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 plasma and dried blood spot (DBS) samples. Paired plasma and venous DBS samples were prepared from remnant diagnostic samples. Plasma HCV RNA was quantified by AmpliPrep/COBAS Taqman (Roche) and HCVcAg measured by ARCHITECT HCV Ag (Abbott Diagnostics). Sensitivity and specificity for HCVcAg (>3 fmol/L) at two HCV RNA thresholds ( ≥15 IU/mL and ≥3,000 IU/mL) were calculated. (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

Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials
The National Institute of Standards and Technology has developed reference materials for five human genomes. DNA aliquots are available for purchase and the data, analyses, and high-confidence small variant and homozygous reference calls are freely available on the web. These reference materials are useful for evaluating whole-genome sequencing methods and can also be used to benchmark targeted sequencing panels, which are commonly used in clinical settings. This paper describes how to use the Genome in a Bottle samples to obtain performance metrics on any germline-targeted sequencing panel of interest, as well as the limi...
Source: Journal of Molecular Diagnostics - June 26, 2018 Category: Pathology Authors: Megan H. Cleveland, Justin M. Zook, Marc Salit, Peter M. Vallone Tags: Regular Article Source Type: research

Multi-center 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 very 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 (HLA) Loci: A GeT-RM Collaborative Project
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 due to the homology of HLA genes and pseudogenes and the extensive polymorphism in the population. The Centers for Disease Control and Prevention (CDC) 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

Assessing the accuracy of variant detection in cost-effective gene panel testing by next-generation sequencing
There is significant debate within the diagnostics community regarding the accuracy of variant identification by next-generation sequencing and the necessity of confirmatory testing of detected variants. Since the quality threshold to discriminate false-positives depends on the nature of the workflow, no regulatory standard regarding this matter has yet been published. The goal of this study was to empirically determine the threshold to perform additional Sanger sequencing and to reduce the experimental cost to a practical level. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 25, 2018 Category: Pathology Authors: Ryoji Fujiki, Makoto Ikeda, Akiko Yoshida, Maeda Akiko, Yue Yao, Motio Nishimura, Kazuyuki Matsushita, Tomohiko Ichikawa, Tomoaki Tanaka, Hiroko Morisaki, Takayuki Morisaki, Osamu Ohara Tags: Regular Article Source Type: research

Pre-Analytical Handling Conditions and Small RNA Recovery from Urine for miRNA Profiling
We present a comparison of small RNA recovery and stability in urine under alternate pre-analytical handling conditions and extend recommendations on what conditions optimize yield of miRNA from cell-free urine and urine extracellular vesicles (EVs). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: David A. Armstrong, John A. Dessaint, Carol S. Ringelberg, Haley F. Hazlett, Louisa Howard, Moemen A.K. Abdalla, Roxanna L. Barnaby, Bruce A. Stanton, Mark A. Cervinski, Alix Ashare Tags: Technical Advance Source Type: research

A Monochrome Multiplex Real-Time Quantitative PCR Assay for the Measurement of Mitochondrial DNA Content
Mitochondrial DNA copies per cell (mtDNA content) can fluctuate with cellular aging, oxidative stress, and mitochondrial dysfunction, and has been investigated in cancer, diabetes, HIV, and metabolic disease. mtDNA content testing in both clinical and basic settings is expected to increase as research uncovers its biological relevance. Herein, we present a novel mtDNA content assay developed on monochrome multiplex real-time quantitative PCR (MMqPCR) principles. This assay offers a greater than twofold improvement on time effectiveness and cost-effectiveness over conventional (monoplex) qPCR, as well as improved reproducib...
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: Anthony Y.Y. Hsieh, Matthew Budd, David Deng, Izabella Gadawska, H élène C.F. Côté Tags: Regular article Source Type: research

