A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards: From Sequencer to Electronic Health Record
Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. Although text documents are useful for human readability and initial use, they are not conducive for data retrieval and reuse. As a result, clinicians often struggle to find historical gene sequence results on a series of oncology patients within the EHR that might influence the care of the current patient. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 20, 2019 Category: Pathology Authors: Walter S. Campbell, Alexis B. Carter, Allison M. Cushman-Vokoun, Timothy C. Greiner, Rajesh C. Dash, Mark Routbort, Monica E. de Baca, James R. Campbell Tags: Regular article Source Type: research

Personalized chimerism test: selection of short tandem repeat or quantitative PCR depending on patient ’s chimerism status
Chimerism testing is used to monitor engraftment and risk of relapse after allogeneic hematopoietic stem cell transplant for hematological malignancy. Although short tandem repeat (STR) method is widely used among clinical laboratories, quantitative PCR (qPCR) provides better sensitivity (0.1%) than STR (1% to 5%), but is less accurate than STR for patients in mixed chimerism. qPCR chimerism test allows evaluation of residual recipient cells as a surrogate of measurable residual disease. To achieve higher sensitivity and accuracy, we applied qPCR or STR, based on patient chimerism status (recipient alleles (Source: Journal...
Source: Journal of Molecular Diagnostics - February 20, 2019 Category: Pathology Authors: Jennifer Tyler, Lorie Kumer, Carolyn Fisher, Heather Casey, Hiroko Shike Tags: Regular Article Source Type: research

Rational “Error Elimination” Approach to Evaluating Molecular Barcoded Next-Generation Sequencing Data Identifies Low-Frequency Mutations in Hematologic Malignancies
The emergence of highly sensitive molecular diagnostic approaches such as droplet digital PCR has allowed the accurate identification of low-frequency variant alleles in clinical specimens; however, the multiplex capabilities of droplet digital PCR for variant detection are inadequate. The incorporation of molecular barcodes or unique IDs into next-generation sequencing libraries through PCR has enabled the detection of low-frequency variant alleles across multiple genomic regions. However, rational library preparation and sequencing data analytical strategies that integrate molecular barcodes have rarely been applied to c...
Source: Journal of Molecular Diagnostics - February 20, 2019 Category: Pathology Authors: Saradhi Mallampati, Dzifa Y. Duose, Michael A. Harmon, Meenakshi Mehrotra, Rashmi Kanagal-Shamanna, Stephanie Zalles, Ignacio I. Wistuba, Xiaoping Sun, Rajyalakshmi Luthra Tags: Regular article Source Type: research

Analytical Validation of Variants to Aid in Genotype-Guided Therapy for Oncology
The Clinical Laboratory Improvement Amendments (CLIA) of 1988 requires that pharmacogenetic genotyping methods need to be established according to technical standards and laboratory practice guidelines before testing can be offered to patients. Testing methods for variants in ABCB1, CBR3, COMT, CYP3A7, C8ORF34, FCGR2A, FCGR3A, HAS3, NT5C2, NUDT15, SBF2, SEMA3C, SLC16A5, SLC28A3, SOD2, TLR4, and TPMT were validated in a CLIA-accredited laboratory. As no known reference materials were available, DNA samples that were from Coriell Cell Repositories (Camden, NJ) were used for the analytical validation studies. (Source: Journal...
Source: Journal of Molecular Diagnostics - February 20, 2019 Category: Pathology Authors: Marelize Swart, Wesley M. Stansberry, Victoria M. Pratt, Elizabeth B. Medeiros, Patrick J. Kiel, Fei Shen, Bryan P. Schneider, Todd C. Skaar Tags: Regular article Source Type: research

Personalized Chimerism Test that Uses Selection of Short Tandem Repeat or Quantitative PCR Depending on Patient's Chimerism Status
Chimerism testing is used to monitor engraftment and risk of relapse after allogeneic hematopoietic stem cell transplantation for hematologic malignancies. Although short tandem repeat (STR) method is widely used among clinical laboratories, quantitative PCR (qPCR) provides better sensitivity (0.1%) than STR (1% to 5%) but is less accurate than STR for patients in mixed chimerism. qPCR chimerism allows evaluation of residual recipient cells as a surrogate of measurable residual disease. To achieve higher sensitivity and accuracy, we applied qPCR or STR based on patient chimerism status (recipient alleles (Source: Journal o...
Source: Journal of Molecular Diagnostics - February 19, 2019 Category: Pathology Authors: Jennifer Tyler, Lorie Kumer, Carolyn Fisher, Heather Casey, Hiroko Shike Tags: Regular article Source Type: research

