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Journal of Molecular Diagnostics: JMD

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https://www.readbyqxmd.com/read/29154853/standards-and-guidelines-for-validating-next-generation-sequencing-bioinformatics-pipelines-a-joint-recommendation-of-the-association-for-molecular-pathology-and-the-college-of-american-pathologists
#1
REVIEW
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
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...
November 17, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29104083/development-and-evaluation-of-a-pan-sarcoma-fusion-gene-detection-assay-using-the-nanostring-ncounter-platform
#2
Kenneth Tou En Chang, Angela Goytain, Tracy Tucker, Aly Karsan, Cheng-Han Lee, Torsten O Nielsen, Tony L Ng
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...
November 2, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29155049/is-tubulocystic-renal-cell-carcinoma-real-genomic-analysis-confirms-the-who-classification
#3
Yi Ding, Hiroshi Miyamoto, Paul G Rothberg
This commentary highlights the article by Lawrie et al that validates that tubulocystic renal cell carcinoma is a distinct type of renal neoplasm.
November 15, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29155048/telomere-diagnostics-for-pancreatic-neoplasms-and-cysts
#4
Loren Joseph
This commentary highlights the article by Hata et al that examines markers for assessing neoplastic progression.
November 15, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29061376/heterogeneity-of-braf-nras-and-tert-promoter-mutational-status-in-multiple-melanomas-and-association-with-mc1r-genotype-findings-from-molecular-and-immunohistochemical-analysis
#5
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
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...
October 20, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29061375/evaluation-of-a-next-generation-sequencing-assay-for-brca1-and-brca2-mutation-detection
#6
Gabriele Lorenzo Capone, Anna Laura Putignano, Sharon Trujillo Saavedra, Irene Paganini, Roberta Sestini, Francesca Gensini, Irene De Rienzo, Laura Papi, Berardino Porfirio
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...
October 20, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29061374/analytical-validation-of-a-next-generation-sequencing-assay-to-monitor-immune-responses-in-solid-tumors
#7
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 Ernstoff, Mark Gardner, Lorenzo Galluzzi, Carl Morrison
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 immunologic tumor microenvironment as a guide for therapeutic decisions on patients with solid tumors. The assay relies on RNA-sequencing (seq) to semiquantitatively measure the levels of 43 transcripts related to anticancer immune responses and 11 transcripts that reflect the relative abundance of tumor-infiltrating lymphocytes, as well as on DNA-seq to estimate mutational burden...
October 20, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29056575/identification-of-enteric-viruses-in-oral-swabs-from-children-with-acute-gastroenteritis
#8
Ran Zhuo, Brendon D Parsons, Bonita E Lee, Steven J Drews, Linda Chui, Marie Louie, Bryanne Crago, Stephen B Freedman, Samina Ali, Xiaoli Pang
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 Luminex xTAG Gastrointestinal Pathogen Panel (GPP)...
October 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29056574/plasmodium-detection-and-differentiation-by-direct-on-blood-pcr-nucleic-acid-lateral-flow-immunoassay-development-validation-and-evaluation
#9
Johanna M Roth, Laura de Bes, Patrick Sawa, George Omweri, Victor Osoti, Boris Oberheitmann, Henk D F H Schallig, Pètra F Mens
Decreasing malaria transmission warrants the search for highly sensitive point-of-care diagnostics, especially in resource-limited settings. The direct-on-blood PCR nucleic acid lateral flow immunoassay (db-PCR-NALFIA) is a simplified PCR-based technique with a lateral flow readout that does not require sample preparation. Two duplex db-PCR-NALFIAs were developed: a pan-Plasmodium/Plasmodium falciparum (pan/P. falciparum) and a pan-Plasmodium/Plasmodium vivax (pan/P. vivax) assay. Confirmed positive (n = 61) and negative controls (n = 40) were used for laboratory validations...
October 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29056573/non-coding-rna-expression-and-targeted-next-generation-sequencing-distinguish-tubulocystic-renal-cell-carcinoma-tc-rcc-from-other-renal-neoplasms
#10
Charles H Lawrie, María 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 López
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) and compared with other renal neoplasms...
October 19, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28963021/hcv-and-the-impact-of-host-genetics
#11
Linda Cook
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.
September 27, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28867605/high-throughput-and-sensitive-quantification-of-circulating-tumor-dna-by-microfluidic-based-multiplex-pcr-and-next-generation-sequencing
#12
Yinghui Guan, Oleg Mayba, Thomas Sandmann, Shan Lu, Younjeong Choi, Walter C Darbonne, Vincent Leveque, Lisa Ryner, Eric Humke, Nga W R Tam, Sundari Sujathasarma, Anna Cheung, Richard Bourgon, Mark R Lackner, Yulei Wang
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. Herein, we report the adaptation and characterization of the microfluidics multiplex PCR sequencing technology for high-throughput and sensitive quantitation of ctDNA. A multiplex PCR preamplification step was developed and incorporated into the microfluidics multiplex PCR sequencing work flow to enable low-input ctDNA analysis with enhanced sensitivity...
