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

Describing the Reportable Range Is Important for Reliable Treatment Decisions
Because interpretation of next-generation sequencing (NGS) data remains challenging, optimization of the NGS process is needed to obtain correct sequencing results. Therefore, extensive validation and continuous monitoring of the quality is essential. NGS performance was compared with traditional detection methods and technical quality of nine NGS technologies was assessed. First, nine formalin-fixed, paraffin-embedded patient samples were analyzed by 114 laboratories by using different detection methods. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 25, 2018 Category: Pathology Authors: V éronique Tack, Lien Spans, Ed Schuuring, Cleo Keppens, Karen Zwaenepoel, Patrick Pauwels, Jeroen Van Houdt, Elisabeth M.C. Dequeker Tags: Regular article Source Type: research

Next-Generation Sequencing Using S1 Nuclease for Poor-Quality Formalin-Fixed, Paraffin-Embedded Tumor Specimens
Next-generation sequencing (NGS) testing of formalin-fixed, paraffin-embedded (FFPE) tissues is widely used in clinical diagnosis. However, the failure of high-quality DNA library construction, a critical step for NGS, often limits NGS application for FFPE tissues, particularly for old FFPE tissues. tour aim was to develop a high-quality DNA library construction method optimized for NGS of FFPE specimens. DNA library construction was developed for FFPE specimens using S1 nuclease and compared with the Covaris method —the widely accepted DNA library construction protocol. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 25, 2018 Category: Pathology Authors: Sung-Min Chun, Chang Ohk Sung, Hyejoon Jeon, Tae-Im Kim, Ji-Young Lee, Whan Park, Yujin Kim, Deokhoon Kim, Se Jin Jang Tags: Regular Article Source Type: research

Describing the Reportable Range Is Important for Reliable Treatment Decisions: A Multi-Laboratory Study for Molecular Tumor Profiling Using Next-Generation Sequencing
As interpretation of next-generation sequencing (NGS) data remains challenging, optimization of the NGS process is needed to obtain correct sequencing results. Therefore, extensive validation and continuous monitoring of the quality is essential. NGS performance was compared to traditional detection methods and technical quality of nine NGS technologies was assessed. First, nine formalin-fixed, paraffin-embedded patient samples were analyzed by 114 laboratories using different detection methods. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 25, 2018 Category: Pathology Authors: V éronique Tack, Lien Spans, Ed Schuuring, Cleo Keppens, Karen Zwaenepoel, Patrick Pauwels, Jeroen Van Houdt, Elisabeth M.C. Dequeker Tags: Regular article Source Type: research

Benchmarking of Amplicon-Based Next-Generation Sequencing Panels Combined with Bioinformatics Solutions for Germline BRCA1 and BRCA2 Alteration Detection
In this study, we evaluated the combinations of several BRCA testing assays and bioinformatics solutions for the identification of single nucleotide variants, insertion/deletion variants (indels), and copy number variations (CNVs). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 25, 2018 Category: Pathology Authors: Julie A. Vendrell, Paul Vilquin, Marion Larrieux, Charles Van Goethem, J érôme Solassol Tags: Regular article Source Type: research

Multiple Ways to Detect IDH2 Mutations in Angioimmunoblastic T-Cell Lymphoma from Immunohistochemistry to Next-Generation Sequencing
Angioimmunoblastic T-cell lymphoma (AITL) is a peripheral T-cell lymphoma associated with chemoresistance and a poor prognosis. Various nonsynonymous mutations in the R172 residue of IDH2 are present in 20% to 30% of AITL patients. In addition to their diagnostic value, these mutations are potentially targetable, especially by IDH2 inhibitor, and therefore their identification in a routine setting is clinically relevant. However, in AITL, the neoplastic cells may be scarce, making the identification of molecular anomalies difficult. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 5, 2018 Category: Pathology Authors: Aur élie Dupuy, François Lemonnier, Virginie Fataccioli, Nadine Martin-Garcia, Cyrielle Robe, Romain Pelletier, Elsa Poullot, Anissa Moktefi, Karima Mokhtari, Marie C. Rousselet, Alexandra Traverse-Glehen, Richard Delarue, Olivier Tournilhac, Marie H. D Tags: Regular article Source Type: research

Multiple ways to detect IDH2 mutations in angioimmunoblastic T-cell lymphoma: from immunohistochemistry to next-generation sequencing
Angioimmunoblastic T-cell lymphoma (AITL) is a peripheral T-cell lymphoma associated with chemoresistance and a poor prognosis. Various non-synonymous mutations in the R172 residue of IDH2 are present in 20% to 30% of AITL patients. In addition to their diagnostic value, these mutations are potentially targetable, especially by IDH2 inhibitor, and therefore their identification in a routine setting is clinically relevant. However, in AITL, the neoplastic cells may be scarce making the identification of molecular anomalies difficult. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 5, 2018 Category: Pathology Authors: Aur élie Dupuy, François Lemonnier, Virginie Fataccioli, Nadine Martin-Garcia, Cyrielle Robe, Romain Pelletier, Elsa Poullot, Anissa Moktefi, Karima Mokhtari, Marie Christine Rousselet, Alexandra Traverse-Glehen, Richard Delarue, Olivier Tournilhac, Mar Tags: Regular Article Source Type: research

