Droplet Digital PCR for Mutation Detection in Formalin-Fixed, Paraffin-Embedded Melanoma Tissues
The identification of somatic mutations is crucial for guiding therapeutic decisions about personalized melanoma treatment. However, genetic analysis of tumors is usually performed on limited and often low-quality DNA from tumors with low tumor cellularity and high tumor heterogeneity. Different mutation-detection platforms exist, with varying analytical sensitivities. Here we evaluated the detection of common mutations in BRAF, NRAS, and TERT promoter in 40 melanoma FFPE tissues using Droplet Digital (dd)PCR, and compared the results to the detection rates obtained by Sanger sequencing and pyrosequencing. (Source: Journal...
Source: Journal of Molecular Diagnostics - January 2, 2018 Category: Pathology Authors: Ashleigh C. McEvoy, Benjamin A. Wood, Nima M. Ardakani, Michelle Pereira, Robert Pearce, Lester Cowell, Cleo Robinson, Fabienne Grieu-Iacopetta, Alexander J. Spicer, Benhur Amanuel, Melanie Ziman, Elin S. Gray Tags: Regular article Source Type: research

SNPitty: An intuitive web-application for interactive B-allele frequency and copy-number visualization of next-generation sequencing data
Exploration and visualization of next-generation sequencing data is crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions-of-interest coupled with dynamic heuristic filtering of genetic aberrations is however lacking. Therefore, we developed the web-application SNPitty that allows interactive visualization and interrogation of variant call format (VCF) files by utilizing B-allele frequencies of single nucleotide polymorphisms and single nucleotide variants, coverage metrics and copy-numbers analysis results. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - January 2, 2018 Category: Pathology Authors: Job van Riet, Niels M.G. Krol, Peggy N. Atmodimedjo, Erwin Brosens, Wilfred. F.J. van IJcken, Maurice P.H.M. Jansen, John W.M. Martens, Leendert H. Looijenga, Guido Jenster, Hendrikus J. Dubbink, Winand N.M. Dinjens, Harmen J.G. van de Werken Tags: Technical Advance Source Type: research

Droplet Digital PCR for Mutation Detection in Formalin-Fixed, Paraffin-Embedded Melanoma Tissues: A Comparison with Sanger Sequencing and Pyrosequencing
Identification of somatic mutations is crucial to guide therapeutic decisions for personalized melanoma treatment. However, genetic analysis of the tumor is usually performed on limited and often low-quality DNA, from tumors with low tumor cellularity and high tumor heterogeneity. Different mutation detection platforms exist with varying analytical sensitivities. Here we evaluated the detection of common mutations in BRAF, NRAS, and TERT-promoter in 40 melanoma formalin-fixed, paraffin-embedded tissues using droplet digital PCR (ddPCR), and compared the results to the detection rate obtained by Sanger sequencing and pyrose...
Source: Journal of Molecular Diagnostics - January 2, 2018 Category: Pathology Authors: Ashleigh C. McEvoy, Benjamin A. Wood, Nima M. Ardakani, Michelle Pereira, Robert Pearce, Lester Cowell, Cleo Robinson, Fabienne Grieu-Iacopetta, Alexander J. Spicer, Benhur Amanuel, Melanie Ziman, Elin S. Gray Tags: Regular Article Source Type: research

Evaluation of Diagnostic Utility of a High-Risk Human Papillomavirus PCR Test on Formalin-Fixed, Paraffin-Embedded Head and Neck Tumor Tissues
The increasing prevalence of high-risk human papillomavirus (HR-HPV) –associated head and neck squamous cell carcinoma (HNSCC) has prompted strong clinical demands for detecting HR-HPV directly in the tumor. Although p16 immunohistochemistry (IHC) has been the standard testing method, it has limitations including false positivity, lack of sensitivity in low tumor c ell samples such as fine-needle aspirate (FNA), and its subjectivity. We developed a modified method based on the Roche Cobas 4800 HR-HPV PCR assay and evaluated the performance characteristics and the diagnostic utility of this assay for direct HR-HPV det...
Source: Journal of Molecular Diagnostics - December 19, 2017 Category: Pathology Authors: Albert Njoroge Huho, Nour Yadak, Th èrése Jeanne Bocklage, Shangxin Yang Tags: Regular article Source Type: research

