Development and Analytical Validation of an Expanded Mutation Detection Panel for Next-Generation Sequencing of Thyroid Nodule Aspirates
Molecular analysis is used to evaluate the risk of malignancy for thyroid fine needle aspirates, identified as indeterminate by microscopic cytology, based on the detection of various oncogenic DNA mutations and fusion transcripts, or upon the use of various mRNAs or microRNA-based classifier algorithms. Our approach has been to use a combination test utilizing the detection of oncogenic mutations/ fusion transcripts and a micro-RNA expression –based classifier algorithm. To improve the performance of the combination test, the next-generation sequencing (NGS)-based mutational panel was expanded from the detection of ...
Source: Journal of Molecular Diagnostics - December 18, 2019 Category: Pathology Authors: Kenny Kwabena Ablordeppey, Venkata Arun Timmaraju, Joanna Wanmin Song-Yang, Sharon Yaqoob, Christina Narick, Alidad Mireskandari, Sydney David Finkelstein, Gyanendra Kumar Tags: Regular article Source Type: research

Molecular discordance between myeloid sarcomas and concurrent bone marrows occurs in actionable genes and is associated with worse overall survival
Myeloid sarcoma is a rare, architecture-effacing proliferation of myeloid blasts localized to an extramedullary site, with or without concurrent bone marrow involvement. Clonal heterogeneity results from acquisition of somatic mutations within different subclones of leukemic cells. We hypothesized that clonal heterogeneity between myeloid sarcomas and concurrent bone marrow biopsies might be present given their differing biologic features and microenvironment. High-throughput sequencing of the largest series (n = 24) of paired myeloid sarcomas and bone marrow biopsies was performed. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2019 Category: Pathology Authors: Brian Werstein, Jennifer Dunlap, Michael J. Cascio, Robert S. Ohgami, Guang Fan, Richard Press, Philipp W. Raess Source Type: research

Renewed Commitments to Key Partners
This Editorial highlights the updates to the publication frequency, member benefits, and societal oversight of The Journal of Molecular Diagnostics beginning in January  2020. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2019 Category: Pathology Authors: Barbara A. Zehnbauer Tags: Editorial Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2019 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2019 Category: Pathology Source Type: research

Instructions to Authors
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2019 Category: Pathology Source Type: research

Scientific Integrity Policy
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2019 Category: Pathology Source Type: research

Acoustofluidic Salivary Exosome Isolation
In this study, an acoustofluidic (the fusion of acoustics and microfluidics) platform was developed to perform size-based isolation of salivary exosomes. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 12, 2019 Category: Pathology Authors: Zeyu Wang, Feng Li, Joseph Rufo, Chuyi Chen, Shujie Yang, Liang Li, Jinxin Zhang, Jordan Cheng, Yong Kim, Mengxi Wu, Elliot Abemayor, Michael Tu, David Chia, Rachel Spruce, Nikolaos Batis, Hisham Mehanna, David T.W. Wong, Tony Jun Huang Tags: Regular article Source Type: research

Concordance of Genomic Alterations by Next-Generation Sequencing in Tumor Tissue versus Cell-Free DNA in Stage I –IV Non–Small Cell Lung Cancer
Molecular biomarkers hold promise for personalization of cancer treatment. However, a typical tumor biopsy may be difficult to acquire and may not capture genetic variations within or across tumors. Given these limitations, tumor genotyping using next-generation sequencing of plasma-derived circulating tumor (ct)-DNA has the potential to transform non –small cell lung cancer (NSCLC) management. Importantly, mutations detected in biopsied tissue must also be detected in plasma-derived ctDNA at different disease stages. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: John Jiang, Hans-Peter Adams, Lijing Yao, Stephanie Yaung, Preeti Lal, Aarthi Balasubramanyam, Frederike Fuhlbr ück, Nalin Tikoo, Alexander F. Lovejoy, Sebastian Froehler, Li Tai Fang, H. Jost Achenbach, Ralph Floegel, Rainer Krügel, John Palma Tags: Regular article Source Type: research

Development and Validation of a Novel and Rapid Molecular Detection Method for High-Risk Human Papillomavirus in Formalin-Fixed Paraffin-Embedded Tumor Tissue
In this study, we developed and validated a molecular HPV detection method for FFPE specimens of oropharyngeal and nonoropharyngeal HNSCC. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Steven W. Mes, Dani ëlle A.M. Heideman, Elisabeth Bloemena, Arjen Brink, Martijn Bogaarts, C. René Leemans, Ruud H. Brakenhoff Tags: Regular article Source Type: research