A Model Information Management Plan for Molecular Pathology Sequence Data Using Standards
Incorporating genetic variant data into the electronic health record (EHR) in discrete computable fashion has vexed the informatics community for years. Genetic sequence test results are typically communicated by the molecular laboratory and stored in the EHR as textual documents. Although text documents are useful for human readability and initial use, they are not conducive for data retrieval and reuse. As a result, clinicians often struggle to find historical gene sequence results on a series of oncology patients within the EHR that might influence the care of the current patient. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 19, 2019 Category: Pathology Authors: Walter S. Campbell, Alexis B. Carter, Allison M. Cushman-Vokoun, Timothy C. Greiner, Rajesh C. Dash, Mark Routbort, Monica E. de Baca, James R. Campbell Tags: Regular article Source Type: research

VarGrouper
Accurate genetic variant representation through nomenclature and annotation is essential for understanding functional consequence and properly noting the presence of variants across time, assays, and laboratories. Current variant calling algorithms detect single deletion –insertion variants as multiple indel and/or substitution variants from next-generation sequencing data. Consequently, these variants are separately annotated in bioinformatics pipelines, leading to inaccurate variant representation. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 19, 2019 Category: Pathology Authors: Ryan J. Schmidt, Allison Macleay, Long Phi Le Tags: Technical advance Source Type: research

A Novel Approach to Detect Programed Death Ligand 1 (PD-L1) Status and Multiple Tumor Mutations Using a Single Non –Small-Cell Lung Cancer (NSCLC) Bronchoscopy Specimen
Multiple biomarkers are under evaluation to guide the use of immune checkpoint inhibitors in non –small-cell lung cancer (NSCLC), including programed death ligand 1 (PD-L1) tumor cell staining. We have developed a new approach that accurately quantifies PD-L1 status and identifies multiple mutations by using a single bronchoscopy specimen. A novel molecular marker was identified to detect the presence of malignant cells in radial endobronchial ultrasound bronchial brushings from NSCLC (n = 15) and benign (n = 13) nodules by quantitative real-time RT-PCR (RT-qPCR). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 13, 2019 Category: Pathology Authors: Amanda Vannitamby, Shona Hendry, Tanvi Makadia, Janine Danks, John Slavin, Louis Irving, Daniel Steinfort, Steven Bozinovski Tags: Technical advance Source Type: research

Genetic Diagnostic Testing for Inherited Cardiomyopathies: Considerations for Offering Multi-Gene Tests in a Health Care Setting
Inherited cardiomyopathies (ICs) are a major cause of heart disease. Given their marked clinical and genetic heterogeneity, the content and clinical utility of IC multi-gene panels has been the topic of continuous debate. Our genetics diagnostic laboratory has been providing clinical diagnostic testing for ICs since 2012. We began by testing nine genes, and expanded our panel by 5-fold in 2015. Here, we describe the implementation of a cost-effective next-generation sequencing (NGS)-based assay for testing of IC genes, including a protocol that minimizes the amount of Sanger sequencing required to confirm variants identifi...
Source: Journal of Molecular Diagnostics - February 4, 2019 Category: Pathology Authors: Hussein Daoud, Mahdi Ghani, Landry Nfonsam, Ryan Potter, Shelley Ordorica, Virginia Haslett, Nathaniel Santos, Heather Derksen, Donelda Lahey, Martha McGill, Vanessa Trudel, Brittany Antoniuk, Nasim Vasli, Caitlin Chisholm, Gabrielle Mettler, Elizabeth Si Tags: Regular Article Source Type: research

Genomic Analysis of Circulating Tumor DNA Using a Melanoma-Specific UltraSEEK Oncogene Panel
The analysis of circulating tumor DNA (ctDNA) provides a minimally-invasive molecular interrogation that has the potential to guide treatment selection and disease monitoring. Here, we evaluated a custom UltraSEEK melanoma panel for the MassARRAY system, probing for 61 mutations over 13 genes. The analytical sensitivity and clinical accuracy of the UltraSEEK melanoma panel was compared to droplet digital PCR. The blinded analysis of 68 mutations detected in 48 plasma samples from stage IV melanoma patients revealed a concordance of 88% between the two platforms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 4, 2019 Category: Pathology Authors: Elin S. Gray, Tom Witkowski, Michelle Pereira, Leslie Calapre, Karl Herron, Darryl Irwin, Brett Chapman, Muhammad A. Khattak, Jeanette Raleigh, Athena Hatzimihalis, Jonathan Cebon, Shahneen Sandhu, Grant A. McArthur, Michael Millward, Melanie Ziman, Alexa Tags: Regular article Source Type: research