A Novel and Reliable Method to Detect Microsatellite Instability in Colorectal Cancer by Next-Generation Sequencing
Two types of molecular tests have been established to assess the deficiency of DNA mismatch repair (MMR) system: microsatellite instability (MSI) and immunohistochemical (IHC) analysis. We have developed a reliable method to analyze the MSI status by next-generation sequencing (NGS) based on read count distribution. A total of 91 patients with primary colorectal cancer were recruited. These patients included 54 cases with the loss of expression of any MMR protein in IHC suggesting deficient MMR (dMMR), and 37 cases of colorectal cancer with staining of all four MMR proteins in IHC, suggesting proficient MMR (pMMR) in posto...
Source: Journal of Molecular Diagnostics - December 19, 2017 Category: Pathology Authors: Lizhen Zhu, Yanqin Huang, Xuefeng Fang, Chenglin Liu, Wanglong Deng, Chenhan Zhong, Jinghong Xu, Dong Xu, Ying Yuan Tags: Regular article Source Type: research

Evaluation of Diagnostic Utility of a High-Risk Human Papillomavirus PCR Test on Formalin Fixed, Paraffin-Embedded Head and Neck Tumor Tissues
The increasing prevalence of high-risk human papillomavirus (HR-HPV) –associated head and neck squamous cell carcinoma (HNSCC) has prompted strong clinical demands for detecting HR-HPV directly in the tumor. Although p16 immunohistochemistry (IHC) has been the standard testing method, it has limitations including false positivity, lack of sensitivity in low tumor c ell samples such as fine needle aspirate (FNA), and its subjectivity. We developed a modified method based on the Roche Cobas 4800 HR-HPV PCR assay and evaluated the performance characteristics and the diagnostic utility of this assay for direct HR-HPV det...
Source: Journal of Molecular Diagnostics - December 19, 2017 Category: Pathology Authors: Albert Njoroge Huho, Nour Yadak, Th èrése Jeanne Bocklage, Shangxin Yang Tags: Regular Article Source Type: research

Evaluation of a Urine-Based Rapid Molecular Diagnostic Test with Potential to be used at Point-of-Care for Pulmonary Tuberculosis: Cape Town Cohort
In this study, a new urine-based Tr-DNA molecular assay was evaluated for diagnosis of pulmonary tuberculosis among 428 adult pulmonary TB suspects (164 HIV-positive, 263 HIV-negative) from Cape Town, South Africa. Tr-DNA was isolated from 4 mL EDTA urine, and rapid double-stranded primer-based PCR method performed targeting Mycobacterium tuberculosis–specific direct repeat region. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2017 Category: Pathology Authors: Krutarth Patel, Matilde Nagel, Maria Wesolowski, Stefan Dees, Eric Rivera-Milla, Christof Geldmacher, Keertan Dheda, Michael Hoelscher, Ines Labugger Tags: Regular Article Source Type: research

Comprehensive Genomic Profiling of Malignant Effusions in Patients with Metastatic Lung Adenocarcinoma
Cytology samples are being increasingly utilized for comprehensive molecular testing. Although fine-needle aspirates are adequate substrates for high-throughput sequencing, the suitability of malignant body fluids remains largely unexplored. Herein, we investigated the adequacy and utility of performing targeted next-generation sequencing (NGS) on malignant effusions from patients with metastatic lung adenocarcinoma. Thirty-two effusion samples that were submitted for hybrid capture –based NGS using a clinically validated solid tumor genotyping panel were examined. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2017 Category: Pathology Authors: Soo-Ryum Yang, Chieh-Yu Lin, Henning Stehr, Steven R. Long, Christina S. Kong, Gerald J. Berry, James L. Zehnder, Christian A. Kunder Tags: Regular Article Source Type: research

Conventional and single-molecule targeted sequencing method for specific variant detection in IKBKG whilst bypassing the IKBKGP1 pseudogene
In addition to Sanger sequencing, next-generation sequencing of gene panels and exomes has emerged as a standard diagnostic tool in many laboratories. However, these captures can miss regions, have poor efficiency, or capture pseudogenes which hamper proper diagnoses. One such example is the primary immunodeficiency –associated gene IKBKG. Its pseudogene IKBKGP1 makes traditional capture methods aspecific. We therefore developed a long-range PCR method to efficiently target IKBKG, as well as two associated genes (IRAK4 and MYD88), whilst bypassing the IKBKGP1 pseudogene. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 18, 2017 Category: Pathology Authors: Glynis Frans, Wim Meert, Jutte Van der Werff Ten Bosch, Isabelle Meyts, Xavier Bossuyt, Joris R. Vermeesch, Matthew S. Hestand Tags: Regular Article Source Type: research