Development and Analytical Validation of a DNA Dual-Strand Approach for the US Food and Drug Administration –Approved Next-Generation Sequencing–Based Praxis Extended RAS Panel for Metastatic Colorectal Cancer Samples
A next-generation sequencing method was developed that can distinguish single-stranded modifications from low-frequency somatic mutations present on both strands of DNA in formalin-fixed paraffin-embedded colorectal cancer samples. We applied this method for analytical validation of the Praxis Extended RAS Panel, a US Food and Drug Administration –approved companion diagnostic for panitumumab, on the Illumina MiSeqDx platform. With the use of the TruSeq amplicon workflow, both strands of DNA from the starting material were interrogated independently. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Nitin Udar, Anita Iyer, Margaret Porter, Robert Haigis, Shannon Smith, Shivani Dhillon, Kristen Meier, Diane Ward, Jing Lu, Paul Wenz, Leonard Buchner, Tamsen Dunn, Aaron Wise, Amy Mueller, Karen Gutekunst Tags: Regular article Source Type: research

Multi-Institutional Evaluation of Interrater Agreement of Variant Classification Based on the 2017 Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer
This multi-institutional study was undertaken to evaluate interrater reliability of the 2017 Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists guidelines for interpretation and reporting of oncology sequence variants and to assess current practices and perceptions surrounding these guidelines. Fifty-one variants were distributed to 20 participants from 10 institutions for classification using the new guidelines. Agreement was assessed using chance-corrected agreement (Cohen κ). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Deepika Sirohi, Robert L. Schmidt, Dara L. Aisner, Amir Behdad, Bryan L. Betz, Noah Brown, Joshua F. Coleman, Christopher L. Corless, Georgios Deftereos, Mark D. Ewalt, Helen Fernandes, Susan J. Hsiao, Mahesh M. Mansukhani, Sarah S. Murray, Nifang Niu, La Tags: Regular article Source Type: research

Digital Rolling Circle Amplification –Based Detection of Ebola and Other Tropical Viruses
Emerging tropical viruses have caused serious outbreaks during the recent years, such as Ebola virus (EBOV) in 2014 and the most recent in 2018 to 2019 in Congo. Thus, immediate diagnostic attention is demanded at the point of care in resource-limited settings, because the performance and the operational parameters of conventional EBOV testing are limited. Especially, their sensitivity, specificity, and coverage of other tropical disease viruses make them unsuitable for diagnostic at the point of care. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Sibel Ciftci, Felix Neumann, Samir Abdurahman, K. Sofia Appelberg, Ali Mirazimi, Mats Nilsson, Narayanan Madaboosi Tags: Regular article Source Type: research

Retrospective validation of a metagenomic sequencing protocol for combined detection of rna and dna viruses using respiratory samples from pediatric patients
In this study, the performance of an in-house mNGS protocol for routine diagnostics of viral respiratory infections with potential for automated pan-pathogen detection was studied.The sequencing protocol and bioinformatics analysis were designed and optimized including exogenous internal controls. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Sander van Boheemen, Anneloes L. van Rijn, Nikos Pappas, Ellen C. Carbo, Ruben H.P. Vorderman, Igor Sidorov, Peter J. van `t Hof, Hailiang Mei, Eric C.J. Claas, Aloys C.M. Kroes, Jutte J.C. de Vries Source Type: research

Therapeutic Monitoring of Circulating DNA Mutations in Metastatic Cancer with Personalized Digital PCR
The objective of this study was to validate the use of personalized dPCR mutation assays to monitor patients with metastatic cancer. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Christina M. Wood-Bouwens, Derrick Haslem, Bryce Moulton, Alison F. Almeda, Hojoon Lee, Gregory M. Heestand, Lincoln D. Nadauld, Hanlee P. Ji Source Type: research

Development and validation of a novel and rapid molecular detection method for high-risk HPV in formalin-fixed paraffin-embedded tumor tissue
In this study, we developed and validated a molecular HPV detection method for FFPE specimens of oropharyngeal and non-oropharyngeal HNSCC. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Steven W. Mes, Dani ëlle A.M. Heideman, Elisabeth Bloemena, Arjen Brink, Martijn Bogaarts, C. René Leemans, Ruud H. Brakenhoff Source Type: research

