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https://www.readbyqxmd.com/read/28529628/cross-platform-comparison-of-four-leading-technologies-for-detecting-egfr-mutations-in-circulating-tumor-dna-from-non-small-cell-lung-carcinoma-patient-plasma
#1
Ting Xu, Xiaozheng Kang, Xiaofang You, Liang Dai, Dequan Tian, Wanpu Yan, Yongbo Yang, Hongchao Xiong, Zhen Liang, Grace Q Zhao, Shengrong Lin, Ke-Neng Chen, Guobing Xu
Analysis of circulating tumor DNA (ctDNA) is emerging as a powerful tool for guiding targeted therapy and monitoring tumor evolution in patients with non-small cell lung cancer (NSCLC), especially when representative tissue biopsies are not available. Here, we have compared the ability of four leading technology platforms to detect epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, T790M and G719X) in ctDNA from NSCLC patients. Two amplification refractory mutation systems (cobas-ARMS and ADx-ARMS), a droplet digital polymerase chain reaction (ddPCR) and a next-generation sequencing (Firefly NGS) platform were included in the comparison...
2017: Theranostics
https://www.readbyqxmd.com/read/28522907/droplet-digital-pcr-for-quantification-of-itga6-in-a-stool-mrna-assay-for-the-detection-of-colorectal-cancers
#2
Elizabeth Herring, Shigeru Kanaoka, Éric Tremblay, Jean-François Beaulieu
AIM: To investigate the use of droplet digital polymerase chain reaction (ddPCR) for detecting host mRNA markers in stools as a non-invasive test for colorectal cancer screening. METHODS: ddPCR and quantitative PCR were compared side by side for their performance in the detection of ITGA6 and ITGA6A transcripts in stool samples obtained from patients with various types of colorectal lesions (advanced adenomas and stage II-IV colorectal cancers) and control (patients displaying no pathological findings) using duplex TaqMan reactions for both methods...
April 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28497422/utility-of-urinary-circulating-tumor-dna-for-egfr-mutation-detection-in-different-stages-of-non-small-cell-lung-cancer-patients
#3
Fajiu Li, Jie Huang, Dongyuan Ji, Qinghua Meng, Chuanhai Wang, Shi Chen, Xiaojiang Wang, Zhiyang Zhu, Cheng Jiang, Yi Shi, Shuang Liu, Chenghong Li
PURPOSE: Non-invasive methods of molecular profiling for non-small cell lung cancer (NSCLC) are useful for monitoring disease progression. The aim of the current study was to ascertain if transrenal DNA is sensitive for clinical correlation and EGFR detection in NSCLC patients. METHODS: 160 patients at various stages of the disease participated and samples were collected prospectively at 2-month intervals. A baseline sample was taken before treatment commencement...
May 11, 2017: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/28490568/noninvasive-detection-of-f8-int22h-related-inversions-and-sequence-variants-in-maternal-plasma-of-hemophilia-carriers
#4
Irena Hudecova, Peiyong Jiang, Joanna Davies, Y M Dennis Lo, Rezan A Kadir, Rossa W K Chiu
Direct detection of F8 and F9 sequence variants in maternal plasma of hemophilia carriers has been demonstrated by microfluidics digital PCR. Noninvasive prenatal assessment of the most clinically relevant group of sequence variants among hemophilia patients, namely those involving int22h-related inversions disrupting the F8 gene, poses additional challenges due to its molecular complexity. We investigated the use of droplet digital PCR (ddPCR) and targeted massively parallel sequencing (MPS) for maternal plasma DNA analysis to noninvasively determine fetal mutational status in pregnancies at risk for hemophilia...
May 10, 2017: Blood
https://www.readbyqxmd.com/read/28487054/reduced-cost-chlamydia-trachomatis-specific-multiplex-real-time-pcr-diagnostic-assay-evaluated-for-ocular-swabs-and-use-by-trachoma-research-programmes
#5
Robert Butcher, Jo Houghton, Tamsyn Derrick, Athumani Ramadhani, Beatriz Herrera, Anna R Last, Patrick A Massae, Matthew J Burton, Martin J Holland, Chrissy H Roberts
INTRODUCTION: Trachoma, caused by the intracellular bacterium Chlamydia trachomatis (Ct) is the leading infectious cause of preventable blindness. Many commercial platforms are available that provide highly sensitive and specific detection of Ct DNA. However, the majority of these commercial platforms are inaccessible for population-level surveys in resource-limited settings typical to trachoma control programmes. We developed two low-cost quantitative PCR (qPCR) tests for Ct using readily available reagents on standard real-time thermocyclers...
