Evaluation for Genetic Disorders in the Absence of a Clinical Indication for Testing
The increasing quality and diminishing cost of next-generation sequencing has transformed our ability to interrogate large quantities of genetic information. This has led to a dramatic increase in the number of elective genomic tests performed. In this article, elective test denotes a test that a patient chooses to undertake without a clinical indication. The variety of elective genomic testing options is considerable. Because these offerings provide differing levels of sensitivity and specificity, it can be difficult to choose among them. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 16, 2018 Category: Pathology Authors: James T. Lu, Matthew Ferber, Jill Hagenkord, Elissa Levin, Sarah South, Hyunseok P. Kang, Kimberly A. Strong, David P. Bick Tags: Perspectives Source Type: research

Evaluation for Genetic Disorders in the Absence of a Clinical Indication for Testing: Elective Genomic Testing
The increasing quality and diminishing cost of next-generation sequencing has transformed our ability to interrogate large quantities of genetic information. This has led to a dramatic increase in the number of elective genomic tests performed. In this article elective test denotes a test that a patient chooses to undertake without a clinical indication. The variety of elective genomic testing options is considerable. Because these offerings provide differing levels of sensitivity and specificity it can be difficult to choose among them. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 16, 2018 Category: Pathology Authors: James T. Lu, Matthew Ferber, Jill Hagenkord, Elissa Levin, Sarah South, Hyunseok P. Kang, Kimberly A. Strong, David P. Bick Tags: Perspectives Source Type: research

Optimizing a Metatranscriptomic Next-Generation Sequencing Protocol for Bronchoalveolar Lavage Diagnostics
We describe here a RNA-based metatranscriptomic NGS (mtNGS) protocol for culture-independent detection of potential infectious pathogens, using clinical bronchoalveolar lavage specimens as an example. We present both an optimized workflow for experimental sequence data collection and a simplified pipeline for bioinformatics sequence data processing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 30, 2018 Category: Pathology Authors: Weihua Huang, Changhong Yin, Guiqing Wang, Jeremy Rosenblum, Sankaran Krishnan, Nevenka Dimitrova, John T. Fallon Tags: Regular Article Source Type: research

Mutation burden and I index for Detection of microsatellite instability in colorectal cancer by targeted next-generation sequencing
Next-generation sequencing (NGS) panels are widely used for defining tumor mutation profiles and determining treatment approaches. We performed targeted NGS with 382 genes in colorectal cancer with known microsatellite instability (MSI) status. After exclusion of germline alterations, load of somatic mutations and small insertion/deletion (indel) alterations were determined. In the test set, 79 patients with 41 microsatellite-stable (MSS) and 38 MSI tumors were included. There were 120 MSS and eight MSI-high tumors in the validation set. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 30, 2018 Category: Pathology Authors: Jeong Eun Kim, Sung-Min Chun, Yong Sang Hong, Kyu-pyo Kim, Sun Young Kim, Jihun Kim, Chang-Ohk Sung, Eun Jeong Cho, Tae Won Kim, Se Jin Jang Tags: Regular Article Source Type: research

Development of novel mutation-specific droplet digital PCR assays detecting TERT promoter mutations in tumor and plasma samples
We describe the development of novel probe-based droplet digital PCR (ddPCR) assays that specifically detect and quantify these two mutations along with the less common 242-243 CC>TT mutation, and demonstrate their application using human tumor and plasma samples from melanoma patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 25, 2018 Category: Pathology Authors: Broderick Corless, Gregory A. Chang, Samantha Cooper, Mahrukh S. Syeda, Yongzhao Shao, Iman Osman, George Karlin-Neumann, David Polsky Tags: Regular article Source Type: research

Expedited Analysis and Reporting of Multiple Mutations that Modify Medical Management of Myeloid Malignancies
This commentary highlights the article by Patel et  al that reports a novel custom next-generation sequencing platform for fast detection of select genes in hematologic malignancies. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2018 Category: Pathology Authors: Michael J. Kluk, Adam Bagg Tags: Commentary Source Type: research

Optimized digital droplet PCR for BCR-ABL
Quantitative real-time-PCR methods are commonly used to monitor BCR-ABL transcript levels in patients with chronic myelogenous leukemia. However, standard techniques involve separate measurements of target and reference DNAs, require standard curves, and are susceptible to PCR inhibition. An optimized duplex droplet digital (dd)PCR should provide absolute quantification without the need for standard curves. The combination of high sensitivity and low background is particularly important for reliable monitoring of minimal residual disease. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2018 Category: Pathology Authors: Jacqueline Maier, Thoralf Lange, Michael Cross, Kathrin Wildenberger, Dietger Niederwieser, Georg-Nikolaus Franke Tags: Technical Advance Source Type: research