Multi-Institutional Evaluation of Inter-rater Agreement of Variant Classification Based on the 2017 AMP, ASCO and CAP Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer
This multi-institutional study was undertaken to evaluate inter-rater reliability of the 2017 AMP/ASCO/CAP guidelines for interpretation and reporting of oncology sequence variants and to assess current practices and perceptions surrounding these guidelines. Fifty-one variants were distributed to 20 participants from 10 institutions for classification using the new guidelines. Agreement was assessed using chance corrected agreement (Cohen ’s kappa). Overall chance corrected agreement (kappa) was 0.35. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Deepika Sirohi, Robert L. Schmidt, Dara L. Aisner, Amir Behdad, Bryan L. Betz, Noah Brown, Joshua F. Coleman, Christopher L. Corless, Georgios Deftereos, Mark D. Ewalt, Helen Fernandes, Susan J. Hsiao, Mahesh M. Mansukhani, Sarah S. Murray, Nifang Niu, La Source Type: research

Sample Tracking Using Unique Sequence Controls
Sample tracking and identity is essential when processing multiple samples in parallel. Sequencing applications often involve high sample numbers and the data is frequently used in a clinical setting. As such a simple and accurate intrinsic sample tracking process through a sequencing pipeline is essential. Various solutions have been implemented to verify sample identity including variant detection at the start and end of the pipeline using arrays or genotyping, bioinformatic comparisons, and optical barcoding of samples. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Richard A. Moore, Thomas Zeng, T. Roderick Docking, Ian Bosdet, Yaron S. Butterfield, Sarah Munro, Irene Li, Lucas Swanson, Elizabeth R. Starks, Kane Tse, Andrew J. Mungall, Robert A. Holt, Aly Karsan Tags: Technical Advance Source Type: research

Level of seven neuroblastoma-associated mRNAs detected by droplet digital PCR is associated with tumor relapse/regrowth of high-risk neuroblastoma patients
Monitoring of several sets of neuroblastoma-associated mRNAs (NB-mRNAs) by quantitative PCR (qPCR) can be used for evaluating minimal residual disease (MRD) in neuroblastoma (NB) patients. Droplet digital PCR (ddPCR) is an adaption of qPCR that potentially provides more simple and reproducible detection of low-level of mRNAs. However, it remains tested whether MRD in NB patients can be monitored by ddPCR using a set of NB-mRNAs. In the present study, 208 bone marrow (BM) and 67 peripheral blood (PB) samples were retrospectively collected from 20 high-risk NB patients with clinical disease evaluation at two Japanese centers...
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Khin Kyae Mon Thwin, Toshiaki Ishida, Suguru Uemura, Nobuyuki Yamamoto, Kyaw San Lin, Akihiro Tamura, Aiko Kozaki, Atsuro Saito, Kenji Kishimoto, Takeshi Mori, Daiichiro Hasegawa, Yoshiyuki Kosaka, Nanako Nino, Satoru Takafuji, Kazumoto Iijima, Noriyuki N Tags: Regular Article Source Type: research

Concordance of Genomic Alterations by Next-generation Sequencing (NGS) in Tumor Tissue vs. Cell-free DNA in Stage I –IV Non-small Cell Lung Cancer
Molecular biomarkers hold promise for the personalization of cancer treatment. However, a typical tumor biopsy may be difficult to acquire and may not capture genetic variations within or across tumors. Given these limitations, tumor genotyping using next-generation sequencing (NGS) of plasma-derived circulating tumor DNA (ctDNA) has the potential to transform non-small cell lung cancer (NSCLC) management. Importantly, mutations detected in biopsied tissue must also be detected in plasma-derived ctDNA at different disease stages. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: John Jiang, Hans-Peter Adams, Lijing Yao, Stephanie Yaung, Preeti Lal, Aarthi Balasubramanyam, Frederike Fuhlbr ück, Nalin Tikoo, Alexander F. Lovejoy, Sebastian Froehler, Li Tai Fang, H. Jost Achenbach, Ralph Floegel, Rainer Krügel, John Palma Tags: Regular Article Source Type: research

