the BD MAX StaphSR (MAX StaphSR) assay, a PCR-based test that detects and differentiates Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA), compared to our standard of care culture and the subsequent clinical impact on SSIs one year after implementation. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 22, 2020 Category: Pathology Authors: Giannoula S. Tansarli, Lindsay LeBlanc, Dianne B. Auld, Kimberle C. Chapin Tags: Regular Article Source Type: research

Enzymatic and chemical-based methods to inactivate endogenous blood ribonucleases for nucleic acid diagnostics
There are ongoing research efforts into simple and low-cost point-of-care (POC) nucleic acid amplification tests (NATs) addressing widespread diagnostic needs in resource-limited clinical settings. Nucleic acid testing for RNA targets in blood specimens typically requires sample preparation that inactivates robust blood ribonucleases (RNases) that can rapidly degrade exogenous RNA. Most NATs rely on decades-old methods that lyse pathogens and inactivate RNases with high concentrations of guanidinium salts. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 21, 2020 Category: Pathology Authors: Andrew T. Bender, Benjamin P. Sullivan, Lorraine Lillis, Jonathan D. Posner Source Type: research

Laboratories and Pandemic Preparedness
The coronavirus pandemic of 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 was first detected in Wuhan, China, in December 2019 and spread globally during the early part of 2020. As of May 11, 2020,>4 million cases have been confirmed worldwide, with>1.3 million cases in the United States (https://coronavirus.jhu.edu/map.html, last accessed May 11, 2020). The United States now has the most confirmed cases and confirmed deaths worldwide. The key to slowing the spread of this disease is widespread testing so that patients can be quickly identified and isolated. (...
Source: Journal of Molecular Diagnostics - May 16, 2020 Category: Pathology Authors: Karen L. Kaul Tags: Guest editorial Source Type: research

Laboratories and pandemic preparedness: A framework for collaboration and oversight
The coronavirus pandemic of 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 was first detected in Wuhan, China in December 2019 and spread globally during the early part of 2020. As of May 11, 2020, over 4 million cases have been confirmed worldwide, with over 1.3 million cases in the United States (https://coronavirus.jhu.edu/map.html, last accessed May 11, 2020). The United States now has the most confirmed cases and confirmed deaths worldwide. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 16, 2020 Category: Pathology Authors: Karen L. Kaul Tags: Guest Editorial Source Type: research

Detection of Microsatellite Instability from Circulating Tumor DNA by Targeted Deep  Sequencing
Currently, microsatellite instability (MSI) detection is limited to tissue samples with sufficient tumor content. Detection of MSI from blood has been explored but confounded by low sensitivity due to limited circulating tumor DNA (ctDNA). We developed a next-generation sequencing –based algorithm, blood MSI signature enrichment analysis, to detect MSI from blood. Blood MSI signature enrichment analysis development involved three major steps. First, marker sites that can effectively distinguish high MSI (MSI-H) from microsatellite stable tumors were extracted. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 15, 2020 Category: Pathology Authors: Zhenghao Cai, Zhenxin Wang, Chenglin Liu, Dongtao Shi, Dapeng Li, Minhua Zheng, Han Han-Zhang, Analyn Lizaso, Jianxing Xiang, Juan Lv, Wenjun Wu, Zhihong Zhang, Zhou Zhang, Fei Yuan, Songbing He, Jing Sun Tags: Technical advance Source Type: research

Detection of microsatellite instability from circulating tumor DNA by targeted deep sequencing
In this study, we developed an NGS-based algorithm, bMSISEA (blood MSI signature enrichment analysis), to detect MSI from blood samples. BMSISEA development involved 3 major steps. First, marker sites that can effectively distinguish MSI-high (MSI-H) from microsatellite stable (MSS) tumors were extracted. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 15, 2020 Category: Pathology Authors: Zhenghao Cai, Zhenxin Wang, Chenglin Liu, Dongtao Shi, Dapeng Li, Minhua Zheng, Han Han-Zhang, Analyn Lizaso, Jianxing Xiang, Juan Lv, Wenjun Wu, Zhihong Zhang, Zhou Zhang, Fei Yuan, Songbing He, Jing Sun Tags: Technical Advance Source Type: research

Implementation of an Emergency Use Authorization Test During an Impending National Crisis
The laboratory response to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic may be termed heroic. From the identification of the novel coronavirus to implementation of routine laboratory testing around the world to the development of potential vaccines, laboratories have played a critical role in the efforts to curtail this pandemic. In this brief report, we review our own effort at a mid-sized, rural, academic medical center to implement a molecular test for the virus; and, we share insights and lessons learned from that process which might be helpful in similar situations in the future. (...
Source: Journal of Molecular Diagnostics - May 14, 2020 Category: Pathology Authors: Joel A. Lefferts, Edward J. Gutmann, Isabella W. Martin, Wendy A. Wells, Gregory J. Tsongalis Tags: Perspectives Source Type: research