September 1, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28867604/characterization-and-genomic-localization-of-a-smad4-processed-pseudogene
#13
Christopher M Watson, Nick Camm, Laura A Crinnion, Agne Antanaviciute, Julian Adlard, Alexander F Markham, Ian M Carr, Ruth Charlton, David T Bonthron
Like many clinical diagnostic laboratories, the Yorkshire Regional Genetics Service undertakes 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 regarding rare nonpathogenic variants that may interfere with variant calling. In a cohort of 2042 such cases, we identified 5 that initially appeared to be carriers of a 95-bp deletion of SMAD4 intron 6...
September 1, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28867603/molecular-signatures-for-tumor-classification-an-analysis-of-the-cancer-genome-atlas-data
#14
Yasin Mamatjan, Sameer Agnihotri, Anna Goldenberg, Peter Tonge, Sheila Mansouri, Gelareh Zadeh, Kenneth Aldape
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...
September 1, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28866070/next-generation-sequencing-a-novel-approach-to-distinguish-multifocal-primary-lung-adenocarcinomas-from-intrapulmonary-metastases
#15
Snehal B Patel, Wendy Kadi, Ann E Walts, Alberto M Marchevsky, Andy Pao, Angela Aguiluz, Tudor Mudalige, Zhenqui Liu, Nan Deng, Jean Lopategui
Distinguishing between multiple lung primary tumors 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. 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)...
September 1, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28860020/triplex-high-resolution-melting-assay-for-the-simultaneous-assessment-of-ifnl3-rs12979860-abcb11-rs2287622-and-rnf7-rs16851720-genotypes-in-chronic-hepatitis-c-patients
#16
Elena L Enache, Anca Sin, Liviu S Enache, Ligia Bancu
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...
August 30, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29054399/determination-of-molecular-subtypes-of-diffuse-large-b-cell-lymphoma-using-a-reverse-transcriptase-multiplex-ligation-dependent-probe-amplification-classifier-a-calym-study
#17
Victor Bobée, 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 Picquenot, Thierry Jo Molina, Gilles Salles, Corinne Haioun, Hervé Tilly, Fabrice Jardin
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...
November 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28826610/calling-chromosome-alterations-dna-methylation-statuses-and-mutations-in-tumors-by-simple-targeted-next-generation-sequencing-a-solution-for-transferring-integrated-pangenomic-studies-into-routine-practice
#18
Simon Garinet, Mario Néou, Bruno de La Villéon, Simon Faillot, Julien Sakat, Juliana P Da Fonseca, Anne Jouinot, Christophe Le Tourneau, Maud Kamal, Windy Luscap-Rondof, Valentina Boeva, Sebastien Gaujoux, Michel Vidaud, Eric Pasmant, Franck Letourneur, Jérôme Bertherat, Guillaume Assié
Pangenomic studies identified distinct molecular classes for many cancers, with major clinical applications. However, routine use requires cost-effective assays. We assessed whether targeted next-generation sequencing (NGS) could call chromosomal alterations and DNA methylation status. A training set of 77 tumors and a validation set of 449 (43 tumor types) were analyzed by targeted NGS and single-nucleotide polymorphism (SNP) arrays. Thirty-two tumors were analyzed by NGS after bisulfite conversion, and compared to methylation array or methylation-specific multiplex ligation-dependent probe amplification...
September 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28826609/a-droplet-digital-pcr-method-for-severe-combined-immunodeficiency-newborn-screening
#19
Noemi Vidal-Folch, Dragana Milosevic, Ramanath Majumdar, Dimitar Gavrilov, Dietrich Matern, Kimiyo Raymond, Piero Rinaldo, Silvia Tortorelli, Roshini S Abraham, Devin Oglesbee
Severe combined immunodeficiency (SCID) benefits from early intervention via hematopoietic cell transplantation to reverse T-cell lymphopenia (TCL). Newborn screening (NBS) programs use T-cell receptor excision circle (TREC) levels to detect SCID. Real-time quantitative PCR is often performed to quantify TRECs in dried blood spots (DBSs) for NBS. Yet, real-time quantitative PCR has inefficiencies necessitating normalization, repeat analyses, or standard curves. To address these issues, we developed a multiplex, droplet digital PCR (ddPCR) method for measuring absolute TREC amounts in one DBS punch...
September 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28826608/high-throughput-multiplex-genotyping-directly-from-blood-or-dried-blood-spot-without-dna-extraction-for-the-screening-of-multiple-g6pd-gene-variants-at-risk-for-drug-induced-hemolysis
#20
Xiaoyi Tian, Jun Zhou, Ye Zhao, Zhibin Cheng, Wenqi Song, Yu Sun, Xiaodong Sun, Zhi Zheng
Clinical or epidemiologic screening of single-nucleotide polymorphism markers requires large-scale multiplexed genotyping. Available genotyping tools require DNA extraction and multiplex PCR, which may limit throughput and suffer amplification bias. Herein, a novel genotyping approach has been developed, multiplex extension and ligation-based probe amplification (MELPA), which eliminates DNA extraction and achieves uniform PCR amplification. MELPA lyses blood or dried blood spot and directly captures specific target DNA to 96-well plates using tailed probes...
September 2017: Journal of Molecular Diagnostics: JMD
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