Optimization of next-generation sequencing technologies for von Hippel Lindau (VHL) mosaic mutation detection and development of confirmation methods
Von Hippel Lindau disease (VHL) is a monogenic disorder characterized by the development of tumors affecting the central nervous system, kidney, pancreas, or adrenal glands, and due to germline mutations in the VHL tumor suppressor gene. About 5% of patients harboring a typical VHL phenotype have no mutation detected by conventional techniques, so a postzygotic VHL mosaicism can be suspected. The aim of this study was therefore to implement a next-generation sequencing (NGS) strategy for VHL mosaic mutation detection, including an optimization of the original Personal Genome Machine design by enrichment with oligonucleotid...
Source: Journal of Molecular Diagnostics - February 4, 2019 Category: Pathology Authors: Lucie Coppin, Pascal Plouvier, Michel Cr épin, Anne-Sophie Jourdain, Emilie Ait Yahya, Stéphane Richard, Brigitte Bressac-de Paillerets, Catherine Cardot-Bauters, Sophie Lejeune, Julie Leclerc, Pascal Pigny Tags: Regular Article Source Type: research

Genomic Analysis of Circulating Tumor DNA  Using a Melanoma-Specific UltraSEEK Oncogene Panel
The analysis of circulating tumor DNA provides a minimally invasive molecular interrogation that has the potential to guide treatment selection and disease monitoring. Here, the authors evaluated a custom UltraSEEK melanoma panel for the MassARRAY system, probing for 61 mutations over 13 genes. The analytical sensitivity and clinical accuracy of the UltraSEEK melanoma panel was compared with droplet digital PCR. The blinded analysis of 68 mutations detected in 48 plasma samples from stage IV melanoma patients revealed a concordance of 88% between the two platforms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - February 3, 2019 Category: Pathology Authors: Elin S. Gray, Tom Witkowski, Michelle Pereira, Leslie Calapre, Karl Herron, Darryl Irwin, Brett Chapman, Muhammad A. Khattak, Jeanette Raleigh, Athena Hatzimihalis, Jonathan Cebon, Shahneen Sandhu, Grant A. McArthur, Michael Millward, Melanie Ziman, Alexa Tags: Regular article Source Type: research

Genetic Diagnostic Testing for Inherited Cardiomyopathies
Inherited cardiomyopathies (ICs) are a major cause of heart disease. Given their marked clinical and genetic heterogeneity, the content and clinical utility of IC multi-gene panels has been the topic of continuous debate. Our genetics diagnostic laboratory has been providing clinical diagnostic testing for ICs since 2012. We began by testing nine genes and expanded our panel by fivefold in 2015. Here, we describe the implementation of a cost-effective next-generation sequencing (NGS)-based assay for testing of IC genes, including a protocol that minimizes the amount of Sanger sequencing required to confirm variants identif...
Source: Journal of Molecular Diagnostics - February 3, 2019 Category: Pathology Authors: Hussein Daoud, Mahdi Ghani, Landry Nfonsam, Ryan Potter, Shelley Ordorica, Virginia Haslett, Nathaniel Santos, Heather Derksen, Donelda Lahey, Martha McGill, Vanessa Trudel, Brittany Antoniuk, Nasim Vasli, Caitlin Chisholm, Gabrielle Mettler, Elizabeth Si Tags: Regular article Source Type: research

Considerations for Genomic Data Privacy and Security When Working in the Cloud
Next-generation sequencing produces large amounts of data. The complexity and data management issues associated with next-generation sequencing have led many laboratories to turn to cloud services, especially when internal information technology infrastructure is inadequate to support data requirements. In addition, public cloud repositories of variants are being increasingly utilized, and their data sets are being populated through crowdsourcing submissions of human genetic variation identified within laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 28, 2019 Category: Pathology Authors: Alexis B. Carter Tags: Review Source Type: research

Targeted RNA Sequencing in Non –Small Cell Lung Cancer
This commentary highlights the article by Blidner et  al that describes a novel assay for detection of chimeric RNAs from gene fusions and exon-skipping events in non–small-cell lung cancer. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 18, 2019 Category: Pathology Authors: Lauren L. Ritterhouse Tags: Commentary Source Type: research