The history and impact of molecular coding changes on coverage and reimbursement of molecular diagnostic tests: transition from stacking codes to the current molecular code set including genomic sequencing procedures
Changes in coding and coverage create uncertain reimbursement environment for molecular pathology laboratories. We analyzed our experience with two representative molecular oncology tests: a T-cell receptor (TCR) beta rearrangement test and a large (467 gene) cancer next-generation sequencing panel the Columbia Combined Cancer Panel, CCCP. Prior to 2013, the TCR beta test was coded using “stacked” current procedural terminology codes and subsequently transitioned to a tier 1 code. CCCP was coded using a combination of tier 1 and 2 codes until 2015, when a new Genomic Sequencing Procedure code was adopted. (Sour...
Source: Journal of Molecular Diagnostics - December 18, 2017 Category: Pathology Authors: Susan J. Hsiao, Mahesh M. Mansukhani, Melissa C. Carter, Anthony N. Sireci Tags: Regular Article Source Type: research

Identification of Germline Variants in Tumor Genomic Sequencing Analysis
This Correspondence relates to the article by Li et  al (Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and the College of American Pathologists. J Mol Diagn 2017, 19:4–23). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 14, 2017 Category: Pathology Authors: Nathan D. Montgomery, Sara R. Selitsky, Nirali M. Patel, D. Neil Hayes, Joel S. Parker, Karen E. Weck Tags: Correspondence Source Type: research

Navigating the Peer Review Process
This editorial provides insights and guidelines for publishing in The Journal of Molecular Diagnostics. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 14, 2017 Category: Pathology Authors: Barbara Zehnbauer, Emily H. Essex, Chhavi Chauhan Tags: Editorial Source Type: research

Authors' Reply
to the Letter to the Editor by Montgomery et  al (Identification of Germline Variants in Tumor Genomic Sequencing Analysis. J Mol Diagn 2017, 19:XXXX–XXXX). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 14, 2017 Category: Pathology Authors: Marilyn M. Li, Michael Datto, Eric J. Duncavage, Shashikant Kulkarni, Neal I. Lindeman, Somak Roy, Apostolia M. Tsimberidou, Cindy L. Vnencak-Jones, Daynna J. Wolff, Anas Younes, Marina N. Nikiforova Tags: Correspondence Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 14, 2017 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 14, 2017 Category: Pathology Source Type: research

Instructions to Authors
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 14, 2017 Category: Pathology Source Type: research

Scientific Integrity Policy
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 14, 2017 Category: Pathology Source Type: research

Simple Detection of Telomere Fusions in Pancreatic Cancer, Intraductal Papillary Mucinous Neoplasm, and Pancreatic Cyst Fluid
Telomere end-to-end fusions are an important source of chromosomal instability that arise in cells with critically shortened telomeres. We developed a nested real-time quantitative PCR method for telomere fusion detection in pancreatic ductal adenocarcinomas, intraductal papillary mucinous neoplasms (IPMNs), and IPMN cyst fluids. Ninety-one pancreatic cancer cell lines and xenograft samples, 93 IPMNs, and 93 surgically aspirated IPMN cyst fluid samples were analyzed. The association between telomere shortening, telomerase activity, and telomere fusion detection was evaluated. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - December 8, 2017 Category: Pathology Authors: Tatsuo Hata, Marco Dal Molin, Anne McGregor-Das, Tae Jun Song, Christopher Wolfgang, James R. Eshleman, Ralph H. Hruban, Michael Goggins Tags: Regular article Source Type: research

Telomere Diagnostics for Pancreatic Neoplasms and Cysts
This commentary highlights the article by Hata et  al that examines markers for assessing neoplastic progression. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 15, 2017 Category: Pathology Authors: Loren Joseph Tags: Commentary Source Type: research