Clinical Evaluation of Massively Parallel RNA Sequencing for Detecting Recurrent Gene Fusions in Hematologic Malignancies
The application of next-generation sequencing (NGS) technology in clinical diagnostics should proceed with care. We have evaluated the clinical validity of two commercially available RNA fusion panels, the TruSight RNA fusion panel (Illumina) and FusionPlex Pan-Heme Kit (ArcherDx), to detect recurrent translocations in hematologic malignancies. Twenty-four bone marrow samples taken at the initial diagnosis of patients with acute leukemia and chronic myeloid leukemia were included. To assess the limit of detection, serial dilutions of BCR-ABL1 (e1a2) positive RNAs were prepared using a commercial reference material. (Source...
Source: Journal of Molecular Diagnostics - October 19, 2018 Category: Pathology Authors: Borahm Kim, Hyeonah Lee, Saeam Shin, Seung-Tae Lee, Jong Rak Choi Tags: Regular Article Source Type: research

Expedited analysis and reporting of multiple mutations that modify medical management in myeloid malignancies:
This commentary highlights the article by Patel et al that reports a novel custom next-generation sequencing platform for fast detection of select genes in hematological malignancies. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2018 Category: Pathology Authors: Michael J. Kluk, Adam Bagg Tags: Commentary Source Type: research

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

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

Title Page
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 18, 2018 Category: Pathology Source Type: research

Disclosure Statement
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 18, 2018 Category: Pathology Source Type: research

Abstracts
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 18, 2018 Category: Pathology Source Type: research

Author Index
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 18, 2018 Category: Pathology Source Type: research

Electric Field –Induced Release and Measurement Liquid Biopsy for Noninvasive Early Lung Cancer Assessment
Previously, we detected circulating tumor DNA that contained two EGFR mutations (p.L858R and exon19 del) in plasma of patients with late-stage non –small-cell lung carcinoma (NSCLC) using the electric field–induced release and measurement (EFIRM) platform. Our aim was to determine whether EFIRM technology can detect these mutations in patients with early-stage NSCLC. Prospectively, 248 patients with radiographically determined pulmonary n odules were recruited. Plasma was collected before biopsy and histologic examination of the nodule. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 8, 2018 Category: Pathology Authors: Fang Wei, Charles M. Strom, Jordan Cheng, Chien-Chung Lin, Ching-Yun Hsu, Guy W. Soo Hoo, David Chia, Yong Kim, Feng Li, David Elashoff, Tristan Grognan, Michael Tu, Wei Liao, Rena Xian, Wayne W. Grody, Wu-Chou Su, David T.W. Wong Tags: Technical advance Source Type: research

Screening for Regulatory Variants in 460 kb Encompassing the CFTR Locus in Cystic Fibrosis Patients
It is estimated that up to 5% of cystic fibrosis transmembrane conductance regulator (CFTR) pathogenic alleles are unidentified. Some of these errors may lie in noncoding regions of the locus and affect gene expression. To identify regulatory element variants in the CFTR locus, SureSelect-targeted enrichment of 460 kb encompassing the gene was optimized to deep sequence genomic DNA from 80 CF patients with an unequivocal clinical diagnosis but only one or no CFTR-coding region pathogenic variants. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 5, 2018 Category: Pathology Authors: Jenny L. Kerschner, Sujana Ghosh, Alekh Paranjapye, Wilmel R. Cosme, Marie-Pierre Audr ézet, Miyuki Nakakuki, Hiroshi Ishiguro, Claude Férec, Johanna Rommens, Ann Harris Tags: Regular article Source Type: research

Screening for regulatory variants in 460kb encompassing the CFTR locus in cystic fibrosis patients
It is estimated that up to 5% of cystic fibrosis transmembrane conductance regulator (CFTR) pathogenic alleles are unidentified. Some of these errors may lie in non-coding regions of the locus and impact gene expression. To identify regulatory element variants in the CFTR locus, SureSelect targeted enrichment of 460kb encompassing the gene was optimized to deep-sequence genomic DNA from 80 CF patients with an unequivocal clinical diagnosis but only one or no CFTR-coding region pathogenic variants. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 5, 2018 Category: Pathology Authors: Jenny L. Kerschner, Sujana Ghosh, Alekh Paranjapye, Wilmel R. Cosme, Marie-Pierre Audr ézet, Miyuki Nakakuki, Hiroshi Ishiguro, Claude Férec, Johanna Rommens, Ann Harris Tags: Regular Article Source Type: research