Development and Analytical Validation of a DNA Dual-Strand Approach for the FDA-Approved Next-Generation Sequencing-Based Praxis Extended RAS Panel for Metastatic Colorectal Cancer Samples
A next-generation sequencing method was developed that can distinguish single-stranded modifications from low-frequency somatic mutations present on both strands of DNA in formalin-fixed paraffin-embedded (FFPE) colorectal cancer (CRC) samples. We applied this method for analytical validation of the Praxis Extended RAS Panel, a United States Food and Drug Administration (FDA)-approved companion diagnostic for panitumumab, on the Illumina MiSeqDx platform. Using the TruSeq amplicon workflow, both strands of DNA from the starting material were interrogated independently. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Nitin Udar, Anita Iyer, Margaret Porter, Robert Haigis, Shannon Smith, Shivani Dhillon, Kristen Meier, Diane Ward, Jing Lu, Paul Wenz, Leonard Buchner, Tamsen Dunn, Aaron Wise, Amy Mueller, Karen Gutekunst Source Type: research

Digital rolling circle amplification-based detection of Ebola and other tropical viruses
Emerging tropical viruses have caused serious outbreaks during the recent years, such as Ebola virus (EBOV) in 2014 and the most recent in 2018-19 in Congo. Thus, immediate diagnostic attention is demanded at the point-of-care in resource-limited settings, since the performance and the operational parameters of conventional EBOV testing are limited. Especially, their sensitivity, specificity and coverage of other tropical disease viruses make them unsuitable for diagnostic at the point-of-care. Here, we present a padlock probe (PLP)-based rolling circle amplification (RCA) method for the detection of EBOV. (Source: Journal...
Source: Journal of Molecular Diagnostics - December 10, 2019 Category: Pathology Authors: Sibel Ciftci, Felix Neumann, Samir Abdurahman, K. Sofia Appelberg, Ali Mirazimi, Mats Nilsson, Narayanan Madaboosi Source Type: research

Clinical Validation of a Myeloid Next-Generation Sequencing Panel for Single-Nucleotide Variants, Insertions/Deletions, and Fusion Genes
Myeloid neoplasms are a heterogeneous group of neoplasms including acute myeloid leukemia (AML), myeloproliferative neoplasms, myelodysplastic syndrome, and myeloproliferative neoplasms/myelodysplastic syndrome. Genetic abnormalities are used as diagnostic, prognostic, and predictive biomarkers in patients with these diseases. Herein, we describe the clinical validation of the Oncomine Myeloid Research (OMR) next-generation sequencing panel that interrogates for 40 genes and 29 fusion genes commonly seen in myeloid neoplasms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Iyare Izevbaye, Li Y. Liang, Cheryl Mather, Soufiane El-Hallani, Remegio Maglantay, Lalit Saini Tags: Regular article Source Type: research

VarCover
To facilitate reference-material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants (rsIDs or VCF) and returns an approximately minimal set of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and preselection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a minimal set of reference samples from the 1000 Genomes Project to cover 237 variants considered putatively pathogenic (of which 12 were classified as pathogen...
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Erick R. Scott, Vikas Bansal, Carl Meacham, Stuart A. Scott Tags: Technical advance Source Type: research

Subgroup Analysis Can Optimize the Relapse-Prediction Cutoff Value for WT1 Expression After Allogeneic Hematologic Stem Cell Transplantation in Acute Myeloid Leukemia
High WT1 expression after allogeneic hematologic stem cell transplantation (allo-HSCT) can strongly predict relapse in acute myeloid leukemia (AML). However, the cutoff values obtained have been inconsistent. Precise cutoff values may be optimized through subtype analysis; the RUNX1-RUNX1T1 fusion transcript provides an ideal reference. RUNX1-RUNX1T1 and WT1 transcript levels were simultaneously measured in 1299 bone marrow samples serially collected from 176 t(8;21) AML patients after allo-HSCT. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Ya-Zhen Qin, Yu Wang, Lan-Ping Xu, Xiao-Hui Zhang, Xiao-Su Zhao, Kai-Yan Liu, Xiao-Jun Huang Tags: Regular article Source Type: research