A Monochrome Multiplex qPCR Assay for the Measurement of Mitochondrial DNA Content
Mitochondrial DNA copies per cell (mtDNA content) can fluctuate with cellular aging, oxidative stress, and mitochondrial dysfunction, and has been investigated in cancer, diabetes, Human immunodeficiency virus, and metabolic disease. mtDNA content testing in both clinical and basic settings is expected to rise as research uncovers its biological relevance. Here, we present a novel mtDNA content assay developed on monochrome, multiplex qPCR (MMqPCR) principles. This assay offers a>2-fold improvement on time- and cost-effectiveness over conventional (monoplex) qPCR, as well as improved reproducibility given the reduced ef...
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: Anthony Y.Y. Hsieh, Matthew Budd, David Deng, Izabella Gadawska, H élène C.F. Côté Tags: Regular Article Source Type: research

Analysis of mutation and loss of heterozygosity by whole-exome sequencing yields insights into pseudomyxoma peritonei
Pseudomyxoma peritonei is a clinical syndrome characterized by gross mucinous ascites originating from a disseminated intraperitoneal neoplasm. Although typically confined to the abdomen, mortality is high if untreated. Biomarkers, including genetic mutation profiles, may aid treatment selection and decision making. We applied whole-exome sequencing to five patients diagnosed with low grade appendiceal mucinous neoplasms, utilizing paired tumor and germline samples identify biomarkers. Multiple bioinformatic approaches were applied to these data to assess both somatic mutation profiles and loss of heterozygosity events. (S...
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: Reuben J. Pengelly, Babatunde Rowaiye, Karen Pickard, Brendan Moran, Sanjeev Dayal, William Tapper, Alex Mirnezami, Tom Cecil, Faheez Mohamed, Norman Carr, Sarah Ennis Tags: Regular Article Source Type: research

Analytical validation of a hybrid capture –based next-generation sequencing clinical assay for genomic profiling of cell-free circulating tumor DNA
Genomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a non-invasive method for the detection of genomic biomarkers to guide clinical decision-making for cancer patients. We developed a hybrid capture –based next-generation sequencing assay for genomic profiling of circulating tumor DNA from blood (FoundationACT®). High sequencing coverage and molecular barcode–based error detection enabled accurate detection of genomic alterations, including base substitutions, short insertions/deletions, a nd genomic rearrangements at low allele frequencies (AF), and copy numbe...
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: Travis A. Clark, Jon H. Chung, Mark Kennedy, Jason D. Hughes, Niru Chennagiri, Daniel S. Lieber, Bernard Fendler, Lauren Young, Mandy Zhao, Michael Coyne, Virginia Breese, Geneva Young, Amy Donahue, Dean Pavlick, Alyssa Tsiros, Timothy Brennan, Shan Zhong Tags: Regular Article Source Type: research

Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing –Based Assays for Cancer
Human Genome Variation Society (HGVS) nomenclature is a de facto clinical standard for reporting DNA sequence variants. With increasing use of high-throughput sequencing, manual generation of HGVS nomenclatures for all variants is impractical and error-prone. It is therefore beneficial to include one or more HGVS generator tools in next-generation sequencing (NGS) bioinformatics pipelines to enable automated, consistent, and accurate generation of HGVS nomenclature after appropriate validation. We implemented an HGVS nomenclature tool, hgvs package, by integrating it into our custom-developed NGS variant management and rep...
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: Keith M. Callenberg, Lucas Santana-Santos, Liang Chen, Wayne L. Ernst, Michelle Barbi De Moura, Yuri E. Nikiforov, Marina N. Nikiforova, Somak Roy Tags: Regular article Source Type: research

Pre-Analytical Handling Conditions and Small RNA Recovery from Urine for microRNA Profiling
There are currently no standardized protocols for pre-analytical handling of urine to best preserve small RNA for microRNA profiling studies. MicroRNA is an attractive candidate as a potential biomarker due to high level of stability in body fluids and its ability to be quantified on multiple high-throughput platforms. Here, we present a comparison of small RNA recovery/stability in urine under alternate pre-analytical handling conditions and extend recommendations on what conditions optimize yield of microRNA from cell-free urine and urine extracellular vesicles (EVs). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: David A. Armstrong, John A. Dessaint, Carol S. Ringelberg, Haley F. Hazlett, Louisa Howard, Moemen A.K. Abdalla, Roxanna L. Barnaby, Bruce A. Stanton, Mark A. Cervinski, Alix Ashare Tags: Technical Advance Source Type: research