An optimized workflow to evaluate estrogen receptor gene mutations in small amounts of cell-free DNA
The detection of mutated genes in cell-free DNA (cfDNA) in plasma has emerged as an important minimally-invasive way to obtain detailed information regarding tumor biology. Reliable determination of circulating tumor –derived DNA, often present at a very low quantity amidst an excess of normal DNA in plasma, would be of added value for screening and monitoring of cancer patients and for hypothesis-generating studies in valuable retrospective cohorts. Our aim was to establish a workflow to simultaneously assess four hotspot estrogen receptor mutations (mESR1) in cfDNA isolated from only 200 μL of plasma by means of...
Source: Journal of Molecular Diagnostics - October 5, 2018 Category: Pathology Authors: Silvia R. Vitale, Anieta M. Sieuwerts, Nick Beije, Jaco Kraan, Lindsay Angus, Bianca Mostert, Esther A. Reijm, Ngoc M. Van, Ronald van Marion, Luc Y. Dirix, Paul Hamberg, Felix E. de Jongh, Agnes Jager, John A. Foekens, Paolo Vigneri, Stefan Sleijfer, Mau Tags: Regular Article Source Type: research

insiM
Lack of reliable reference samples containing different mutations of interest across large sets of disease-relevant loci limits the extensive validation clinical next-generation sequencing (NGS) assays and their associated bioinformatics pipelines. Herein, we have generated a publicly available, highly flexible tool, in silico Mutator (insiM), to introduce point mutations, insertions, deletions, and duplications of any size into real data sets of amplicon-based or hybrid-capture NGS assays. insiM accepts an alignment file along with target territory and produces paired-end FASTQ files containing specified mutations via mod...
Source: Journal of Molecular Diagnostics - September 28, 2018 Category: Pathology Authors: Sushant A. Patil, Ibro Mujacic, Lauren L. Ritterhouse, Jeremy P. Segal, Sabah Kadri Tags: Technical advance Source Type: research

In Silico Mutator
Lack of reliable reference samples containing different mutations of interest across large sets of disease-relevant loci limits the extensive validation clinical next-generation sequencing (NGS) assays and their associated bioinformatics pipelines. Herein, we have generated a publicly available, highly flexible tool, in silico Mutator (insiM), to introduce point mutations, insertions, deletions, and duplications of any size into real data sets of amplicon-based or hybrid-capture NGS assays. insiM accepts an alignment file along with target territory and produces paired-end FASTQ files containing specified mutations via mod...
Source: Journal of Molecular Diagnostics - September 28, 2018 Category: Pathology Authors: Sushant A. Patil, Ibro Mujacic, Lauren L. Ritterhouse, Jeremy P. Segal, Sabah Kadri Tags: Technical advance Source Type: research

A nanopore sequencing –based assay for rapid detection of gene fusions
Structural chromosomal rearrangements leading to gene fusions are strong driver mutations in a variety of tumors. Identification of specific gene fusions can be essential for distinguishing benign from malignant conditions, and for recognizing specific subtypes of neoplasms which can have different management and prognosis. Rapid identification of gene fusions is particularly critical for patients with acute leukemia who cannot wait more than few days before initiating treatment, and for whom treatment can be dramatically different depending on the leukemia subtype. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 28, 2018 Category: Pathology Authors: William R. Jeck, Jesse Lee, Hayley Robinson, Long P. Le, A. John Iafrate, Valentina Nardi Tags: Regular Article Source Type: research

Accurate and sensitive analysis of minimal residual disease in acute myeloid leukemia using deep sequencing of single nucleotide variations
Minimal residual disease (MRD) in acute myeloid leukemia (AML) is of major prognostic importance. The genetic landscape of AML is characterized by numerous somatic mutations, which constitute potential MRD markers. Leukemia-specific mutations can be identified with exome sequencing at diagnosis and assessed during follow-up at low frequencies using targeted deep sequencing. Our aim was to further validate this patient-tailored assay for substitution mutations. By applying a statistical model, which corrects for position-specific errors, a limit of detection for single nucleotide variations of variant allele frequency (VAF)...
Source: Journal of Molecular Diagnostics - September 28, 2018 Category: Pathology Authors: Erik Delsing Malmberg, Anna Rehammar, Mariana B. Pereira, Jonas Abrahamsson, Tore Samuelsson, Sara St åhlman, Julia Asp, Anne Tierens, Lars Palmqvist, Erik Kristiansson, Linda Fogelstrand Tags: Regular Article Source Type: research