Digital Gene Expression Analysis on Cytology  Smears Can Rule Out Malignancy in Follicular-Patterned Thyroid Tumors
Patients with indeterminate thyroid nodules (Bethesda III and IV) are often treated with diagnostic lobectomy, which in most cases represents an overtreatment. A reliable rule-out molecular test could spare patients unnecessary surgery. Stained smears of 88 indeterminate thyroid nodules with histologic diagnosis of follicular-patterned tumors were selected: 34 follicular adenomas (FAs), 34 follicular variant papillary thyroid carcinomas (FVPTCs), and 20 noninvasive follicular neoplasms with papillary-like nuclear features (NIFTPs). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Elisabetta Macerola, Anello Marcello Poma, Agnese Proietti, Rossana Romani, Liborio Torregrossa, Clara Ugolini, Teresa Rago, Paolo Vitti, Fulvio Basolo Source Type: research

Single-Molecule Sequencing
We investigated the potential of next-generation sequencing (NGS) as an alternative method for preimplantation genetic testing of monogenic disease (PGT-M) with human leukocyte antigen (HLA) matching and for noninvasive prenatal diagnosis follow-up. The case involved parents who were carriers of the FANCG 260delG mutation. After clinical PGT using conventional STR and mutation analysis, two euploid disease-free embryos were transferred, resulting in a twin pregnancy. Using the original embryo whole genome amplification products from 10 embryos, NGS confirmed the genotypes of the eight nontransferred embryos for both mutati...
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Svetlana Rechitsky, Anver Kuliev, Geraldine San Ramon, Ilan Tur-Kaspa, Yin Wang, Wenjie Wang, Xueqing Wu, Li Wang, Don Leigh, David S. Cram Tags: Regular article Source Type: research

Clinical Validation of a Myeloid Next-Generations Sequencing Panel for Single-Nucleotide Variants, Insertions/Deletions, and Fusion Genes
Myeloid neoplasms are a heterogeneous group of neoplasms including acute myeloid leukemia (AML), myeloproliferative neoplasms, myelodysplastic syndrome, and myeloproliferative neoplasms/myelodysplastic syndrome. Genetic abnormalities are used as diagnostic, prognostic, and predictive biomarkers in patients with these diseases. Herein, we describe the clinical validation of the Oncomine Myeloid Research (OMR) next-generation sequencing panel that interrogates for 40 genes and 29 fusion genes commonly seen in myeloid neoplasms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Iyare Izevbaye, Li Ying Liang, Cheryl Mather, Soufiane El-Hallani, Remegio Maglantay, Lalit Saini Tags: Regular article Source Type: research

Single Molecule Sequencing A New Approach for Preimplantation Testing and Noninvasive Prenatal Diagnosis Confirmation of Fetal Genotype
We investigated the potential of next-generation sequencing (NGS) as an alternative methodology for preimplantation genetic testing of monogenic disease (PGT-M) with HLA matching and for noninvasive prenatal diagnosis follow up. The case involved parents who were carriers of the FANCG 260delG mutation. Following clinical PGT using conventional STR and mutation analysis, two euploid disease-free embryos were transferred resulting in a twin pregnancy. Using the original embryo whole genome amplification products from 10 embryos, NGS confirmed the genotypes of the eight non-transferred embryos for both mutation status and HLA...
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Svetlana Rechitsky, Anver Kuliev, Geraldine San Ramon, Ilan Tur-Kaspa, Yin Wang, Wenjie Wang, Xueqing Wu, Li Wang, Don Leigh, David S. Cram Tags: Regular article Source Type: research

Clinical Validation of a Myeloid Next-Generations Sequencing Panel for Single Nucleotide Variants, Indels, and Fusion Genes
Myeloid neoplasms are a heterogenous group of neoplasms including acute myeloid leukemia (AML), myeloproliferative neoplasms, myelodysplastic syndrome, and myeloproliferative neoplasms / myelodysplastic syndrome. Genetic abnormalities are used as diagnostic, prognostic, and predictive biomarkers in patients with these diseases. Here, we describe the clinical validation of the Oncomine Myeloid Research (OMR) next-generation sequencing panel that interrogates for 40 genes and 29 fusion genes commonly seen in myeloid neoplasms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Iyare Izevbaye, Li Ying Liang, Cheryl Mather, Soufiane El-Hallani, Remegio Maglantay JR, Lalit Saini Tags: Regular Article Source Type: research