The development and validation of clinical exome-based panels using ExomeSlicer
Exome-based panels are becoming the preferred diagnostic strategy in clinical laboratories. This approach enables dynamic gene content update and, if needed, cost-effective reflex to whole exome sequencing. There are currently no guidelines or appropriate resources to support the clinical implementation of exome-based panels. Here, we highlight principles and important considerations for the clinical development and validation of exome-based panels. In addition, we developed ExomeSlicer, a novel, web-based resource, which uses empirical exon-level next-generation sequencing quality metrics to predict and visualize technica...
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: Rojeen Niazi, Michael A. Gonzalez, Jorune Balciuniene, Perry Evans, Mahdi Sarmady, Ahmad N. Abou Tayoun Tags: Regular Article Source Type: research

Validation and Implementation of BRCA1/2 Variant Screening in Ovarian Tumor Tissue
BRCA1/2 variant analysis in tumor tissue could streamline the referral of patients with epithelial ovarian, fallopian tube, or primary peritoneal cancer to genetic counselors and select patients who benefit most from targeted treatment. We investigated the sensitivity of BRCA1/2 variant analysis in formalin-fixed, paraffin-embedded tumor tissue using a combination of next-generation sequencing and copy number variant multiplex ligation-dependent probe amplification. After optimization using a training cohort of known BRCA1/2 mutation carriers, validation was performed in a prospective cohort (Clinical implementation Of BRC...
Source: Journal of Molecular Diagnostics - June 21, 2018 Category: Pathology Authors: Marthe M. de Jonge, Dina Ruano, Ronald van Eijk, Nienke van der Stoep, Maartje Nielsen, Juul T. Wijnen, Natalja T. ter Haar, Astrid Baalbergen, Monique E.M.M. Bos, Marjolein J. Kagie, Maaike P.G. Vreeswijk, Katja N. Gaarenstroom, Judith R. Kroep, Vincent Tags: Regular article Source Type: research

Development and Verification of an RNA Sequencing (RNA-Seq) Assay for the Detection of Gene Fusions in Tumors
We assessed the performance characteristics of an RNA sequencing (RNA-Seq) assay designed to detect gene fusions in 571 genes to help manage patients with cancer. Polyadenylated RNA was converted to cDNA, which was then used to prepare next-generation sequencing libraries that were sequenced on an Illumina HiSeq 2500 instrument and analyzed with an in-house developed bioinformatic pipeline. The assay identified 38 of 41 gene fusions detected by another method, such as fluorescence in situ hybridization or RT-PCR, for a sensitivity of 93%. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - June 18, 2018 Category: Pathology Authors: Jennifer L. Winters, Jaime I. Davila, Amber M. McDonald, Asha A. Nair, Numrah Fadra, Rebecca N. Wehrs, Brittany C. Thomas, Jessica R. Balcom, Long Jin, Xianglin Wu, Jesse S. Voss, Eric W. Klee, Gavin R. Oliver, Rondell P. Graham, Jadee L. Neff, Kandelaria Tags: Regular article Source Type: research

Efficient Detection of Copy Number Mutations in PMS2 Exons with a Close Homolog
Detection of 3 ′ PMS2 copy-number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify d eletions and duplications in PMS2 exons 9 to 15. The approach captures sequences using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ranges. (Source: Jou...
Source: Journal of Molecular Diagnostics - May 21, 2018 Category: Pathology Authors: Daniel S. Herman, Christina Smith, Chang Liu, Cecily P. Vaughn, Selvi Palaniappan, Colin C. Pritchard, Brian H. Shirts Tags: Regular article Source Type: research