Is Tubulocystic Renal Cell Carcinoma Real?
This commentary highlights the article by Lawrie et  al that validates that tubulocystic renal cell carcinoma is a distinct type of renal neoplasm. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 15, 2017 Category: Pathology Authors: Yi Ding, Hiroshi Miyamoto, Paul G. Rothberg Tags: Commentary Source Type: research

Commentary: Telomere Diagnostics for Pancreatic Neoplasms and Cysts
Advances in imaging of the pancreas have led to a dramatic increase in the frequency of presymptomatic detection of lesions. This is especially problematic because of the difficulty in sampling pancreatic lesions, the morbidity in resecting even small lesions, and the dismal prognosis of pancreatic ductal adenocarcinoma (PDAC) despite early detection. Although some lesions have both a solid and a cystic component, frequently only a cyst is present. The majority of lesions found incidentally do not represent PDAC, but several classes of neoplasms have an increased risk of progression to PDAC. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 15, 2017 Category: Pathology Authors: Loren Joseph Tags: Commentary Source Type: research

Is Tubulocystic Renal Cell Carcinoma Real? Genomic Analysis Confirms the WHO Classification
This commentary highlights the article by Lawrie et al that validates that tubulocystic renal cell carcinoma is a distinct type of renal neoplasm. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 15, 2017 Category: Pathology Authors: Yi Ding, Hiroshi Miyamoto, Paul G. Rothberg Tags: Commentary Source Type: research

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Because of the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 14, 2017 Category: Pathology Authors: Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize S. Kip, Eric W. Klee, Stephen E. Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L. Temple-Smolkin, Karl V. Voelkerding, Chen Wang, Alexis B. Carter Tags: Special article Source Type: research

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines: A Joint Recommendation of the Association for Molecular Pathology and College of American Pathologists
Bioinformatics pipelines are an integral component of next-generation sequencing (NGS). Processing raw sequence data to detect genomic alterations has significant impact on disease management and patient care. Due to the lack of published guidance, there is currently a high degree of variability in how members of the global molecular genetics and pathology community establish and validate bioinformatics pipelines. Improperly developed, validated, and/or monitored pipelines may generate inaccurate results that may have negative consequences for patient care. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 14, 2017 Category: Pathology Authors: Somak Roy, Christopher Coldren, Arivarasan Karunamurthy, Nefize Sertac Kip, Eric W. Klee, Stephen E. Lincoln, Annette Leon, Mrudula Pullambhatla, Robyn L. Temple-Smolkin, Karl V. Voelkerding, Chen Wang, Alexis B. Carter Tags: Special Article Source Type: research

Development and Evaluation of a Pan-Sarcoma Fusion Gene Detection Assay Using the NanoString nCounter Platform
The NanoString nCounter assay is a high-throughput hybridization technique using target-specific probes that can be customized to test for numerous fusion transcripts in a single assay utilizing RNA from formalin-fixed, paraffin-embedded material. We designed a NanoString assay targeting 174 unique fusion junctions in 25 sarcoma types. The study cohort comprised 212 cases, 96 of which showed fusion gene expression by the NanoString assay, including all 20 Ewing sarcomas, 11 synovial sarcomas, and five myxoid liposarcomas tested. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - November 2, 2017 Category: Pathology Authors: Kenneth Tou En Chang, Angela Goytain, Tracy Tucker, Aly Karsan, Cheng-Han Lee, Torsten O. Nielsen, Tony L. Ng Tags: Regular article Source Type: research

Editorial Board
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 21, 2017 Category: Pathology Source Type: research

Table of Contents
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 21, 2017 Category: Pathology Source Type: research

Title Page
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 21, 2017 Category: Pathology Source Type: research

Disclosure Statement
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 21, 2017 Category: Pathology Source Type: research

Abstracts
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 21, 2017 Category: Pathology Source Type: research

Author Index
(Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 21, 2017 Category: Pathology Source Type: research