insiM: in silico Mutator software for bioinformatics pipeline validation of clinical next-generation sequencing (NGS) assays
Lack of reliable reference samples containing different mutations of interest across large sets of disease-relevant loci limits the extensive validation clinical next-generation sequencing (NGS) assays and their associated bioinformatics pipelines. Here, we have created a publicly available, highly flexible tool, in silico Mutator (insiM) to introduce point mutations, insertions, deletions, and duplications of any size into real datasets of amplicon-based or hybrid-capture NGS assay. insiM accepts an alignment file along with target territory and produces paired-end FASTQ files containing specified mutations via modificati...
Source: Journal of Molecular Diagnostics - September 28, 2018 Category: Pathology Authors: Sushant A. Patil, Ibro Mujacic, Lauren L. Ritterhouse, Jeremy P. Segal, Sabah Kadri Tags: Technical Advance Source Type: research

Diagnostic targETEd seQuencing adjudicaTion (DETEQT)
Next-generation sequencing (NGS) for infectious disease diagnostics is a relatively new and underdeveloped concept. If this technology is to become a regulatory-grade clinical diagnostic, standardization in the form of locked-down assays and firmly established underlying processes is necessary. Targeted sequencing, specifically by amplification of genomic signatures, has the potential to bridge the gap between PCR- and NGS-based diagnostics; however, existing NGS assay panels lack validated analytical techniques to adjudicate high background and error-prone NGS data. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 27, 2018 Category: Pathology Authors: Turner A. Conrad, Chien-Chi Lo, Jeffrey W. Koehler, Amanda S. Graham, Christopher P. Stefan, Adrienne T. Hall, Christina E. Douglas, Patrick S. Chain, Timothy D. Minogue Tags: Regular article Source Type: research

Diagnostic Targetd Sequencing Adjudication
Next-generation sequencing (NGS) for infectious disease diagnostics is a relatively new and underdeveloped concept. If this technology is to become a regulatory-grade clinical diagnostic, standardization in the form of locked-down assays and firmly established underlying processes is necessary. Targeted sequencing, specifically by amplification of genomic signatures, has the potential to bridge the gap between PCR- and NGS-based diagnostics; however, existing NGS assay panels lack validated analytical techniques to adjudicate high background and error-prone NGS data. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 27, 2018 Category: Pathology Authors: Turner A. Conrad, Chien-Chi Lo, Jeffrey W. Koehler, Amanda S. Graham, Christopher P. Stefan, Adrienne T. Hall, Christina E. Douglas, Patrick S.G. Chain, Timothy D. Minogue Tags: Regular article Source Type: research

Targeted next-generation sequencing facilitates genetic diagnosis and provides novel pathogenetic insights into deafness with enlarged vestibular aqueduct
Enlarged vestibular aqueduct (EVA) is an inner ear malformation associated with sensorineural hearing impairment. The majority of EVA are associated with Pendred syndrome and non-syndromic DFNB4, two autosomal recessive disorders caused by mutations in SLC26A4. However, a significant percentage of EVA patients cannot have confirmed diagnosis by screening common SLC26A4 mutations, constituting an enigma in genetic diagnosis. To enable comprehensive genetic examination and explore the etiologies of EVA, we designed a next-generation sequencing panel targeting the entire length of three Pendred syndrome/DFNB4 genes (SLC26A4, ...
Source: Journal of Molecular Diagnostics - September 27, 2018 Category: Pathology Authors: Yin-Hung Lin, Chen-Chi Wu, Yi-Hsin Lin, Ying-Chang Lu, Chih-Shan Chen, Tien-Chen Liu, Pei-Lung Chen, Chuan-Jen Hsu Tags: Regular Article Source Type: research

An Innovative Multiplexed And Flexible Molecular Approach For The Differential Detection Of Arboviruses
Nucleic acid testing during the preseroconversion viremic phase is required to differentially diagnose arboviral infections. The continuing emergence of arboviruses such as Zika (ZIKV), dengue (DENV), and chikungunya (CHIKV) viruses necessitates the development of a flexible diagnostic approach. Similar clinical signs and the priority to protect pregnant women from ZIKV infection indicate that the differential diagnosis of arboviruses is essential for effective patient management, clinical care, and epidemiological surveillance. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 27, 2018 Category: Pathology Authors: Fanny Leon, Albert Meyer, Robin Reynier, Emilie Blanc, Lilian Bruy ère-Ostells, Jean-Charles Brès, Yannick Simonin, Sara Salinas, Pierre Gallian, Isabelle Leparc-Goffart, Antoine Biron, Myrielle Dupont-Rouzeyrol, François Morvan, Jean-Jacques Vasseur, Tags: Regular Article Source Type: research