Efficient Detection of Copy Number Mutations in PMS2 Exons with Close Homologs
Detection of 3 ′ PMS2 copy number mutations that cause Lynch syndrome is difficult because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify d eletions and duplications in PMS2 exons 9 to 15. The approach captures sequence reads using PMS2 targets, maps sequences randomly among regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference range s. (Sourc...
Source: Journal of Molecular Diagnostics - May 21, 2018 Category: Pathology Authors: Daniel S. Herman, Christina Smith, Chang Liu, Cecily P. Vaughn, Selvi Palaniappan, Colin C. Pritchard, Brian H. Shirts Tags: Regular article Source Type: research

A reliable targeted next-generation sequencing strategy for diagnosis of myopathies and muscular dystrophies, especially for the giant titin and nebulin genes
Myopathies and muscular dystrophies (M-MDs) are genetically heterogeneous diseases, with more than 100 identified genes, including the giant and complex titin (TTN) and nebulin (NEB) genes. Next-generation sequencing technology revolutionized M-MD diagnosis and revealed high frequency of TTN and NEB variants. We developed a next-generation sequencing diagnostic strategy targeted on the coding sequences of 135 M-MD genes. Comparison of two targeted capture technologies (SeqCap EZ Choice library capture kit (Roche-Nimblegen) and Nextera Rapid Capture Custom Enrichment kit (Illumina)) and of two whole exome sequencing kits (S...
Source: Journal of Molecular Diagnostics - May 21, 2018 Category: Pathology Authors: Reda Zenagui, Delphine Lacourt, Henri Pegeot, Kevin Yauy, Raul Juntas Morales, Corine Theze, Fran çois Rivier, Claude Cances, Guilhem Sole, Dimitri Renard, Ulrike Walther-Louvier, Xavier Ferrer-Monasterio, Caroline Espil, Marie-Christine Arné-Bes, Pasca Tags: Regular Article Source Type: research

Efficient Detection of Copy Number Mutations in PMS2 Exons with Close Homologs: Detection of copy number variants in 3 ’ PMS2 exons
Detection of 3 ’ PMS2 copy number mutations that cause Lynch syndrome is difficult, because of highly homologous pseudogenes. To improve the accuracy and efficiency of clinical screening for these mutations, we developed a new method to analyze standard capture-based, next-generation sequencing data to identify deletions and duplications in PMS2 exons 9 to 15. The approach captures sequence reads using PMS2 targets, maps sequences randomly amongst regions with equal mapping quality, counts reads aligned to homologous exons and introns, and flags read count ratios outside of empirically derived reference ra nges. (Sou...
Source: Journal of Molecular Diagnostics - May 21, 2018 Category: Pathology Authors: Daniel S. Herman, Christina Smith, Chang Liu, Cecily P. Vaughn, Selvi Palaniappan, Colin C. Pritchard, Brian H. Shirts Tags: Regular Article Source Type: research

Validity of targeted next-generation sequencing in routine care for identifying clinically relevant molecular profiles in non –small-cell lung cancer: results of a 2-year experience on 1,343 samples
Theranostic assays are based on single gene testing but the ability of next-generation sequencing (NGS) to interrogate numerous genetic alterations will progressively replace single gene assays. Although NGS was evaluated to screen for theranostic mutations, its usefulness in clinical practice on large series of samples remains to be demonstrated. NGS performance was assessed following guidelines. TaqMan probes and NGS were compared for their ability to detect EGFR and KRAS mutations and NGS mutation profiles were analyzed on a large series of NSCLC (n=1,343). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - May 19, 2018 Category: Pathology Authors: Antoine Legras, Marc Barritault, Anne Tallet, Elizabeth Fabre, Alice Guyard, Bastien Rance, William Digan, Nicolas Pecuchet, Etienne Giroux-Leprieur, Catherine Julie, St éphane Jouveshomme, Véronique Duchatelle, Véronique Giraudet, Laure Gibault, Alain Tags: Regular Article Source Type: research