Subgroup Analysis Can Optimize the Relapse Prediction Cutoff Value for WT1 Expression Following Allogeneic Hematologic Stem Cell Transplantation in Acute Myeloid Leukemia
High WT1 expression after allogeneic hematologic stem cell transplantation (allo-HSCT) can strongly predict relapse in acute myeloid leukemia (AML). However, the cutoff values obtained were inconsistent. The precise cutoff values may be optimized through subtype analysis, and the RUNX1-RUNX1T1 fusion transcript provides an ideal reference. RUNX1-RUNX1T1 and WT1 transcript levels were simultaneously measured in 1,299 bone marrow samples serially collected from 176 t(8;21) AML patients after receiving allo-HSCTfor. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Ya-Zhen Qin, Yu Wang, Lan-Ping Xu, Xiao-Hui Zhang, Xiao-Su Zhao, Kai-Yan Liu, Xiao-Jun Huang Tags: Regular Article Source Type: research

Evaluation of the BD MAX Check-Points CPO assay for the detection of carbapenemase producers directly from rectal swabs
A novel real time multiplex PCR assay, BD MAX Check-Points CPO, was evaluated to detect carbapenemase-producing organisms in clinical settings on the BD MAX system. A total of 175 well-characterized isolates (including 123 carbapenemase-producers) and 128 rectal swab specimens (including 83 positives) of patients considered at “high-risk” for carriage of carbapenemase-producers were included. Bacterial suspensions were used to spike “true negative” rectal swabs to mimic a clinical sample. Fifty microliters of sample, containing either the spiked or the patient’s samples were processed. (Source...
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Delphine Girlich, Saoussen Oueslati, Sandrine Bernabeu, Isabelle Langlois, Christine Begasse, Nicolas Arangia, Elodie Creton, Garance Cotellon, Aimie Sauvadet, Laurent Dortet, Nicolas Fortineau, Thierry Naas Tags: Regular Article Source Type: research

Evaluation of Commercial Next-Generation Sequencing Bioinformatics Software Solutions
Next-generation sequencing (NGS) diagnostics continue to expand rapidly in clinical medicine. An ever-expanding menu of molecular biomarkers are deemed important for diagnostic, prognostic, and therapeutic assessment in patients. The increasing role of NGS in the clinic is driven mainly by the falling costs of sequencing. However, the data-intensive nature of NGS makes bioinformatic analysis a major challenge to many clinical laboratories. Critically needed NGS bioinformatics personnel are hard to recruit and retain in small- to mid-size clinical laboratories. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Rama R. Gullapalli Source Type: research

Digital Gene Expression Analysis on Cytology Smears Can Rule-out Malignancy in Follicular-Patterned Thyroid Tumors
Patients with indeterminate thyroid nodules (Bethesda III and IV) are often treated with diagnostic lobectomy, which in the majority of cases represent an overtreatment. A reliable rule-out molecular test could spare patients unnecessary surgery. Stained smears of 88 indeterminate thyroid nodules with histological diagnosis of follicular-patterned tumors were selected: 34 follicular adenomas (FA), 34 follicular variant papillary thyroid carcinomas (FVPTC), and 20 noninvasive follicular neoplasms with papillary-like nuclear features (NIFTP). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Elisabetta Macerola, Anello Marcello Poma, Agnese Proietti, Rossana Romani, Liborio Torregrossa, Clara Ugolini, Teresa Rago, Paolo Vitti, Fulvio Basolo Source Type: research

VarCover: Allele Min-Set Cover Software
To facilitate reference material selection for clinical genetic testing laboratories, we developed VarCover, open-source software hosted on GitHub, which accepts a file of variants (rsIDs or VCF) and returns an approximately minimal set of samples covering the targeted alleles. VarCover employs the SetCoverPy package, sample weights, and pre-selection of singleton-possessing samples to efficiently solve the min-set cover problem. As a test case, we attempted to find a minimal set of 1000 Genomes (1KG) Project reference samples to cover 237 putatively pathogenic variants (of which 12 were pathogenic or likely pathogenic) in...
Source: Journal of Molecular Diagnostics - November 17, 2019 Category: Pathology Authors: Erick R. Scott, Vikas Bansal, Carl Meacham, Stuart A. Scott Tags: Technical Advance Source Type: research

Multiplexed Digital Detection of B-cell Acute Lymphoblastic Leukemia Fusion Transcripts Using the NanoString nCounter System
In this study, we used NanoString technology to design, validate, and evaluate a multiplex panel for the detection of B-ALL fusion transcripts. Fifty-one B-ALL fusion transcripts reported in children in the literature were included in the design of the NanoString panel. Twenty-six fusion transcripts were validated using 64 positive-control samples and 74 negative-control samples with 100% sensitivity and 99% specificity in comparison to RT-PCR. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 12, 2019 Category: Pathology Authors: Yunan Zhong, Kassa Beimnet, Zaman Alli, Anthony Arnoldo, Paul E. Kowalski, Gino R. Somers, Cynthia Hawkins, Mohamed Abdelhaleem Source Type: research