A single-tube, EuroClonality-inspired, TRG clonality multiplex PCR aids management of patients with enteropathic diseases, including from formaldehyde-fixed, paraffin-embedded tissues
Celiac disease is a chronic inflammation of the small intestine with villous atrophy that can become refractory to a gluten-free diet. Two categories of refractory celiac disease (I and II) can be distinguished by the phenotype of intra-epithelial lymphocytes and the status of TRG genes. Their distinction is important because 30% to 50% of type II, but only 0% to 14% of type I, evolve to an aggressive enteropathy-associated T-cell lymphoma and therefore require intensive treatment. Currently, differential diagnosis integrates immunohistochemistry, immunophenotyping, and TRG clonality analyses but each have limitations. (So...
Source: Journal of Molecular Diagnostics - September 27, 2018 Category: Pathology Authors: Coralie Derrieux, Am élie Trinquand, Julie Bruneau, Virginie Verkarre, Ludovic Lhermitte, Marion Alcantara, Patrick Villarese, Bertrand Meresse, David Sibon, Olivier Hermine, Nicole Brousse, Thierry Molina, Christophe Cellier, Nadine Cerf-Bensussan, Geor Tags: Regular Article Source Type: research

DETEQT: Algorithms for Adjudicating Targeted Infectious Disease Next-Generation Sequencing Panels
Next-generation sequencing (NGS) for infectious disease diagnostics is a relatively new and under-developed concept. If this technology is to become a regulatory-grade clinical diagnostic, standardization in the form of locked-down assays and firmly established underlying processes is necessary. Targeted sequencing, specifically by amplification of genomic signatures, has the potential to bridge the gap between PCR- and NGS-based diagnostics; however, existing NGS assay panels lack validated analytical techniques to adjudicate high background and error prone NGS data. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 27, 2018 Category: Pathology Authors: Turner A. Conrad, Chien-Chi Lo, Jeffrey W. Koehler, Amanda S. Graham, Christopher P. Stefan, Adrienne T. Hall, Christina E. Douglas, Patrick Sam Guy Chain, Timothy D. Minogue Tags: Regular Article Source Type: research

The next generation in detection of leukemia-associated translocations
Diagnosis of leukemia has come a long way since the days of the French-American-British classification scheme, which relied upon a combination of blast counts, morphology, and cytochemistry to classify myeloid and lymphoid acute leukemias (1). Beginning with the 2008 World Health Organization (WHO) Classification of Tumors of the Hematopoietic and Lymphoid Tissues (2) and expanded in the 2017 edition (3), new categories of acute myeloid leukemia and acute lymphocytic leukemia were created based solely on molecular abnormalities present within the leukemic cells, independent of the proportion of leukemic blasts in the perip...
Source: Journal of Molecular Diagnostics - September 27, 2018 Category: Pathology Authors: Daniel E. Sabath Tags: Commentary Source Type: research

Effects of collection and processing procedures on plasma circulating cell-free DNA from cancer patients
This study investigates the effects of the i) delay in processing, ii) storage temperatures, iii) different blood collection tubes, iv) centrifugation protocols, and v) sample shipment on cfDNA levels. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 28, 2018 Category: Pathology Authors: Bente Risberg, Dana WY. Tsui, Heather Biggs, Andrea Ruiz-Valdepenas Martin de Almagro, Sarah-Jane Dawson, Charlotte Hodgkin, Linda Jones, Christine Parkinson, Anna Piskorz, Francesco Marass, Dineika Chandrananda, Elizabeth Moore, James Morris, Vincent Pla Tags: Regular Article Source Type: research

A Head-to-Head Analytical Comparison of Cobas 4800 HPV, PapilloCheck HPV Screening, and LMNX Genotyping Kit HPV GP for Detection of Human Papillomavirus DNA in Cervical and Cervicovaginal Swabs
High-risk human papillomavirus (hrHPV) infection is a cause of cervical cancer development. The addition of hrHPV testing to cervical cancer screening and monitoring of cervical intraepithelial neoplasia treatment improves the efficacy of screening and treatment, respectively. Self-sampling for hrHPV testing seems a promising tool for increasing patient participation in cervical cancer screening. In this project, 1198 cervical swabs obtained by physicians and 176 cervicovaginal swabs obtained by self-sampling (not collected in parallel) were analyzed for the presence of 14 hrHPV genotypes using three commercially available...
Source: Journal of Molecular Diagnostics - August 27, 2018 Category: Pathology Authors: Hana Jaworek, Vladimira Koudelakova, Jiri Drabek, Jana Vrbkova, Blazena Zborilova, Ivana Oborna, Jana Brezinova, Radim Marek, Karel Huml, Peter Vanek, Marian Hajduch Tags: Regular article Source Type: research