May 6, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28484715/plasma-circulating-tumor-dna-levels-for-the-monitoring-of-melanoma-patients-landscape-of-available-technologies-and-clinical-applications
#6
REVIEW
Benoit Busser, Julien Lupo, Lucie Sancey, Stéphane Mouret, Patrice Faure, Joel Plumas, Laurence Chaperot, Marie Thérèse Leccia, Jean Luc Coll, Amandine Hurbin, Pierre Hainaut, Julie Charles
Melanoma is a cutaneous cancer with an increasing worldwide prevalence and high mortality due to unresectable or metastatic stages. Mutations in BRAF, NRAS, or KIT are present in more than 60% of melanoma cases, but a useful blood-based biomarker for the clinical monitoring of melanoma patients is still lacking. Thus, the analysis of circulating tumor cells (CTCs) and/or cell-free circulating tumor DNA (ctDNA) analysis from blood (liquid biopsies) appears to be a promising noninvasive, repeatable, and systemic sampling tool for detecting and monitoring melanoma...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28477149/current-and-emerging-applications-of-droplet-digital-pcr-in-oncology
#7
REVIEW
Susana Olmedillas-López, Mariano García-Arranz, Damián García-Olmo
The clinical management of cancer has evolved in recent years towards more personalized strategies that require a comprehensive knowledge of the complex molecular features involved in tumor growth and evolution, and the development of drug resistance mechanisms leading to disease progression. Droplet digital PCR (ddPCR) has become one of the most accurate and reliable tools for the examination of genetic alterations in a wide variety of cancers because of its high sensitivity and specificity. ddPCR is currently being applied for absolute allele quantification, rare mutation detection, analysis of copy number variations, DNA methylation, and gene rearrangements in different kinds of clinical samples...
May 5, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28475662/twoddpcr-an-r-bioconductor-package-and-shiny-app-for-droplet-digital-pcr-analysis
#8
Anthony Chiu, Mahmood Ayub, Caroline Dive, Ged Brady, Crispin J Miller
Summary: Droplet Digital PCR (ddPCR) is a sensitive platform used to quantify specific nucleic acid molecules amplified by polymerase chain reactions. Its sensitivity makes it particularly useful for the detection of rare mutant molecules, such as those present in a sample of circulating free tumour DNA obtained from cancer patients. ddPCR works by partitioning a sample into individual droplets for which the majority contain only zero or one target molecule. Each droplet then becomes a reaction chamber for PCR, which through the use of fluorochrome labelled probes allows the target molecules to be detected by measuring the fluorescence intensity of each droplet...
May 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28472366/androgen-receptor-gene-status-in-plasma-dna-associates-with-worse-outcome-on-enzalutamide-or-abiraterone-for-castration-resistant-prostate-cancer-a-multi-institution-correlative-biomarker-study
#9
V Conteduca, D Wetterskog, M T A Sharabiani, E Grande, M P Fernandez-Perez, A Jayaram, S Salvi, D Castellano, A Romanel, C Lolli, V Casadio, G Gurioli, D Amadori, A Font, S Vazquez-Estevez, A González Del Alba, B Mellado, O Fernandez-Calvo, M J Méndez-Vidal, M A Climent, I Duran, E Gallardo, A Rodriguez, C Santander, M I Sáez, J Puente, D Gasi Tandefelt, A Wingate, D Dearnaley, F Demichelis, U De Giorgi, E Gonzalez-Billalabeitia, G Attard
Background: There is an urgent need to identify biomarkers to guide personalized therapy in castration-resistant prostate cancer (CRPC). We aimed to clinically qualify androgen receptor (AR) gene status measurement in plasma DNA using multiplex droplet digital PCR (ddPCR) in pre- and post-chemotherapy CRPC. Methods: We optimized ddPCR assays for AR copy number and mutations and retrospectively analyzed plasma DNA from patients recruited to one of the three biomarker protocols with prospectively collected clinical data...
May 3, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28448765/digital-assays-part-i-partitioning-statistics-and-digital-pcr
#10
Amar S Basu
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error...