Multiplexed Digital Detection of B-ALL Leukemia Fusion Transcripts using the NanoString nCounter System
In this study, we used nanoString technology to design, validate, and evaluate a multiplex panel for detection of B-ALL fusion transcripts. Fifty-one B-ALL fusion transcripts reported in children in the literature were included in the design of the nanoString panel. Twenty-six fusion transcripts were validated using 64 positive control samples and 74 negative control samples with 100% sensitivity and 99% in comparison to Reverse Transcription-PCR. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 12, 2019 Category: Pathology Authors: Yunan Zhong, Kassa Beimnet, Zaman Alli, Anthony Arnoldo, Paul E. Kowalski, Gino R. Somers, Cynthia Hawkins, Mohamed Abdelhaleem Source Type: research

Improving copy number variant detection from sequencing data with a combination of programs and a predictive model
We present an efficient bioinformatics pipeline for CNV detection from gene panel MPS data in neuromuscular disorders. CNVs were generated in silico into samples sequenced with a previously published MPS gene panel. The in silico CNVs from these samples were analyzed with four programs having complementary CNV detection ranges, CoNIFER, XHMM, ExomeDepth, and CODEX. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 12, 2019 Category: Pathology Authors: Salla V älipakka, Marco Savarese, Lydia Sagath, Meharji Arumilli, Teresa Giugliano, Bjarne Udd, Peter Hackman Source Type: research

Using Nanopore Whole-Transcriptome Sequencing for Human Leukocyte Antigen Genotyping and Correlating Donor Human Leukocyte Antigen Expression with Flow Cytometric Crossmatch Results
Transplant centers are increasingly using virtual crossmatching to evaluate recipient and donor compatibility. However, the current state of virtual crossmatching fails to incorporate donor human leukocyte antigen (HLA) expression in the assessment, despite numerous studies that have demonstrated the impact of donor HLA expression on physical crossmatch outcomes. Whole-transcriptome sequencing (RNA-Seq) for HLA enables simultaneous determination of HLA genotyping and relative HLA expression. Ultimately the RNA-Seq needs to be faster to be incorporated into the virtual crossmatching process. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 23, 2019 Category: Pathology Authors: Maureen C. Montgomery, Chang Liu, Rosanne Petraroia, Eric T. Weimer Tags: Regular article Source Type: research

Tetraploid Partial Hydatidiform Moles
DNA genotyping studies have established that most partial hydatidiform moles (PHMs) are diandric dispermic triploid conceptions. Rare triandric tetraploid PHMs have been described, but genotyping cannot determine the manner in which three paternal chromosome complements are derived (one sperm with triplication, two sperm with one duplication, three different sperm, one diploid, and one haploid sperm). In a large prospective analysis of potentially molar products of conception, five tetraploid PHMs were encountered among 235 PHMs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 23, 2019 Category: Pathology Authors: Jennifer Bynum, Denise Batista, Rena Xian, Deyin Xing, James R. Eshleman, Brigitte M. Ronnett, Gang Zheng Tags: Regular article Source Type: research

Detection of ESR1 Mutations in Single Circulating Tumor Cells on Estrogen Deprivation Therapy but Not in Primary Tumors from Metastatic Luminal Breast Cancer Patients
Mutations in the ligand-binding domain (LBD) of the ESR1 gene result in resistance to estrogen deprivation therapy (EDT) in breast cancer. Their detection might enable optimization of therapy strategies. However, the predictive utility of the primary tumor (PT) is limited, and obtaining serial biopsies of metastatic lesions is challenging. To underline their application as a liquid biopsy, single circulating tumor cells (CTCs) were analyzed with a next-generation sequencing approach for the ESR1 coding region. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 23, 2019 Category: Pathology Authors: Andr é Franken, Ellen Honisch, Florian Reinhardt, Franziska Meier-Stiegen, Liwen Yang, Sandra Jaschinski, Irene Esposito, Barbara Alberter, Bernhard Polzer, Hanna Huebner, Peter A. Fasching, Sunil Pancholi, Lesley-Ann Martin, Eugen Ruckhaeberle, Fabienne Tags: Regular article Source Type: research