Targeted RNA Sequencing in Non –Small-Cell Lung Cancer
This commentary highlights the article by Blidner et  al that describes a novel assay for detection of chimeric RNAs from gene fusions and exon-skipping events in non–small-cell lung cancer. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 18, 2019 Category: Pathology Authors: Lauren L. Ritterhouse Tags: Commentary Source Type: research

Targeted RNA-Seq in Non –Small-Cell Lung Cancer
This commentary highlights the article by Blidner et al that describes a novel assay for detection of chimeric RNAs from gene fusions and exon-skipping events in non –small-cell lung cancer. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 18, 2019 Category: Pathology Authors: Lauren L. Ritterhouse Tags: Commentary Source Type: research

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing –Detected Variants with an Orthogonal Method in Clinical Genetic Testing
Orthogonal confirmation of next-generation sequencing (NGS)-detected germline variants has been standard practice, although published studies have suggested that confirmation of the highest quality calls may not always be necessary. The key question is how laboratories can establish criteria that consistently identify those NGS calls that require confirmation. Most prior studies addressing this question have limitations: These studies are generally small, omit statistical justification, and explore limited aspects of the underlying data. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 2, 2019 Category: Pathology Authors: Stephen E. Lincoln, Rebecca Truty, Chiao-Feng Lin, Justin M. Zook, Joshua Paul, Vincent H. Ramey, Marc Salit, Heidi L. Rehm, Robert L. Nussbaum, Matthew S. Lebo Tags: Regular Article Source Type: research

Structural Variation Detection by Proximity Ligation from Formalin-Fixed, Paraffin-Embedded Tumor Tissue
The clinical management and therapy of many solid tumor malignancies is dependent on detection of medically actionable or diagnostically relevant genetic variation. However, a principal challenge for genetic assays from tumors is the fragmented and chemically damaged state of DNA in formalin-fixed, paraffin-embedded (FFPE) samples. From highly fragmented DNA and RNA there is no current technology for generating long-range DNA sequence data as is required to detect genomic structural variation or long-range genotype phasing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 31, 2018 Category: Pathology Authors: Christopher J. Troll, Nicholas H. Putnam, Paul D. Hartley, Brandon Rice, Marco Blanchette, Sameed Siddiqui, Javkhlan-Ochir Ganbat, Martin P. Powers, Ramesh Ramakrishnan, Christian A. Kunder, Carlos D. Bustamante, James L. Zehnder, Richard E. Green, Helio Tags: Technical advance Source Type: research

Designing and Implementing NGS Tests for Inherited Disorders – a Practical Framework with Step-by-Step Guidance for Clinical Laboratories
Comprehensive next-generation sequencing (NGS) tests are increasingly used as first-line tests in the evaluation of patients with suspected heritable disease. Despite major technical simplifications, these assays still pose significant challenges for molecular testing laboratories. Existing professional guidelines and recommendations provide a framework for laboratories implementing such tests, but in-depth, concrete guidance is generally not provided. Consequently, there is variability in how laboratories interpret and subsequently implement these regulatory frameworks. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 31, 2018 Category: Pathology Authors: Avni Santani, Birgitte B. Simen, Marian Briggs, Matthew Lebo, Jason D. Merker, Marina Nikiforova, Patricia Vasalos, Karl Voelkerding, John Pfeifer, Birgit Funke Tags: Special Article Source Type: research

Designing and Implementing NGS Tests for Inherited Disorders
Comprehensive next-generation sequencing (NGS) tests are increasingly used as first-line tests in the evaluation of patients with suspected heritable disease. Despite major technical simplifications, these assays still pose significant challenges for molecular testing laboratories. Existing professional guidelines and recommendations provide a framework for laboratories implementing such tests, but in-depth, concrete guidance is generally not provided. Consequently, there is variability in how laboratories interpret and subsequently implement these regulatory frameworks. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 30, 2018 Category: Pathology Authors: Avni Santani, Birgitte B. Simen, Marian Briggs, Matthew Lebo, Jason D. Merker, Marina Nikiforova, Patricia Vasalos, Karl Voelkerding, John Pfeifer, Birgit Funke Tags: Special article Source Type: research

Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms
Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the assessment of B-cell lineage neoplasms. Clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially available kit...
Source: Journal of Molecular Diagnostics - December 24, 2018 Category: Pathology Authors: Maria E. Arcila, Wayne Yu, Mustafa Syed, Hannah Kim, Lidia Maciag, JinJuan Yao, Caleb Ho, Kseniya Petrova, Christine Moung, Paulo Salazar, Ivelise Rijo, Tessara Baldi, Ahmet Zehir, Ola Landgren, Jae Park, Mikhail Roshal, Ahmet Dogan, Khedoudja Nafa Tags: Regular article Source Type: research