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Is Comparable in Clinical Samples Preserved in Saline or Viral Transport Medium
As the coronavirus disease 2019 (COVID-19) pandemic sweeps across the world, the availability of viral transport medium (VTM) has become severely limited, contributing to delays in diagnosis and rationing of diagnostic testing. Given that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA has demonstrated stability, we posited that phosphate-buffered saline (PBS) may be a viable transport medium, as an alternative to VTM, for clinical real-time quantitative PCR (qPCR) testing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 13, 2020 Category: Pathology Authors: Jared Radbel, Sugeet Jagpal, Jason Roy, Andrew Brooks, Jay Tischfield, Michael Sheldon, Christian Bixby, Dana Witt, Maria L. Gennaro, Daniel B. Horton, Emily S. Barrett, Jeffrey L. Carson, Reynold A. Panettieri, Martin J. Blaser Tags: Regular article Source Type: research

Detection of Severe Acute Respiratory Syndrome Coronavirus 2 Is Comparable in Clinical Samples Preserved in Saline or Viral Transport Medium
As the coronavirus disease 2019 (COVID-19) pandemic sweeps across the world, the availability of viral transport medium (VTM) has become severely limited, contributing to delays in diagnosis and rationing of diagnostic testing. Given that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral RNA has demonstrated stability, we posited that phosphate-buffered saline (PBS) may be a viable transport medium, as an alternative to VTM, for clinical real-time quantitative PCR (qPCR) testing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 13, 2020 Category: Pathology Authors: Jared Radbel, Sugeet Jagpal, Jason Roy, Andrew Brooks, Jay Tischfield, Michael Sheldon, Christian Bixby, Dana Witt, Maria L. Gennaro, Daniel B. Horton, Emily S. Barrett, Jeffrey L. Carson, Reynold A. Panettieri, Martin J. Blaser Tags: Regular article Source Type: research

Detection of SARS-CoV-2 is comparable in clinical samples preserved in saline or viral transport media
As the COVID-19 pandemic sweeps across the world, the availability of viral transport media (VTM) has become severely limited, contributing to delays in diagnosis and rationing of diagnostic testing. Given that SARS-CoV-2 viral RNA has demonstrated stability, we posited that phosphate buffered saline (PBS) may be a viable transport medium, as an alternative to VTM), for clinical qPCR testing. We assessed the intra- and inter-individual reliability of SARS-CoV-2 qPCR in clinical endotracheal secretion samples transported in VTM or PBS, evaluating the stability of the RT-qPCR signal for three viral targets (N gene, ORF1ab, a...
Source: Journal of Molecular Diagnostics - May 13, 2020 Category: Pathology Authors: Jared Radbel, Sugeet Jagpal, Jason Roy, Andrew Brooks, Jay Tischfield, Michael Sheldon, Christian Bixby, Dana Witt, Maria Laura Gennaro, Daniel B. Horton, Emily S. Barrett, Jeffrey L. Carson, Reynold A. Panettieri, Martin J. Blaser Tags: Regular Article Source Type: research

Sputum Cell-Free DNA
This study established an improved sputum cell-free DNA (cfDNA) extraction method study and applied a super –amplification refractory mutation system to detect the EGFR mutation status in sputum cfDNA. The sputum sediments were used for cytology evaluation. The study included 102 lung adenocarcinoma patients; 65 patients (63.7%) were positive for EGFR mutations in tumor samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 11, 2020 Category: Pathology Authors: Zheng Wang, Lin Zhang, Lin Li, Xiaoguang Li, Yan Xu, Mengzhao Wang, Li Liang, Peng Jiao, Yuanming Li, Shurong He, Jun Du, Lei He, Min Tang, Mingjun Sun, Li Yang, Jing Di, Guanshan Zhu, Hong Shi, Dongge Liu Tags: Regular article Source Type: research

Application of Multiplex Bisulfite PCR –Ligase Detection Reaction–Real-Time Quantitative PCR Assay in Interrogating Bioinformatically Identified, Blood-Based Methylation Markers for Colorectal Cancer
This report demonstrates the ability of a multiplex bisulfite PCR –ligase detection reaction–real-time quantitative PCR assay to detect seven methylated CpG markers (CRC or colon specific), in both simulated (approximately 30 copies of fragmented CRC cell line DNA mixed with approximately 3000 copies of fragmented peripheral blood DNA) and CRC patient-derived cell-free DNAs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 11, 2020 Category: Pathology Authors: Manny D. Bacolod, Aashiq H. Mirza, Jianmin Huang, Sarah F. Giardina, Philip B. Feinberg, Steven A. Soper, Francis Barany Tags: Regular article Source Type: research

Sputum Cell-free DNA: Valued Surrogate Sample for Detection of EGFR Mutation in Patients with Advanced Lung Adenocarcinoma
Sputum is common cytological sample type, but its potential use in EGFR mutation detection in patients with lung cancer is not fully evaluated. An improved sputum cfDNA extraction method was established in this study, and applied super-amplification refractory mutation system (SuperARMS) to detect the EGFR mutation status in sputum cfDNA. The sputum sediments were used for cytology evaluation. The study included 102 lung adenocarcinoma patients, in which 65 (63.7%) patients were positive for EGFR mutations in tumor samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 11, 2020 Category: Pathology Authors: Zheng Wang, Lin Zhang, Lin Li, Xiaoguang Li, Yan Xu, Mengzhao Wang, Li Liang, Peng Jiao, Yuanming Li, Shurong He, Jun Du, Lei He, Min Tang, Mingjun Sun, Li Yang, Jing Di, Guanshan Zhu, Hong Shi, Dongge Liu Source Type: research