April 1, 2017: SLAS Technology
https://www.readbyqxmd.com/read/28445137/monitoring-of-kras-mutated-ctdna-to-discriminate-pseudo-progression-from-true-progression-during-anti-pd-1-treatment-of-lung-adenocarcinoma
#11
Nicolas Guibert, Julien Mazieres, Myriam Delaunay, Anne Casanova, Magali Farella, Laura Keller, Gilles Favre, Anne Pradines
OBJECTIVES: Pseudo-progression is a rare but worrying situation for both clinicians and patients during immunotherapy. Dedicated ir-RECIST criteria have been established to improve this situation. However, this can be sometimes considered inadequate and patients experiencing true progression may then receive inefficient treatments. Additional reliable tools to discriminate pseudo from true progression are thus needed. So far, no biomarker has been identified to distinguish pseudo from true progression...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28441386/graft-derived-cell-free-dna-a-noninvasive-early-rejection-and-graft-damage-marker-in-liver-transplantation-a-prospective-observational-multicenter-cohort-study
#12
Ekkehard Schütz, Anna Fischer, Julia Beck, Markus Harden, Martina Koch, Tilo Wuensch, Martin Stockmann, Björn Nashan, Otto Kollmar, Johannes Matthaei, Philipp Kanzow, Philip D Walson, Jürgen Brockmöller, Michael Oellerich
BACKGROUND: Graft-derived cell-free DNA (GcfDNA), which is released into the blood stream by necrotic and apoptotic cells, is a promising noninvasive organ integrity biomarker. In liver transplantation (LTx), neither conventional liver function tests (LTFs) nor immunosuppressive drug monitoring are very effective for rejection monitoring. We therefore hypothesized that the quantitative measurement of donor-derived cell-free DNA (cfDNA) would have independent value for the assessment of graft integrity, including damage from acute rejection...
April 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28437435/infective-respiratory-syncytial-virus-is-present-in-human-cord-blood-samples-and-most-prevalent-during-winter-months
#13
Angela Mary Fonceca, Abha Chopra, Avram Levy, Paul Stanton Noakes, Matthew Wee-Peng Poh, Natasha Leanne Bear, Susan Prescott, Mark Lloyd Everard
BACKGROUND: Human respiratory syncytial virus (RSV) remains the most common cause of severe lower respiratory tract disease amongst infants, and continues to cause annual epidemics of respiratory disease every winter worldwide. Demonstrating placental transmission of viable RSV in human samples is a major paradigm shift in respiratory routes considered likely for RSV transmission. METHODS: Droplet digital PCR (ddPCR) was used to identify RSV present in cord blood mononucleocytes (CBM)...
2017: PloS One
https://www.readbyqxmd.com/read/28426533/hiv-dna-content-in-different-cd4-t-cell-subsets-correlates-with-cd4-cd8-ratio-or-length-of-efficient-treatment
#14
Lara Gibellini, Simone Pecorini, Sara de Biasi, Elena Bianchini, Margherita Digaetano, Marcello Pinti, Gianluca Carnevale, Vanni Borghi, Giovanni Guaraldi, Cristina Mussini, Andrea Cossarizza, Milena Nasi
OBJECTIVES: HIV establishes a latent infection at different degrees within naïve (TN) or central (TCM) and effector memory (TEM) CD4+ T cell. Studying patients in whom HIV production was suppressed by combined antiretroviral therapy (cART), our main aim was to find which factors are related or can influence intracellular viral reservoir in different CD4+ T cell subsets. METHODS: We enrolled 32 HIV+ patients successfully treated for > 2 years, with a CD4+ T cell count > 500 cells/μL and plasma viremia undetectable from at least one year...
April 19, 2017: AIDS
https://www.readbyqxmd.com/read/28424530/molecular-diagnostic-assays-based-on-cpn60-ut-sequences-reveal-the-geographic-distribution-of-subgroup-16srxiii-a-i-i-phytoplasma-in-mexico
#15
Edel Pérez-López, Douglas Rodríguez-Martínez, Chrystel Y Olivier, Mauricio Luna-Rodríguez, Tim J Dumonceaux
Geographically diverse samples from strawberry exhibiting symptoms of Strawberry Green Petal (SbGP), periwinkle plants with virescence, and blackberry, blueberry, and raspberry plants displaying yellowing and inedible fruits, were assayed for the presence of phytoplasma DNA. PCR targeting the 16S rRNA-encoding gene and chaperonin-60 (cpn60) showed that the plants were infected with phytoplasma subgroup16SrXIII-(A/I)I (SbGP/MPV). To examine the geographic distribution of this pathogen in Mexico, we designed an array of cpn60-targeted molecular diagnostic assays for SbGP/MPV phytoplasma...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423028/four-human-plasmodium-species-quantification-using-droplet-digital-pcr
#16
Suttipat Srisutham, Naowarat Saralamba, Benoit Malleret, Laurent Rénia, Arjen M Dondorp, Mallika Imwong
Droplet digital polymerase chain reaction (ddPCR) is a partial PCR based on water-oil emulsion droplet technology. It is a highly sensitive method for detecting and delineating minor alleles from complex backgrounds and provides absolute quantification of DNA targets. The ddPCR technology has been applied for detection of many pathogens. Here the sensitive assay utilizing ddPCR for detection and quantification of Plasmodium species was investigated. The assay was developed for two levels of detection, genus specific for all Plasmodium species and for specific Plasmodium species detection...