Establishment of Ig Heavy Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms
Ig heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the diagnosis and monitoring of B-cell lineage neoplasms. However, clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially av...
Source: Journal of Molecular Diagnostics - December 24, 2018 Category: Pathology Authors: Maria E. Arcila, Wayne Yu, Mustafa Syed, Hannah Kim, Lidia Maciag, JinJuan Yao, Caleb Ho, Kseniya Petrova, Christine Moung, Paulo Salazar, Ivelise Rijo, Tessara Baldi, Ahmet Zehir, Ola Landgren, Jae Park, Mikhail Roshal, Ahmet Dogan, Khedoudja Nafa Tags: Regular article Source Type: research

Establishment of Immunoglobulin Heavy Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms
Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the diagnosis and monitoring of B-cell lineage neoplasms. However, clinical use remains limited as assays are not standardized and validation/implementation guidelines not yet developed. Here, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1, were validated using commercially...
Source: Journal of Molecular Diagnostics - December 24, 2018 Category: Pathology Authors: Maria E. Arcila, Wayne Yu, Mustafa Syed, Hannah Kim, Lidia Maciag, JinJuan Yao, Caleb Ho, Kseniya Petrova, Christine Moung, Paulo Salazar, Ivelise Rijo, Tessara Baldi, Ahmet Zehir, Ola Landgren, Jae Park, Mikhail Roshal, Ahmet Dogan, Khedoudja Nafa Tags: Regular Article Source Type: research

Automated Clinical Exome Reanalysis Reveals Novel Diagnoses
Clinical exome sequencing (CES) has a reported diagnostic yield of 20% to 30% for most clinical indications. The ongoing discovery of novel gene –disease and variant–disease associations are expected to increase the diagnostic yield of CES. Performing systematic reanalysis of previously nondiagnostic CES samples represents a significant challenge for clinical laboratories. Here, we present the results of a novel automated reanalysis meth odology applied to 300 CES samples initially analyzed between June 2014 and September 2016. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Samuel W. Baker, Jill R. Murrell, Addie I. Nesbitt, Kieran B. Pechter, Jorune Balciuniene, Xiaonan Zhao, Zhenming Yu, Elizabeth H. Denenberg, Elizabeth T. DeChene, Alisha B. Wilkens, Elizabeth J. Bhoj, Qiaoning Guan, Matthew C. Dulik, Laura K. Conlin, Ahm Tags: Regular article Source Type: research

Ultra-Rapid Reporting of GENomic Targets (URGENTseq)
Next-generation sequencing (NGS)-based mutation panels profile multiple genes simultaneously, allowing the reporting of numerous genes while saving labor and resources. However, one drawback of using NGS is that the turnaround time is often longer than conventional single gene tests. This delay can be problematic if molecular results are required to guide therapy in patients with clinically aggressive diseases, such as acute myeloid leukemia. To overcome this limitation, we developed a novel custom platform designated as Ultra-rapid Reporting of GENomic Targets (URGENTseq), an integrated solution that includes workflow opt...
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Keyur P. Patel, Roberto Ruiz-Cordero, Wei Chen, Mark J. Routbort, Kristen Floyd, Sergio Rodriguez, John Galbincea, Bedia A. Barkoh, David Hatfield, Haitham Khogeer, Rashmi Kanagal-Shamanna, C. Cameron Yin, Zhuang Zuo, Sanam Loghavi, Chi Young Ok, Courtney Tags: Regular article Source Type: research

Translating Risk of Consumer-Initiated Genetic Testing
This editorial highlights the article by Bick and colleagues that proposes a framework for evaluating elective genomic testing. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Barbara Zehnbauer Tags: Editorial Source Type: research

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

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

Instructions to Authors
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Source Type: research

Scientific Integrity Policy
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Source Type: research