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

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

Detection of EGFR Variants in Plasma
This study evaluated the interlaboratory performance and reproducibility of the cobas EGFR Mutation Test v2 to detect EGFR variants in plasma. Fourteen laboratories received two identic al panels of 27 single-blinded plasma samples. Samples were wild-type or spiked with plasmid DNA to contain seven common EGFR variants at six predefined concentrations from 50 to 5000 copies per mL. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 25, 2018 Category: Pathology Authors: Cleo Keppens, John F. Palma, Partha M. Das, Sidney Scudder, Wei Wen, Nicola Normanno, J Han Van Krieken, Alessandra Sacco, Francesca Fenizia, David Gonzalez de Castro, Selma H önigschnabl, Izidor Kern, Fernando Lopez-Rios, Maria D. Lozano, Antonio Marche Tags: Regular article Source Type: research

System for Informatics in the Molecular Pathology Laboratory
Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet  all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 23, 2018 Category: Pathology Authors: Wenjun Kang, Sabah Kadri, Rutika Puranik, Michelle N. Wurst, Sushant A. Patil, Ibro Mujacic, Sonia Benhamed, Nifang Niu, Chao Jie Zhen, Bekim Ameti, Bradley C. Long, Filipo Galbo, David Montes, Crystal Iracheta, Venessa L. Gamboa, Daisy Lopez, Michael You Tags: Regular article Source Type: research

Suppression of Wild-Type Amplification by Selectivity Enhancing Agents in PCR Assays That Utilize SuperSelective Primers for the Detection of Rare Somatic Mutations
In PCR assays designed to detect rare somatic mutations, SuperSelective primers, by virtue of their short 3 ′-foot sequences, selectively initiate synthesis on mutant DNA target fragments, while suppressing the synthesis of related wild-type fragments, and the resulting threshold cycle reflects the quantity of mutant targets present. However, when there are ≤10 mutant target fragments in a sample, the threshold cycle that is observed occurs so late that it can be confused with the threshold cycle that arises from samples that contain only abundant related wild-type fragments. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 23, 2018 Category: Pathology Authors: Diana Y. Vargas, Salvatore A.E. Marras, Sanjay Tyagi, Fred R. Kramer Tags: Technical advance Source Type: research

Suppression of Wild-Type Amplification by Selectivity-Enhancing Agents in PCR Assays That Utilize SuperSelective Primers for the Detection of Rare Somatic Mutations
In PCR assays designed to detect rare somatic mutations, SuperSelective primers, by virtue of their short 3 ′-foot sequences, selectively initiate synthesis on mutant DNA target fragments, while suppressing the synthesis of related wild-type fragments, and the resulting threshold cycle reflects the quantity of mutant targets present. However, when there are ≤10 mutant target fragments in a sample, the threshold cycle that is observed occurs so late that it can be confused with the threshold cycle that arises from samples that contained only abundant related wild-type fragments. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 23, 2018 Category: Pathology Authors: Diana Y. Vargas, Salvatore A.E. Marras, Sanjay Tyagi, Fred R. Kramer Tags: Technical advance Source Type: research

System for Informatics in the Molecular Pathology Laboratory (SIMPL)
Next-generation sequencing (NGS) diagnostic assays are increasingly becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems (LIS) and/or Laboratory Information Management Systems (LIMS) are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost prohibitive. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 23, 2018 Category: Pathology Authors: Wenjun Kang, Sabah Kadri, Rutika Puranik, Michelle N. Wurst, Sushant A. Patil, Ibro Mujacic, Sonia Benhamed, Nifang Niu, Chao Jie Zhen, Bekim Ameti, Bradley C. Long, Filipo Galbo, David Montes, Crystal Iracheta, Venessa L. Gamboa, Daisy Lopez, Michael You Tags: Regular article Source Type: research