Heterogeneity of BRAF, NRAS, and TERT Promoter Mutational Status in Multiple Melanomas and Association with MC1R Genotype
Data on somatic heterogeneity and germline –somatic interaction in multiple primary melanoma (MPM) patients are limited. We investigated the mutational status of BRAF, NRAS, and TERT promoter genes, the most common genetic alterations in melanoma, in 97 melanomas of 44 MPM patients and compared molecular and immunohistochemical findings. W e further evaluated the association of somatic alterations with the germline MC1R genotype. Mutations in the BRAF gene were identified in 41.2% (40/97) of melanomas, in NRAS in 2.1% (2/97), and in TERT promoter in 19.6% (19/97). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 20, 2017 Category: Pathology Authors: Cristina Pellegrini, Lucia Di Nardo, Gianluca Cipolloni, Claudia Martorelli, Marina De Padova, Ambra Antonini, Maria Giovanna Maturo, Laura Del Regno, Sara Strafella, Tamara Micantonio, Pietro Leocata, Ketty Peris, Maria Concetta Fargnoli Tags: Regular article Source Type: research

Evaluation of a next-generation sequencing assay for BRCA1 and BRCA2 mutation detection
The efficiency of a novel targeted next-generation sequencing (NGS) test, the Devyser BRCA kit, for a comprehensive analysis of all 48 coding exons of the high-risk breast/ovarian cancer susceptibility genes BRCA1 and BRCA2 has been assessed. The new assay intended to detect nucleotide substitutions, small deletions/insertions, and large deletions/duplications. To document the false-negative and false-positive rates of the NGS assay in the hands of end-users, 48 samples with previously identified 444 small-size variants and seven gross rearrangements were analyzed, showing 100% concordance with gold standards. (Source: Jou...
Source: Journal of Molecular Diagnostics - October 20, 2017 Category: Pathology Authors: Gabriele Lorenzo Capone, Anna Laura Putignano, Sharon Trujillo Saavedra, Irene Paganini, Roberta Sestini, Francesca Gensini, Irene De Rienzo, Laura Papi, Berardino Porfirio Tags: Regular Article Source Type: research

Analytical Validation of a Next-Generation Sequencing Assay to Monitor Immune Responses in Solid Tumors
We have developed a next-generation sequencing assay to quantify biomarkers of the host immune response in formalin-fixed, paraffin-embedded (FFPE) tumor specimens. This assay aims to provide clinicians with a comprehensive characterization of the immunological tumor microenvironment as a guide for therapeutic decisions on patients with solid tumors. The assay relies on RNA-seq to semi-quantitatively measure the levels of 43 transcripts related to anticancer immune responses and 11 transcripts reflecting the relative abundance of tumor-infiltrating lymphocytes, as well as on DNA-seq to estimate mutational burden. (Source: ...
Source: Journal of Molecular Diagnostics - October 20, 2017 Category: Pathology Authors: Jeffrey M. Conroy, Sarabjot Pabla, Sean T. Glenn, Blake Burgher, Mary Nesline, Antonios Papanicolau-Sengos, Jonathan Andreas, Vincent Giamo, Felicia L. Lenzo, Fiona C.L. Hyland, Angela Omilian, Wiam Bshara, Moachun Qin, Ji He, Igor Puzanov, Marc S. Ernsto Tags: Regular Article Source Type: research

Heterogeneity Of Braf, Nras, And Tert-Promoter Mutational Status In Multiple Melanomas And Association With Mc1r Genotype: Findings From Molecular And Immunohistochemical Analysis
Data on somatic heterogeneity and germline-somatic interaction in multiple primary melanoma (MPM) patients are limited. We investigated the mutational status of BRAF, NRAS, and TERT-promoter genes, the most common genetic alterations in melanoma, in 97 melanomas of 44 MPM patients and compared molecular and immunohistochemical findings. We further evaluated the association of somatic alterations with the germline MC1R genotype. Mutations in the BRAF gene were identified in 41.2% (40/97) of melanomas, in NRAS in 2.1% (2/97) and, in TERT-promoter in 19.6% (19/97). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 20, 2017 Category: Pathology Authors: Cristina Pellegrini, Lucia Di Nardo, Gianluca Cipolloni, Claudia Martorelli, Marina De Padova, Ambra Antonini, Maria Giovanna Maturo, Laura Del Regno, Sara Strafella, Tamara Micantonio, Pietro Leocata, Ketty Peris, Maria Concetta Fargnoli Tags: Regular Article Source Type: research