A Head-to-Head Analytical Comparison of Cobas 4800 HPV, PapilloCheck HPV
High-risk human papillomavirus (hrHPV) infection is a cause of cervical cancer development. The addition of hrHPV testing to cervical cancer screening and monitoring of cervical intraepithelial neoplasia treatment improves the efficacy of screening and treatment, respectively. Self-sampling for hrHPV testing seems a promising tool for increasing patient participation in cervical cancer screening. In this project, 1198 cervical swabs obtained by physicians and 176 cervicovaginal swabs obtained by self-sampling (not collected in parallel) were analyzed for the presence of 14 hrHPV genotypes using three commercially available...
Source: Journal of Molecular Diagnostics - August 27, 2018 Category: Pathology Authors: Hana Jaworek, Vladimira Koudelakova, Jiri Drabek, Jana Vrbkova, Blazena Zborilova, Ivana Oborna, Jana Brezinova, Radim Marek, Karel Huml, Peter Vanek, Marian Hajduch Tags: Regular article Source Type: research

Noninvasive Molecular Monitoring in Multiple Myeloma Patients Using Cell-Free Tumor DNA
Novel treatments for multiple myeloma (MM) have increased rates of complete response, raising interest in more accurate methods to evaluate residual disease. Cell-free tumor DNA (cfDNA) analysis may represent a minimally invasive approach complementary to multiparameter flow cytometry (MFC) and molecular methods on bone marrow aspirates. A sequencing approach using the Ion Torrent Personal Genome Machine was applied to identify clonal IGH gene rearrangements in tumor plasma cells (PCs) and in serial plasma samples of 25 patients with MM receiving second-line therapy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 27, 2018 Category: Pathology Authors: Giulia Biancon, Silvia Gimondi, Antonio Vendramin, Cristiana Carniti, Paolo Corradini Tags: Regular article Source Type: research

A head-to-head analytical comparison of cobas ® 4800 HPV, PapilloCheck® HPV – Screening, and LMNX Genotyping Kit HPV GP for detection of human papillomavirus DNA in cervical and cervicovaginal swabs,
High-risk human papillomavirus (hrHPV) infection is a cause of cervical cancer development. The addition of hrHPV testing to cervical cancer screening and monitoring of cervical intraepithelial neoplasia treatment improves the efficacy of screening and treatment, respectively. Self-sampling for hrHPV testing seems a promising tool for increasing patient participation in cervical cancer screening. In this project, 1,198 cervical swabs obtained by physicians and 176 cervicovaginal swabs obtained by self-sampling (not collected in parallel) were analyzed for the presence of 14 hrHPV genotypes using three commercially availabl...
Source: Journal of Molecular Diagnostics - August 27, 2018 Category: Pathology Authors: Hana Jaworek, Vladimira Koudelakova, Jiri Drabek, Jana Vrbkova, Blazena Zborilova, Ivana Oborna, Jana Brezinova, Radim Marek, Karel Huml, Peter Vanek, Marian Hajduch Tags: Regular Article Source Type: research

Non-invasive molecular monitoring in multiple myeloma patients using cell-free tumor DNA: a pilot study
Novel treatments for multiple myeloma (MM) have increased rates of complete response raising interest in more accurate methods to evaluate residual disease. Cell-free tumor DNA (cfDNA) analysis may represent a minimally invasive approach complementary to multiparameter flow cytometry (MFC) and molecular methods on bone marrow aspirates. A sequencing approach using the Ion Torrent Personal Genome Machine was applied to identify clonal immunoglobulin heavy chain (IGH) gene rearrangements in tumor plasma cells (PCs) and in serial plasma samples of 25 MM patients receiving second-line therapy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 27, 2018 Category: Pathology Authors: Giulia Biancon, Silvia Gimondi, Antonio Vendramin, Cristiana Carniti, Paolo Corradini Tags: Regular Article Source Type: research

Diagnostic targeted sequencing panel for hepatocellular carcinoma genomic screening
Commercially available targeted panels miss genomic regions frequently altered in hepatocellular carcinoma (HCC). We sought to design and benchmark a sequencing assay for genomic screening in HCC. We designed an AmpliSeq custom panel targeting all exons of 33 protein-coding and two long non-coding RNA genes frequently mutated in HCC, TERT promoter, and nine genes with frequent copy number alterations. Using this panel, the profiling of DNA from fresh-frozen (n=10, 1495x) and/or formalin-fixed, paraffin-embedded (FFPE) tumors with low-input DNA (n=36, 530x) from 39 HCCs identified at least one somatic mutation in 90% of the...
Source: Journal of Molecular Diagnostics - August 22, 2018 Category: Pathology Authors: Viola Paradiso, Andrea Garofoli, Nadia Tosti, Manuela Lanzafame, Valeria Perrina, Luca Quagliata, Matthias S. Matter, Stefan Wieland, Markus H. Heim, Salvatore Piscuoglio, Charlotte K.Y. Ng, Luigi M. Terracciano Tags: Regular Article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 21, 2018 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 21, 2018 Category: Pathology Source Type: research

Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient-Derived Tumors
We developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay that provides a comprehensive genomic profile of a patient's tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, insertions/deletions, copy number variants, structural variants, and RNA gene fusions was analyzed. New York State's Department of Health next-generation DNA sequencing guidelines were expanded on for establishing performance validation applicable to whole-genome sequencing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2018 Category: Pathology Authors: Kazimierz O. Wrzeszczynski, Vanessa Felice, Avinash Abhyankar, Lukasz Kozon, Heather Geiger, Dina Manaa, Ferrah London, Dino Robinson, Xiaolan Fang, David Lin, Michelle F. Lamendola-Essel, Depinder Khaira, Esra Dikoglu, Anne-Katrin Emde, Nicolas Robine, M Tags: Regular article Source Type: research

OncoKids
The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events ...
Source: Journal of Molecular Diagnostics - August 20, 2018 Category: Pathology Authors: Matthew C. Hiemenz, Dejerianne G. Ostrow, Tracy M. Busse, Jonathan Buckley, Dennis T. Maglinte, Moiz Bootwalla, James Done, Jianling Ji, Gordana Raca, Alex Ryutov, Xinjie Xu, Chao Jie Zhen, Jeffrey M. Conroy, Florette K. Hazard, Joshua L. Deignan, Beverly Tags: Regular article Source Type: research

Clinical Significance of DNA Variants in Chronic Myeloid Neoplasms
To address the clinical relevance of small DNA variants in chronic myeloid neoplasms (CMNs), an Association for Molecular Pathology Working Group comprehensively reviewed published literature, summarized key findings that support clinical utility, and defined critical gene inclusions for high-throughput sequencing testing panels. This review highlights the biological complexity of CMNs [including myelodysplastic syndromes, myeloproliferative neoplasms, entities with overlapping features (myelodysplastic syndromes/myeloproliferative neoplasms), and systemic mastocytosis], the genetic heterogeneity within diagnostic categori...
Source: Journal of Molecular Diagnostics - August 20, 2018 Category: Pathology Authors: Rebecca F. McClure, Mark D. Ewalt, Jennifer Crow, Robyn L. Temple-Smolkin, Mrudula Pullambhatla, Rachel Sargent, Annette S. Kim Tags: Special Article Source Type: research

Clinical Significance of DNA Variants in Chronic Myeloid Neoplasms (CMNs): A Report of the Association for Molecular Pathology
To address the clinical relevance of small DNA variants in chronic myeloid neoplasms (CMNs), an Association for Molecular Pathology (AMP) Working Group comprehensively reviewed published literature, summarized key findings that support clinical utility, and defined critical gene inclusions for high-throughput sequencing testing panels. This review highlights the biological complexity of CMNs (including myelodysplastic syndromes, myeloproliferative neoplasms, entities with overlapping features (myelodysplastic syndromes/myeloproliferative neoplasms), and systemic mastocytosis), the genetic heterogeneity within diagnostic ca...
Source: Journal of Molecular Diagnostics - August 20, 2018 Category: Pathology Authors: Rebecca F. McClure, Mark D. Ewalt, Jennifer Crow, Robyn L. Temple-Smolkin, Mrudula Pullambhatla, Rachel Sargent, Annette S. Kim Tags: Special Article Source Type: research

Analytical Validation of Clinical Whole-Genome and Transcriptome Sequencing of Patient Derived Tumors Clinical Application of Whole-Genome Sequencing for Reporting Targetable Variants in Cancer
We have developed and validated a clinical whole-genome and transcriptome sequencing (WGTS) assay which provides a comprehensive genomic profile of a patient ’s tumor. The ability to fully capture the mappable genome with sufficient sequencing coverage to precisely call DNA somatic single nucleotide variants, Indels, copy number variants, structural variants, and RNA gene fusions, was analyzed. New York State’s Department of Health NGS guidelines wer e expanded on for establishing performance validation applicable to whole-genome sequencing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2018 Category: Pathology Authors: Kazimierz O. Wrzeszczynski, Vanessa Felice, Avinash Abhyankar, Lukasz Kozon, Heather Geiger, Dina Manaa, Ferrah London, Dino Robinson, Xiaolan Fang, David Lin, Michelle F. Lamendola-Essel, Depinder Khaira, Esra Dikoglu, Anne-Katrin Emde, Nicolas Robine, M Tags: Regular article Source Type: research