Combined Targeted Resequencing of Cytosine DNA Methylation and Mutations of DNA Repair Genes with Potential Use for Poly(ADP-Ribose) Polymerase 1 Inhibitor Sensitivity Testing
Current molecular tumor diagnostics encompass panel sequencing to detect mutations, copy number alterations, and rearrangements. However, tumor suppressor genes can also be inactivated by methylation within their promoter region. These epigenetic alterations are so far rarely assessed in the clinical setting. Therefore, we established the AllCap protocol facilitating the combined detection of mutations and DNA methylation at the coding and promoter regions of 342 DNA repair genes in one experiment. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Christina Grimm, Axel Fischer, Angela M. Farrelly, Roshni Kalachand, Roberta Castiglione, Elena Wasserburger, Michelle Hussong, Anne M. Schultheis, Janine Altm üller, Holger Thiele, Hans C. Reinhardt, Kai Hauschulz, Bryan T. Hennessy, Ralf Herwig, Matthi Tags: Technical advance Source Type: research

t(3;8)(q26.2;q24) Often Leads to MECOM/MYC Rearrangement and Is Commonly Associated with Therapy-Related Myeloid Neoplasms and/or Disease Progression
t(3;8)(q26.2;q24) is a rare recurrent cytogenetic abnormality that is associated with myeloid neoplasms. Of 20 patients with t(3;8)(q26.2,q24), 8 had therapy-related acute myeloid leukemia (AML), 3 therapy-related myelodysplastic syndrome, 4 blast phase of chronic myeloid leukemia, 1 relapsed AML, 1 AML transformed from chronic myelomonocytic leukemia, 1 blast phase of an unclassifiable myeloproliferative neoplasm, 1 de novo myelodysplastic syndrome, and 1 de novo AML. Nineteen patients presented with cytopenia. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Guilin Tang, Shimin Hu, Sa A. Wang, Wei Xie, Pei Lin, Jie Xu, Gokce Toruner, Ming Zhao, Jun Gu, Madison Doty, Shaoying Li, L. Jeffrey Medeiros, Zhenya Tang Tags: Regular article Source Type: research

Somatic Tumor Variant Filtration Strategies to Optimize Tumor-Only Molecular Profiling Using Targeted Next-Generation Sequencing Panels
A common approach in clinical diagnostic laboratories to variant assessment from tumor molecular profiling is sequencing of genomic DNA extracted from both tumor (somatic) and normal (germline) tissue, with subsequent variant comparison to identify true somatic variants with potential impact on patient treatment or prognosis. However, challenges exist in paired tumor-normal testing, including increased cost of dual sample testing and identification of germline cancer predisposing variants. Alternatively, somatic variants can be identified by in silico tumor-only variant filtration precluding the need for matched normal tes...
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Mahadeo A. Sukhai, Maksym Misyura, Mariam Thomas, Swati Garg, Tong Zhang, Natalie Stickle, Carl Virtanen, Philippe L. Bedard, Lillian L. Siu, Tina Smets, Gert Thijs, Steven Van Vooren, Suzanne Kamel-Reid, Tracy L. Stockley Tags: Regular Article Source Type: research

Clinical Utility Of A Next-Generation Sequencing Panel For Acute Myeloid Leukemia Diagnostics
Next-generation-sequencing (NGS) has redefined the genetic landscape of acute myeloid leukemia (AML) providing new molecular markers for diagnostic and prognostic classifications. However, its application in the clinical setting is still challenging. We hypothesized that a 19-gene AML-targeted NGS panel could be a valid approach to obtain clinically relevant information. Thus, we assessed the ability of this panel to classify AML patients according to diagnostic and prognostic indexes in a cohort of 162 patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Carmen M. Alonso, Marta Llop, Claudia Sargas, Laia Pedrola, Joaqu ín Panadero, David Hervás, José Cervera, Esperanza Such, Mariam Ibáñez, Rosa Ayala, Joaquín Martínez-López, Esther Onecha, Inmaculada de Juan, Sarai Palanca, David Martínez-Cuadró Tags: Regular Article Source Type: research

Next-Generation Sequencing –Based Assessment of JAK2, PD-L1, and PD-L2 Copy Number Alterations at 9p24.1 in Breast Cancer: Potential Implications for Clinical Management
Genomic amplification at 9p24.1, including the loci for JAK2, PD-L1, and PD-L2, has recently been described as a mechanism of resistance in post-chemotherapy, triple-negative breast cancer. This genomic signature holds significant promise as a prognostic biomarker and has implications for targeted therapy with JAK2 inhibitors, as well as with immunotherapy. To guide future screening strategies, we determined the frequency of these alterations. A total of 5,399 cases were included in the study. This encompassed 2,890 institutional cases tested by the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cance...
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Sounak Gupta, Chad M. Vanderbilt, Paolo Cotzia, Javier A. Arias Stella, Jason C. Chang, Ahmet Zehir, Ryma Benayed, Khedouja Nafa, Pedram Razavi, David M. Hyman, Jos é Baselga, Michael F. Berger, Marc Ladanyi, Maria E. Arcila, Dara S. Ross Tags: Regular Article Source Type: research