Noncoding RNA Expression and Targeted Next-Generation Sequencing Distinguish Tubulocystic Renal Cell Carcinoma (TC-RCC) from Other Renal Neoplasms
Tubulocystic renal cell carcinoma (TC-RCC) is a rare recently described renal neoplasm characterized by gross, microscopic, and immunohistochemical differences from other renal tumor types and was recently classified as a distinct entity. However, this distinction remains controversial particularly because some genetic studies suggest a close relationship with papillary RCC (PRCC). The molecular basis of this disease remains largely unexplored. We therefore performed noncoding (nc) RNA/miRNA expression analysis and targeted next-generation sequencing mutational profiling on 13 TC-RCC cases (11 pure, two mixed TC-RCC/PRCC) ...
Source: Journal of Molecular Diagnostics - October 19, 2017 Category: Pathology Authors: Charles H. Lawrie, Mar ía Armesto, Marta Fernandez-Mercado, María Arestín, Lorea Manterola, Ibai Goicoechea, Erika Larrea, María M. Caffarel, Angela M. Araujo, Carla Sole, Maris Sperga, Isabel Alvarado-Cabrero, Michal Michal, Ondrej Hes, José I. Lóp Tags: Regular article Source Type: research

Non-coding RNA expression and targeted next-generation sequencing distinguish Tubulocystic Renal Cell Carcinoma (TC-RCC) from other renal neoplasms
Tubulocystic renal cell carcinoma (TC-RCC) is a rare recently described renal neoplasm characterized by gross, microscopic and immunohistochemical differences from other renal tumor types that was recently classified as a distinct entity. However, this distinction remains controversial particularly as some genetic studies suggest a close relationship with papillary renal cell carcinoma (PRCC). The molecular basis of this disease remains largely unexplored. We therefore performed non-coding (nc)RNA/miRNA expression analysis and targeted next-generation sequencing mutational profiling on 13 TC-RCC cases (11 pure, two mixed T...
Source: Journal of Molecular Diagnostics - October 19, 2017 Category: Pathology Authors: Charles H. Lawrie, Mar ía Armesto, Marta Fernandez-Mercado, María Arestín, Lorea Manterola, Ibai Goicoechea, Erika Larrea, María M. Caffarel, Angela M. Araujo, Carla Sole, Maris Sperga, Isabel Alvarado-Cabrero, Michal Michal, Ondrej Hes, José I. Lóp Tags: Regular Article Source Type: research

Identification of Enteric Viruses in Oral Swabs from Children with Acute Gastroenteritis
Stool is the diagnostic specimen of choice to identify enteropathogens in pediatric gastroenteritis. However, stool collection is challenging and its diagnostic characteristics in patients with isolated vomiting are unknown. Therefore, we evaluated if oral swabs are a suitable alternative specimen to stool specimens. Seven-hundred and thirty-eight oral swabs and 577 stool specimens were collected from 738 children with vomiting and/or diarrhea. All specimens were tested by a laboratory-developed RT-qPCR Gastroenteritis Virus Panel (GVP) for virus identification; 150 oral swabs and 577 stool specimens were tested by the Lum...
Source: Journal of Molecular Diagnostics - October 19, 2017 Category: Pathology Authors: Ran Zhuo, Brendon D. Parsons, Bonita E. Lee, Steven J. Drews, Linda Chui, Marie Louie, Bryanne Crago, Stephen B. Freedman, Samina Ali, Xiaoli Pang Tags: Regular Article Source Type: research

Plasmodium detection and differentiation by direct-on-blood PCR Nucleic Acid Lateral Flow Immunoassay (db-PCR-NALFIA): development, validation, and evaluation
Declining malaria transmission warrants the search for highly sensitive point-of-care diagnostics, especially in resource-limiting settings. Db-PCR-NALFIA is a simplified PCR-based technique with a lateral flow readout that does not require any sample preparation. Two duplex db-PCR-NALFIAs were developed: a pan-Plasmodium/P. falciparum and a pan-Plasmodium/P. vivax assay. Confirmed positive samples from returning travelers (n=61) and negative controls (n=40) were used for laboratory validations. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 19, 2017 Category: Pathology Authors: Johanna M. Roth, Laura de Bes, Patrick Sawa, George Omweri, Victor Osoti, Boris Oberheitmann, Henk D.F.H. Schallig, P ètra F. Mens Tags: Regular Article Source Type: research