Detection of ESR1 Mutations in Single Circulating Tumor Cells upon Estrogen Deprivation Therapy but not in Primary Tumors from Metastatic Luminal Breast Cancer Patients
Mutations in the ligand-binding domain (LBD) of the ESR1 gene result in resistance to estrogen deprivation therapy (EDT) in breast cancer. Their detection might enable optimization of therapy strategies. However, the predictive utility of the primary tumor (PT) is limited and obtaining serial biopsies of metastatic lesions is challenging. To underline their application as a liquid biopsy, single circulating tumor cells (CTCs) were analyzed with a next generation sequencing approach for the ESR1 coding region. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 23, 2019 Category: Pathology Authors: Andr é Franken, Ellen Honisch, Florian Reinhardt, Franziska Meier-Stiegen, Liwen Yang, Sandra Jaschinski, Irene Esposito, Barbara Alberter, Bernhard Polzer, Hanna Huebner, Peter A. Fasching, Sunil Pancholi, Lesley-Ann Martin, Eugen Ruckhaeberle, Fabienne Tags: Regular article Source Type: research

Comparison of Real-Time quantitative PCR and digital droplet PCR for BCR-ABL1 Monitoring in Patients with Chronic Myeloid Leukemia
Real-time quantitative PCR (RT-qPCR) is routinely used to detect minimal residual disease in chronic myeloid leukemia patients. The absolute quantification with droplet digital PCR (dPCR) could reduce the inherent variability of RT-qPCR. We established a duplex dPCR assay using the EAC primer/probe system for BCR-ABL1 and ABL1 and compared the results to RT-qPCR. Two-hundred and thirty cDNA samples from patients with chronic myeloid leukemia were analyzed using both procedures. A second, commercially developed dPCR assay for BCR-ABL1 was also evaluated. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 23, 2019 Category: Pathology Authors: Georg-Nikolaus Franke, Jacqueline Maier, Kathrin Wildenberger, Michael Cross, Francis J. Giles, Martin C. M üller, Andreas Hochhaus, Dietger Niederwieser, Thoralf Lange Tags: Regular Article Source Type: research

Using nanopore RNA-Seq to HLA genotype and correlate donor HLA expression with flow cytometric crossmatch results
Transplant centers are increasingly using virtual crossmatching (VXM) to evaluate recipient and donor compatibility. However, the current state of VXM fails to incorporate donor HLA expression in the assessment, despite numerous studies that demonstrated the impact of donor HLA expression on physical crossmatch outcomes. Whole-transcriptome sequencing (RNA-Seq) for HLA enables simultaneous determination of HLA genotyping and relative HLA expression. Ultimately the RNA-Seq needs to be faster to incorporate into the VXM process. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 23, 2019 Category: Pathology Authors: Maureen C. Montgomery, Chang Liu, Rosanne Petraroia, Eric T. Weimer Tags: Regular Article Source Type: research

Tetraploid Partial Hydatidiform Moles Molecular Genotyping and Determination of Parental Contributions
DNA genotyping studies have established that most partial hydatidiform moles (PHM) are diandric dispermic triploid conceptions. Rare triandric tetraploid PHMs have been described but genotyping cannot determine the manner in which three paternal chromosome complements are derived (one sperm with triplication, two sperm with one duplication, three different sperm, one diploid, and one haploid sperm). In a large prospective analysis of potentially molar products of conception, five tetraploid PHMs were encountered among 235 PHMs. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 23, 2019 Category: Pathology Authors: Jennifer Bynum, Denise Batista, Rena Xian, Deyin Xing, James R. Eshleman, Brigitte M. Ronnett, Gang Zheng Source Type: research

The Journal of Molecular Diagnostics
This editorial highlights 20 years of JMD defining professional practice. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Authors: Barbara A. Zehnbauer Tags: Editorial Source Type: research

The Journal of Molecular Diagnostics
This guest editorial highlights 20 years of clinical innovation in JMD. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Authors: Timothy J. O'Leary Tags: Guest editorial Source Type: research

The Journal of Molecular Diagnostics
This guest editorial highlights 20 years of education and training by JMD. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Authors: Karen L. Kaul Tags: Guest editorial Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2019 Category: Pathology Source Type: research