Suppression of Wild-type Amplification by Selectivity Enhancing Agents in PCR Assays that Utilize SuperSelective Primers for the Detection of Rare Somatic Mutations
In PCR assays designed to detect rare somatic mutations, SuperSelective primers, by virtue of their short 3 ′-foot sequences, selectively initiate synthesis on mutant DNA target fragments, while suppressing the synthesis of related wild-type fragments, and the resulting threshold cycle reflects the quantity of mutant targets present. However, when there are 10 or fewer mutant target fragments in a sampl e, the threshold cycle that is observed occurs so late that it can be confused with the threshold cycle that arises from samples containing only abundant related wild-type fragments. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 23, 2018 Category: Pathology Authors: Diana Y. Vargas, Salvatore A.E. Marras, Sanjay Tyagi, Fred R. Kramer Tags: Technical advance Source Type: research

System for Informatics in the Molecular Pathology Laboratory (SIMPL)
Next-generation sequencing (NGS) diagnostic assays are increasingly becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems (LIS) and/or Laboratory Information Management Systems (LIMS) are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost prohibitive. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - April 23, 2018 Category: Pathology Authors: Wenjun Kang, Sabah Kadri, Rutika Puranik, Michelle N. Wurst, Sushant A. Patil, Ibro Mujacic, Sonia Benhamed, Nifang Niu, Chao Jie Zhen, Bekim Ameti, Bradley C. Long, Filipo Galbo, David Montes, Crystal Iracheta, Venessa L. Gamboa, Daisy Lopez, Michael You Tags: Regular article Source Type: research

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

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

Molecular Minimal Residual Disease Monitoring in Acute Myeloid Leukemia
The ability to sensitively monitor minimal residual disease (MRD) has played a key role in improving the management and outcomes for a number of leukemias, particularly acute promyelocytic leukemia and childhood acute lymphoblastic leukemia. By contrast, MRD monitoring in acute myeloid leukemia (AML) has been limited by variable assay methodologies and a relative paucity of patient-specific MRD markers. Inter- and intratumor genetic heterogeneity poses significant challenges for the identification of molecular markers suitable for MRD monitoring in AML, particularly for those cases without structural chromosomal rearrangem...
Source: Journal of Molecular Diagnostics - April 21, 2018 Category: Pathology Authors: Adrian Selim, Andrew S. Moore Tags: Review Source Type: research

Molecular Minimal Residual Disease Monitoring in Acute Myeloid Leukemia: Challenges and Future Directions
The ability to sensitively monitor minimal residual disease (MRD) has played a key role in improving the management and outcomes for a number of leukemias, particularly acute promyelocytic leukemia and childhood acute lymphoblastic leukemia. In contrast, MRD monitoring in acute myeloid leukemia (AML) has been limited by variable assay methodologies and a relative paucity of patient-specific MRD markers. Inter and intratumor genetic heterogeneity pose significant challenges for the identification of molecular markers suitable for MRD monitoring in AML, particularly for those cases without structural chromosomal rearrangemen...
Source: Journal of Molecular Diagnostics - April 21, 2018 Category: Pathology Authors: Adrian Selim, Andrew S. Moore Tags: Review Source Type: research

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

Molecular Minimal Residual Disease Monitoring in Acute Myeloid Leukemia: Challenges and Future Directions
The ability to sensitively monitor minimal residual disease (MRD) has played a key role in improving the management and outcomes for a number of leukemias, particularly acute promyelocytic leukemia and childhood acute lymphoblastic leukemia. In contrast, MRD monitoring in acute myeloid leukemia (AML) has been limited by variable assay methodologies and a relative paucity of patient-specific MRD markers. Inter and intratumor genetic heterogeneity pose significant challenges for the identification of molecular markers suitable for MRD monitoring in AML, particularly for those cases without structural chromosomal rearrangemen...
Source: Journal of Molecular Diagnostics - April 21, 2018 Category: Pathology Authors: Adrian Selim, Andrew S. Moore Tags: Review Source Type: research

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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