Combined Targeted Re-Sequencing of Cytosine DNA Methylation and Mutations of DNA Repair Genes with Potential Use for PARP1 Inhibitor Sensitivity Testing
Current molecular tumor diagnostics encompass panel sequencing to detect mutations, copy number alterations, and rearrangements. However, tumor suppressor genes can also be inactivated by methylation within their promoter region. These epigenetic alterations are so far rarely assessed in the clinical setting. Therefore, we established the AllCap protocol facilitating the combined detection of mutations and DNA methylation at the coding and promoter regions of 342 DNA repair genes in one experiment. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Christina Grimm, Axel Fischer, Angela M. Farrelly, Roshni Kalachand, Roberta Castiglione, Elena Wasserburger, Michelle Hussong, Anne M. Schultheis, Janine Altm üller, Holger Thiele, Hans C. Reinhardt, Kai Hauschulz, Bryan T. Hennessy, Ralf Herwig, Matthi Tags: Technical advance Source Type: research

t(3;8)(q26.2;q24) Often Leads to MECOM /MYC Rearrangement and is Commonly Associated with Therapy-Related Myeloid Neoplasms and/or Disease Progression
We report 20 patients with t(3;8)(q26.2,q24): eight had therapy-related acute myeloid leukemia (AML), three therapy-related myelodysplastic syndrome, four blast phase of chronic myeloid leukemia, one relapsed AML, one AML transformed from chronic myelomonocytic leukemia, one blast phase of an unclassifiable myeloproliferative neoplasm, one de novo myelodysplastic syndrome, and one de novo AML. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2018 Category: Pathology Authors: Guilin Tang, Shimin Hu, Sa A. Wang, Wei Xie, Pei Lin, Jie Xu, Gokce Toruner, Ming Zhao, Jun Gu, Madison Doty, Shaoying Li, L. Jeffrey Medeiros, Zhenya Tang Tags: Regular Article Source Type: research

Molecular pathology of bone tumors
Although classic histomorphology is the cornerstone of bone tumor diagnostics, this field has rapidly evolved since the advance of new molecular techniques. The identification of novel genetic alterations in bone tumors has led to more insight into the genetic background of these tumors, which resulted in a more prominent role of molecular pathology in daily practice. Numerous studies have been conducted in the last decades and illustrated that based on molecular alterations, bone tumors are roughly divided into tumors with simple and complex karyotypes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 17, 2018 Category: Pathology Authors: Suk Wai Lam, David G.P. van IJzendoorn, Anne-Marie Cleton-Jansen, Karoly Szuhai, Judith V.M.G. Bov ée Tags: Review Source Type: research

Rapid Next-Generation Sequencing Method for Prediction of Prostate Cancer Risks
Prostate cancer is the most commonly diagnosed male cancer and the second leading cause of cancer deaths among men in the United States, with approximately 220,000 new diagnoses and approximately 27,000 deaths each year. Men with clinical low-risk disease can receive active surveillance to safely preserve quality of life, provided that the risk of an undetected aggressive cancer can be managed. Thus, prediction of a tumor's metastatic potential, ideally using only a biopsy sample, is critical to choosing appropriate treatment. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 12, 2018 Category: Pathology Authors: Viacheslav Y. Fofanov, Kinnari Upadhyay, Alexander Pearlman, Johnny Loke, Vivian O, Yongzhao Shao, Stephen Freedland, Harry Ostrer Tags: Regular article Source Type: research

Software-Assisted Manual Review of Clinical Next-Generation Sequencing Data
Clinical genomic tests increasingly use a next-generation sequencing (NGS) platform due in part to the high fidelity of variant calls, yet rare errors are still possible. In germline DNA screening, failure to correct such errors could have serious consequences for patients, who may follow an unwarranted screening or surgical management path. It has been suggested that routine orthogonal confirmation by Sanger sequencing is required to verify NGS results, especially low-confidence positives with depressed allele fraction ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2018 Category: Pathology Authors: Dale Muzzey, Shera Kash, Jillian I. Johnson, Laura M. Melroy, Piotr Kaleta, Kelly A. Pierce, Kaylene Ready, Hyunseok P. Kang, Kevin R. Haas Tags: Regular article Source Type: research