2017: PloS One
https://www.readbyqxmd.com/read/28419517/comparative-analysis-between-rq-pcr-and-digital-droplet-pcr-of-bcl2-igh-gene-rearrangement-in-the-peripheral-blood-and-bone-marrow-of-early-stage-follicular-lymphoma
#17
Marzia Cavalli, Lucia Anna De Novi, Irene Della Starza, Luca Vincenzo Cappelli, Vittorio Nunes, Alessandro Pulsoni, Ilaria Del Giudice, Anna Guarini, Robin Foà
BCL2/IGH rearrangements were analysed by polymerase chain reaction (PCR) at diagnosis in paired peripheral blood (PB) and bone marrow (BM) samples from 67 patients with stage I/II follicular lymphoma (FL). Real time quantitative PCR (RQ-PCR) and digital droplet PCR (ddPCR) were performed in cases with a major breakpoint region (MBR+) at diagnosis and after localized radiotherapy and rituximab administration in order to investigate the applicability of ddPCR. The overall ddPCR/RQ-PCR concordance was 81·9% (113/138 samples) and 97·5% in the 40/138 with quantifiable disease (RQ-PCR≥10(-5) )...
April 17, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28414780/sensitive-quantification-of-the-hiv-1-reservoir-in-gut-associated-lymphoid-tissue
#18
Sara Morón-López, Maria C Puertas, Cristina Gálvez, Jordi Navarro, Anna Carrasco, Maria Esteve, Josep Manyé, Manel Crespo, Maria Salgado, Javier Martinez-Picado
BACKGROUND: The implementation of successful strategies to achieve an HIV cure has become a priority in HIV research. However, the current location and size of HIV reservoirs is still unknown since there are limited tools to evaluate HIV latency in viral sanctuaries such as gut-associated lymphoid tissue (GALT). As reported in the so called "Boston Patients", despite undetectable levels of proviral HIV-1 DNA in blood and GALT, viral rebound happens in just few months after ART interruption...
2017: PloS One
https://www.readbyqxmd.com/read/28414163/droplet-digital-pcr-ddpcr-vs-quantitative-real-time-pcr-qpcr-approach-for-detection-and-quantification-of-merkel-cell-polyomavirus-mcpyv-dna-in-formalin-fixed-paraffin-embedded-ffpe-cutaneous-biopsies
#19
Rosaria Arvia, Mauro Sollai, Federica Pierucci, Carmelo Urso, Daniela Massi, Krystyna Zakrzewska
BACKGROUND: Merkel cell polyomavirus (MCPyV) is associated with Merkel cell carcinoma and high viral load in the skin was proposed as a risk factor for the occurrence of this tumour. MCPyV DNA was detected, with lower frequency, in different skin cancers but since the viral load was usually low, the real prevalence of viral DNA could be underestimated. OBJECTIVE: To evaluate the performance of two assays (qPCR and ddPCR) for MCPyV detection and quantification in formalin fixed paraffin embedded (FFPE) tissue samples...
April 14, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28405680/optimal-method-for-quantitative-detection-of-plasma-egfr-t790m-mutation-using-droplet-digital-pcr-system
#20
Ken Suzawa, Hiromasa Yamamoto, Kadoaki Ohashi, Shinsuke Hashida, Shuta Tomida, Toshio Kubo, Yuho Maki, Junichi Soh, Kazunori Tsukuda, Katsuyuki Kiura, Shinichiro Miyoshi, Shinichi Toyooka
Though patients with EGFR mutations are initially responsive to EGFR-tyrosine kinase inhibitors (TKIs), most tumors ultimately acquire resistance to EGFR-TKIs. The most frequently reported mechanism is EGFR T790M mutation. In this study, using a droplet digital PCR (ddPCR) system, we assessed optimal conditions for a mutation detection assay for EGFR T790M obtained from circulating cell-free DNA (cfDNA) in plasma. The advantages of locked nucleic acids (LNA) probe, short amplicon size, and blocking oligo using peptide nucleic acids (PNA) were assessed using control DNAs from cell lines to improve the sensitivity of mutation detection...
May 2017: Oncology Reports
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