Determination of Molecular Subtypes of Diffuse Large B-Cell Lymphoma Using a Reverse Transcriptase Multiplex Ligation-Dependent Probe Amplification Classifier
Diffuse large B-cell lymphoma (DLBCL) is the most common non-Hodgkin lymphoma. It includes three major subtypes termed germinal center B-cell-like, activated B-cell-like, and primary mediastinal B-cell lymphoma. With the emergence of novel targeted therapies, accurate methods capable of interrogating this cell-of-origin classification should soon become essential in the clinics. To address this issue, we developed a novel gene expression profiling DLBCL classifier based on reverse transcriptase multiplex ligation-dependent probe amplification. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - October 17, 2017 Category: Pathology Authors: Victor Bob ée, Philippe Ruminy, Vinciane Marchand, Pierre-Julien Viailly, Ahmad Abdel Sater, Liana Veresezan, Fanny Drieux, Caroline Bérard, Elodie Bohers, Sylvain Mareschal, Sydney Dubois, Jean-Philippe Jais, Karen Leroy, Martin Figeac, Jean-Michel Pic Tags: Regular article Source Type: research

Hepatitis C and the Impact of Host Genetics
This commentary highlights the article by Enache et  al that describes a diagnostic test for simultaneous genotyping of specific single nucleotide polymorphisms in chronic hepatitis C patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 26, 2017 Category: Pathology Authors: Linda Cook Tags: Commentary Source Type: research

HCV and the Impact of Host Genetics
This commentary highlights the article by Enache et al that describes a diagnostic test for simultaneous genotyping of specific single nucleotide polymorphisms in chronic hepatitis C patients. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 26, 2017 Category: Pathology Authors: Linda Cook Tags: Commentary Source Type: research

Molecular Signatures for Tumor Classification
Cancer classification in the clinic is primarily based on histological analysis in the proper clinical context, often supplemented by immunohistochemical and molecular studies. Recent genomic studies have shown the potential of integrated multiomics platforms for molecular classification. We performed unsupervised analyses of molecular platforms in The Cancer Genome Atlas data (n  = 6216 samples) in comparison with tumor type. Our data showed that mRNA signatures and DNA methylation signatures mapped to histological diagnosis with high accuracy (95% and 88%, respectively) as individual platforms. (Source: Journal...
Source: Journal of Molecular Diagnostics - September 1, 2017 Category: Pathology Authors: Yasin Mamatjan, Sameer Agnihotri, Anna Goldenberg, Peter Tonge, Sheila Mansouri, Gelareh Zadeh, Kenneth Aldape Tags: Regular Article Source Type: research

Molecular Signatures for Tumor Classification An Analysis of TCGA Data
Cancer classification in the clinic is primarily based on histological analysis in the proper clinical context, often supplemented by immunohistochemical and molecular studies. Recent genomic studies have shown the potential of integrated multiomics platforms for molecular classification. We performed unsupervised analyses of molecular platforms in TCGA data (n  = 6216 samples) in comparison with tumor type. Our data showed that mRNA signatures and DNA methylation signatures mapped to histological diagnosis with high accuracy (95% and 88%, respectively) as individual platforms. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 1, 2017 Category: Pathology Authors: Yasin Mamatjan, Sameer Agnihotri, Anna Goldenberg, Peter Tonge, Sheila Mansouri, Gelareh Zadeh, Kenneth Aldape Tags: Regular Article Source Type: research

High-Throughput and Sensitive Quantification of Circulating Tumor DNA by Microfluidic-Based Multiplex PCR and Next-Generation Sequencing
Circulating tumor DNA (ctDNA) has potential to serve as a biomarker for noninvasive monitoring of treatment response and disease progression. However, broad clinical applicability of ctDNA has been limited by the low sensitivity, throughput and patient coverage offered by existing ctDNA detection methods. Here we report the adaptation and characterization of the MMP-Seq technology for high-throughput and sensitive quantitation of ctDNA. A multiplex PCR preamplification (PreAmp) step was developed and incorporated into the MMP-seq workflow to enable low input ctDNA analysis with enhanced sensitivity. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 1, 2017 Category: Pathology Authors: Yinghui Guan, Oleg Mayba, Thomas Sandmann, Shan Lu, Younjeong Choi, Walter C. Darbonne, Vincent Leveque, Lisa Ryner, Eric Humke, Nga Wan Rachel Tam, Sundari Sujathasarma, Anna Cheung, Richard Bourgon, Mark R. Lackner, Yulei Wang Tags: Regular Article Source Type: research