Rapid and Sensitive Detection of Azole-Resistant Aspergillus fumigatus by Tandem Repeat Loop-Mediated Isothermal Amplification
Invasive fungal infections caused by multiazole-resistant Aspergillus fumigatus are associated with increasing rates of mortality in susceptible patients. Current methods of diagnosing infections caused by multiazole-resistant A. fumigatus are, however, not well suited for use in clinical point-of-care testing or in the field. Loop-mediated isothermal amplification (LAMP) is a widely used method of nucleic acid amplification with rapid and easy-to-use features, making it suitable for use in different resource settings. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2018 Category: Pathology Authors: Ling-Shan Yu, Jesus Rodriguez-Manzano, Kenny Malpartida-Cardenas, Thomas Sewell, Oliver Bader, Darius Armstrong-James, Matthew C. Fisher, Pantelis Georgiou Tags: Regular article Source Type: research

Software-assisted manual review of clinical next-generation sequencing data An alternative to routine Sanger sequencing confirmation with equivalent results in > 15,000 germline DNA screens
Clinical genomic tests increasingly utilize a next-generation sequencing (NGS) platform due in part to the high fidelity of variant calls, yet rare errors are still possible. In germline DNA screening, failure to correct such errors could have serious consequences for patients, who may follow an unwarranted screening or surgical-management path. It has been suggested that routine orthogonal confirmation via Sanger sequencing is required to verify NGS results, especially low-confidence positives with depressed allele fraction ( (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2018 Category: Pathology Authors: Dale Muzzey, Shera Kash, Jillian I. Johnson, Laura M. Melroy, Piotr Kaleta, Kelly A. Pierce, Kaylene Ready, Hyunseok P. Kang, Kevin R. Haas Tags: Regular Article Source Type: research

Rapid and sensitive detection of azole-resistant Aspergillus fumigatus by tandem-repeat loop-mediated isothermal amplification
Invasive human fungal infections caused by multi-azole resistant Aspergillus fumigatus are associated with increasing rates of mortality in susceptible patients. Current methods of diagnosing infections caused by multi-azole resistant A. fumigatus are, however, not well suited for use in clinical point-of-care testing or in the field. Loop-mediated isothermal amplification (LAMP) is a widely used method of nucleic acid amplification with rapid and easy-to-use features, making it suitable for use in different resource settings. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2018 Category: Pathology Authors: Ling-Shan Yu, Jesus Rodriguez-Manzano, Kenny Malpartida-Cardenas, Thomas Sewell, Oliver Bader, Darius Armstrong-James, Matthew C. Fisher, Pantelis Georgiou Tags: Regular Article Source Type: research

Design, optimization, and multisite evaluation of a targeted next-generation sequencing assay system for chimeric RNAs from gene fusions and exon-skipping events in non –small-cell lung cancer
Lung cancer accounts for approximately 14% of all newly diagnosed cancers and is the leading cause of cancer-related deaths. Chimeric RNA resulting from gene fusions (RNA fusions) and other RNA splicing errors are driver events and clinically addressable targets for non –small-cell lung cancer (NSCLC). The reliable assessment of these RNA markers by next-generation sequencing requires integrated reagents, protocols, and interpretive software that can harmonize procedures and assure consistent results across laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 4, 2018 Category: Pathology Authors: Richard A. Blidner, Brian C. Haynes, Stephen Hyter, Sarah Schmitt, Ziyan Y. Pessetto, Andrew K. Godwin, Dan Su, Patrick Hurban, L éon C. van Kempen, Maria L. Aguirre, Shobha Gokul, Robyn D. Cardwell, Gary J. Latham Tags: Regular Article Source Type: research

A Novel Multiplex droplet digital PCR Assay to Identify and Quantify KRAS Mutations in Clinical Specimens
Recurrent activating point mutations in KRAS are critical drivers in pancreatic cancer and have been attributed to resistance to anti –epidermal growth factor receptor therapy in colorectal cancer. Although KRAS genotyping provides limited clinical utility in the diagnosis and management of pancreatic cancer patients at present, inferences about the fractional abundance of KRAS mutations may inform on tumor purity in traditional ly challenging clinical specimens and their potential use in precision medicine. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 22, 2018 Category: Pathology Authors: Miguel Alcaide, Matthew Cheung, Kevin Bushell, Sarah E. Arthur, Hui-Li Wong, Joanna Karasinska, Daniel Renouf, David F. Schaeffer, Suzan McNamara, Mathilde Couetoux du Tertre, Gerald Batist, Hagen F. Kennecke, Aly Karsan, Ryan D. Morin Tags: Regular article Source Type: research

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

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

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

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