OncoKidsSM: A Comprehensive Next-Generation Sequencing Panel for Pediatric Malignancies
The OncoKidsSM panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 nanograms) and RNA (20 nanograms) and is compatible with formalin-fixed, paraffin-embedded as well as frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; an...
Source: Journal of Molecular Diagnostics - August 20, 2018 Category: Pathology Authors: Matthew C. Hiemenz, Dejerianne G. Ostrow, Tracy M. Busse, Jonathan Buckley, Dennis T. Maglinte, Moiz Bootwalla, James Done, Jianling Ji, Gordana Raca, Alex Ryutov, Xinjie Xu, Chao Jie Zhen, Jeffrey M. Conroy, Florette K. Hazard, Joshua L. Deignan, Beverly Tags: Regular Article Source Type: research

Validation of a Long-Read PCR Assay for Sensitive Detection and Sizing of C9orf72 Hexanucleotide Repeat Expansions
A hexanucleotide GGGGCC repeat expansion in C9orf72 is the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Accurate determination and quantitation of the repeat length is critical in both clinical and research settings. However, due to the complexity of the C9orf72 expansion with high GC content, large size of repeats, and high rate of insertion/deletions (indels) and sequence variations in the flanking regions, molecular genetic analysis of the locus is challenging. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 20, 2018 Category: Pathology Authors: EunRan Suh, Kaitlyn Grando, Vivianna M. Van Deerlin Tags: Regular Article Source Type: research

Molecular Analysis of Gene Fusions in Bone and Soft Tissue Tumors by Anchored Multiplex PCR –Based Targeted Next-Generation Sequencing
In this study, the applicability of a novel technique termed anchored multiplex PCR (AMP) for next-generation sequencing (NGS), using the Archer FusionPlex Sarcoma kit, aimed at 26 genes, was evaluated and compared with FISH and reverse transcriptase-PCR. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 19, 2018 Category: Pathology Authors: Suk Wai Lam, Anne-Marie Cleton-Jansen, Arjen H.G. Cleven, Dina Ruano, Tom van Wezel, Karoly Szuhai, Judith V.M.G. Bov ée Tags: Regular article Source Type: research

High-Throughput Copy Number Profiling by Digital Multiplex Ligation-Dependent Probe Amplification in Multiple Myeloma
Multiple myeloma (MM) is a genetically heterogeneous disease with diverse clinical outcome. Copy number alterations (CNAs) including whole chromosome and subchromosomal gains and losses are common contributors of the pathogenesis and have demonstrated prognostic impact in MM. We tested the performance of digital multiplex ligation-dependent probe amplification (digitalMLPA), a novel technique combining MLPA and next-generation sequencing, to detect disease-related CNAs. Copy number status at 371 genomic loci were simultaneously analyzed in 56 diagnostic bone marrow samples which were also examined by conventional MLPA and ...
Source: Journal of Molecular Diagnostics - August 7, 2018 Category: Pathology Authors: Szabolcs Kosztolanyi, Richard Kiss, Lilit Atanesyan, Ambrus Gango, Karel de Groot, Maryvonne Steenkamer, Pal Jakso, Andras Matolcsy, Bela Kajtar, Laszlo Pajor, Karoly Szuhai, Suvi Savola, Csaba Bodor, Donat Alpar Tags: Regular Article Source Type: research

Curating clinically relevant transcripts for the interpretation of sequence variants
Variant interpretation depends on accurate annotations using biologically relevant transcripts. We have developed a systematic strategy for designating primary transcripts, and applied it to 109 hearing loss –associated genes that were divided into three categories. Category 1 genes (n=38) had a single transcript, Category 2 genes (n=32) had multiple transcripts, but a single transcript was sufficient to represent all exons, and Category 3 genes (n=38) had multiple transcripts with unique exons. Trans cripts were curated with respect to gene expression reported in the literature and the Genotype-Tissue Expression Pro...
Source: Journal of Molecular Diagnostics - August 7, 2018 Category: Pathology Authors: Marina T. DiStefano, Sarah E. Hemphill, Brandon J. Cushman, Mark J. Bowser, Elizabeth Hynes, Andrew R. Grant, Rebecca K. Siegert, Andrea M. Oza, Michael A. Gonzalez, Sami S. Amr, Heidi L. Rehm, Ahmad N. Abou Tayoun Tags: Regular Article Source Type: research