Characterization and Genomic Localization of a SMAD4 Processed Pseudogene
Like many clinical diagnostic laboratories, we undertake routine investigation of cancer-predisposed individuals by high-throughput sequencing of patient DNA that has been target-enriched for genes associated with hereditary cancer. Accurate diagnosis using such reagents requires alertness against rare nonpathogenic variants that may interfere with variant calling. In a cohort of 2042 such cases, we identified five that initially appeared to be carriers of a 95-bp deletion of SMAD4 intron 6. More detailed analysis indicated that these individuals all carried one copy of a SMAD4 processed gene. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - September 1, 2017 Category: Pathology Authors: Christopher M. Watson, Nick Camm, Laura A. Crinnion, Agne Antanaviciute, Julian Adlard, Alexander F. Markham, Ian M. Carr, Ruth Charlton, David T. Bonthron Tags: Regular Article Source Type: research

Next-Generation Sequencing
This study evaluated whether next-generation sequencing (NGS) using the 50-gene AmpliSeq Cancer Hotspot Panel version 2 can help facilitate this distinction. NGS was performed on known primary-metastatic pairs (8 patients) and multiple lung adenocarcinomas (11 patients). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 30, 2017 Category: Pathology Authors: Snehal B. Patel, Wendy Kadi, Ann E. Walts, Alberto M. Marchevsky, Andy Pao, Angela Aguiluz, Tudor Mudalige, Zhenqui Liu, Nan Deng, Jean Lopategui Tags: Regular Article Source Type: research

Next Generation Sequencing A Novel Approach to Distinguish Multifocal Primary Lung Adenocarcinomas from Intrapulmonary Metastases
Distinguishing between multiple lung primaries and intrapulmonary metastases is imperative for accurate staging. The American Joint Committee on Cancer (AJCC) criteria are routinely used for this purpose but can yield equivocal conclusions. We evaluated whether next generation sequencing (NGS) using the 50 gene AmpliSeq Cancer Hotspot Panel v2 can be used to facilitate this distinction. NGS was performed on known primary-metastatic pairs (8 patients) and multiple lung adenocarcinomas (11 patients). (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 30, 2017 Category: Pathology Authors: Snehal B. Patel, Wendy Kadi, Ann E. Walts, Alberto M. Marchevsky, Andy Pao, Angela Aguiluz, Tudor Mudalige, Zhenqui Liu, Nan Deng, Jean Lopategui Tags: Regular Article Source Type: research

Triplex High-Resolution Melting Assay for the Simultaneous Assessment of IFNL3 rs12979860, ABCB11 rs2287622, and RNF7 rs16851720 Genotypes in Chronic Hepatitis C Patients
Chronic hepatitis C (CHC) is a leading cause of liver disease. Despite the improved efficacy of new antivirals, their high costs preclude their adoption in resource-limited settings, where CHC prevalence is highest. We developed a triplex high-resolution melting assay for the simultaneous assessment of three genetic polymorphisms related to the response to treatment and development of advanced fibrosis in CHC: IFNL3 rs12979860, ABCB11 rs2287622, and RNF7 rs16851720. We validated the assay in clinical samples from 130 CHC patients treated with classic therapy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 28, 2017 Category: Pathology Authors: Elena L. Enache, Anca Sin, Liviu S. Enache, Ligia Bancu Tags: Regular Article Source Type: research

Triplex HRM assay for the simultaneous assessment of IL28B rs12979860, ABCB11 rs2287622, and RNF7 rs16851720 genotypes in chronic hepatitis C patients
Chronic hepatitis C (CHC) is a leading cause of liver disease. Despite the improved efficacy of new antivirals, their high costs preclude their adoption in resource-limited settings, where CHC prevalence is highest. We developed a triplex high resolution melting assay for the simultaneous assessment of three genetic polymorphisms related to the response to treatment and development of advanced fibrosis in CHC: IL28B rs12979860, ABCB11 rs2287622, and RNF7 rs16851720. We validated the assay in clinical samples from 130 CHC patients treated with classical therapy. (Source: Journal of Molecular Diagnostics)
Source: Journal of Molecular Diagnostics - August 28, 2017 Category: Pathology Authors: Elena Luminita Enache, Anca Sin, Liviu Sorin Enache, Ligia Bancu Tags: Regular Article Source Type: research