Comprehensive Validation of Cytology Specimens for Next-Generation Sequencing and Clinical Practice Experience
Biopsy specimens are subjected to an expanding portfolio of assays that regularly include mutation profiling via next-generation sequencing (NGS). Specimens derived from fine needle aspiration, a common biopsy technique, are subjected to a variety of cytopreparatory methods as compared to surgical biopsies that are almost uniformly processed as formalin-fixed, paraffin-embedded tissue. Therefore, fine needle aspiration –derived specimens most commonly accepted for molecular analysis are cell blocks (CB) as they are processed most similarly to surgical biopsy tissue. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 5, 2018 Category: Pathology Authors: Agnes Balla, Ken J. Hampel, Mukesh K. Sharma, Catherine E. Cottrell, Nikoletta Sidiropoulos Tags: Regular Article Source Type: research

Laboratory Information Systems and Instrument Software Lack Basic Functionality for  Molecular Laboratories
This study determined functionality gaps of LISs in molecular laboratories and the associated impact to workflow, efficiency, and security by collecting anonymous survey data from clinical laboratory professionals. A 34-question survey (30 required  + 4 optional) was compiled using an online survey tool. Participants were recruited through several professional molecular society listservs and given 4 weeks to complete the survey. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 2, 2018 Category: Pathology Authors: Charles Myers, Matthew Swadley, Alexis B. Carter Tags: Regular article Source Type: research

Laboratory Information Systems and Instrument Software Lack Basic Functionality for Molecular Laboratories
This study determined functionality gaps of LISs in molecular laboratories and the associated impact to workflow, efficiency, and security by collecting anonymous survey data from clinical laboratory professionals. A 34-question survey (30 required + four optional) was compiled using an online survey tool. Participants were recruited through several professional molecular society listservs and given four weeks to complete the survey. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - July 2, 2018 Category: Pathology Authors: Charles Myers, Matthew Swadley, Alexis B. Carter Tags: Regular article Source Type: research

Development of a Fluorescence in Situ Hybridization Probe for Detecting IKZF1 Deletion Mutations in Patients with Acute Lymphoblastic Leukemia
Intragenic deletion of IKZF1 is a recurrent genomic alteration in acute lymphoblastic leukemia. The deletions are mediated by illegitimate variable(diversity)joining recombination via cryptic recombination signal sequences (RSSs). We developed a fluorescence in situ hybridization (FISH) probe set that can detect any type of IKZF1 deletion, including the commonly deleted exon 4 to 7 region. The probe set consists of a designed probe for the commonly deleted region (Cy3; red) and a bacterial artificial chromosomes clone probe for detecting the 3 ′ flanking region (Spectrum Green). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 26, 2018 Category: Pathology Authors: Junichi Hashiguchi, Masahiro Onozawa, Satoshi Oguri, Shinichi Fujisawa, Masahisa Tsuji, Kohei Okada, Masao Nakagawa, Daigo Hashimoto, Kaoru Kahata, Takeshi Kondo, Chikara Shimizu, Takanori Teshima Tags: Regular article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 26, 2018 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 26, 2018 Category: Pathology Source Type: research

Multicenter Evaluation of the Idylla NRAS-BRAF Mutation Test in Metastatic Colorectal Cancer
Treatment of colorectal cancer (CRC) with monoclonal antibodies against epidermal growth factor receptor requires the assessment of the mutational status of exons 2, 3, and 4 of the NRAS and KRAS oncogenes. Moreover, the mutational status of exon 15 of the BRAF oncogene is a marker of poor prognosis in CRC. The Idylla NRAS-BRAF Mutation Test is a reliable, simple ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 26, 2018 Category: Pathology Authors: Iv án Prieto-Potin, Clara Montagut, Beatriz Bellosillo, Matthew Evans, Matthew Smith, Linea Melchior, Werner Reiltin, Michael Bennett, Veronica Pennati, Francesca Castiglione, Karl-Friedrich Bürrig, Ulrike Cooper, Barbara Dockhorn-Dworniczak, Christiana Tags: Regular article Source Type: research

Characterization of 108 Genomic DNA Reference Materials for 11 Human Leukocyte Antigen Loci
The highly polymorphic human leukocyte antigen (HLA) genes, located in the human major histocompatibility complex, encode the class I and II antigen-presenting molecules. which are centrally involved in the immune response. HLA typing is used for several clinical applications, such as transplantation, pharmacogenetics, and diagnosis of autoimmune disease. HLA typing is highly complex because of the homology of HLA genes and pseudogenes and the extensive polymorphism in the population. The Centers for Disease Control and Prevention established the Genetic Testing Reference Materials Coordination Program (GeT-RM) in partners...
Source: Journal of Molecular Diagnostics - June 26, 2018 Category: Pathology Authors: Maria P. Bettinotti, Deborah Ferriola, Jamie L. Duke, Timothy L. Mosbruger, Nikolaos Tairis, Lawrence Jennings, Lisa V. Kalman, Dimitri Monos Tags: Regular article Source Type: research

Evaluation of a Hepatitis C Virus Core Antigen Assay in Plasma and Dried Blood Spot Samples
This study evaluated the analytical performance of HCV core antigen (HCVcAg) detection in samples of plasma and dried venous blood spots (DBSs). Paired plasma and DBS samples were prepared from remnant diagnostic samples. Plasma HCV RNA was quantified and measured. Sensitivity and specificity for HCVcAg (>3 fmol/L) at two HCV RNA thresholds ( ≥15 and ≥3000 IU/mL) were calculated. Of 120 paired samples tested, 25 had nonquantifiable HCV RNA and 95 had quantifiable HCV RNA. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 26, 2018 Category: Pathology Authors: Fran çois M.J. Lamoury, Behzad Hajarizadeh, Angelica Soker, Danica Martinez, Camelia Quek, Philip Cunningham, Beth Catlett, Gavin Cloherty, Pip Marks, Janaki Amin, Jason Grebely, Gregory J. Dore, Tanya L. Applegate Tags: Regular article Source Type: research