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https://www.readbyqxmd.com/read/29351293/fibroblast-growth-factor-receptor-1-amplification-in-laryngeal-squamous-cell-carcinoma
#1
Jesus Monico, Brandon Miller, Luminita Rezeanu, Warren May, Donna C Sullivan
Fibroblast growth factor receptor 1 (FGFR1) has been noted to be amplified in a variety of squamous cell carcinomas (SCCa) of the head, neck, and lung and increased copy number (CN) is a predictor of poor outcomes. FGFR1 is a therapeutic target for lung SCCa and inhibition therapy is currently in clinical trials. Absolute quantification of FGFR1 from formalin fixed paraffin embedded (FFPE) tissue of laryngeal SCCa was examined in this retrospective study. A droplet digital polymerase chain reaction (ddPCR) was used for absolute quantitation of the FGFR1 gene CN...
2018: PloS One
https://www.readbyqxmd.com/read/29340107/a-comparison-of-arms-plus-and-droplet-digital-pcr-for-detecting-egfr-activating-mutations-in-plasma
#2
Xinxin Zhang, Ning Chang, Guohua Yang, Yong Zhang, Mingxiang Ye, Jing Cao, Jie Xiong, Zhiping Han, Shuo Wu, Lei Shang, Jian Zhang
In this study, we introduce a novel amplification refractory mutation system (ARMS)-based assay, namely ARMS-Plus, for the detection of epidermal growth factor receptor (EGFR) mutations in plasma samples. We evaluated the performance of ARMS-Plus in comparison with droplet digital PCR (ddPCR) and assessed the significance of plasma EGFR mutations in predicting efficacy of EGFR-tyrosine kinase inhibitor (TKI) regimen. A total of 122 advanced non-small cell lung cancer (NSCLC) patients were enrolled in this study...
December 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29339441/allele-specific-droplet-digital-pcr-combined-with-a-next-generation-sequencing-based-algorithm-for-diagnostic-copy-number-analysis-in-genes-with-high-homology-proof-of-concept-using-stereocilin
#3
Sami S Amr, Elissa Murphy, Elizabeth Duffy, Rojeen Niazi, Jorune Balciuniene, Minjie Luo, Heidi L Rehm, Ahmad N Abou Tayoun
BACKGROUND: Copy number variants (CNVs) can substantially contribute to the pathogenic variant spectrum in several disease genes. The detection of this type of variant is complicated in genes with high homology to other genomic sequences, yet such genomics regions are more likely to lead to CNVs, making it critical to address detection in these settings. METHODS: We developed a copy number analysis approach for high homology genes/regions that consisted of next-generation sequencing (NGS)-based dosage analysis accompanied by allele-specific droplet digital PCR (ddPCR) confirmatory testing...
January 16, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29334548/plasma-and-intracellular-pharmacokinetics-of-tenofovir-in-patients-switched-from-tenofovir-disoproxil-fumarate-to-tenofovir-alafenamide
#4
Anthony T Podany, Sara H Bares, Joshua Havens, Ravi Dyavar Shetty, Jennifer O'neill, Sarah Lee, Courtney V Fletcher, Susan Swindells, Kimberly K Scarsi
OBJECTIVES: The aim of the study was to compare the intra-individual plasma and intracellular peripheral blood mononuclear cell (PBMC) pharmacokinetics (PK) of tenofovir (TFV) and its intracellular metabolite, tenofovir-diphosphate (TFV-DP) in patients switched from a fixed dose combination (FDC) tablet of tenofovir disoproxil fumarate (TDF)/ emtricitabine (FTC)/ elvitegravir (EVG)/ cobicistat (COBI) to a FDC containing tenofovir alafenamide (TAF)/FTC/EVG/COBI. DESIGN: A single arm, prospective, non-randomized, cross-over, PK study in patients receiving a TDF-containing regimen (TDF 300 mg/ FTC 200 mg/ EVG 150 mg/ COBI 150 mg) switched to a TAF-containing FDC regimen (TAF 10 mg/ FTC 200 mg/ EVG 150 mg/ COBI 150 mg)...
January 13, 2018: AIDS
https://www.readbyqxmd.com/read/29325035/amplicon-based-next-generation-sequencing-of-plasma-cell-free-dna-for-detection-of-driver-and-resistance-mutations-in-advanced-non-small-cell-lung-cancer
#5
N Guibert, Y Hu, N Feeney, Y Kuang, V Plagnol, G Jones, K Howarth, J F Beeler, C P Paweletz, G R Oxnard
Background: Genomic analysis of plasma cell-free DNA is transforming lung cancer care, however available assays are limited by cost, turnaround time, and imperfect accuracy. Here we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Methods: Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1 and other rare genotypes) were collected while on therapy and analyzed, blinded to tumor genotype...
January 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29324546/applying-precision-medicine-to-ovarian-cancer-proof-of-principle-for-a-molecular-second-look
#6
Melissa Schwartz, Olga Camacho-Vanegas, Ashley M Wood, Matthew Dashkoff, Courtney Whitelock, Timothy T Harkins, Carmel J Cohen, Ann Marie Beddoe, Peter Dottino, John A Martignetti
OBJECTIVES: The objectives of this study were to assess if targeted investigation for tumor-specific mutations by ultradeep DNA sequencing of peritoneal washes of ovarian cancer patients after primary surgical debulking and chemotherapy, and clinically diagnosed as disease free, provides a more sensitive and specific method to assess actual treatment response and tailor future therapy and to compare this "molecular second look" with conventional cytology and histopathology-based findings...
January 10, 2018: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/29321551/aster-leafhopper-survival-and-reproduction-and-aster-yellows-transmission-under-static-and-fluctuating-temperatures-using-ddpcr-for-phytoplasma-quantification
#7
Md H Bahar, Tyler J Wist, Diana R Bekkaoui, Dwayne D Hegedus, Chrystel Y Olivier
Aster yellows (AY) is an important disease of Brassica crops and is caused by Candidatus Phytoplasma asteris and transmitted by the insect vector, Aster leafhopper (Macrosteles quadrilineatus). Phytoplasma-infected Aster leafhoppers were incubated at various constant and fluctuating temperatures ranging from 0 to 35 °C with the reproductive host plant barley (Hordium vulgare). At 0 °C, leafhopper adults survived for 18 days, but failed to reproduce, whereas at 35 °C insects died within 18 days, but successfully reproduced before dying...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29305225/droplet-digital-pcr-for-mutation-detection-in-formalin-fixed-paraffin-embedded-melanoma-tissues-a-comparison-with-sanger-sequencing-and-pyrosequencing
#8
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
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 pyrosequencing...
January 2, 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29305193/ultra-sensitive-droplet-digital-pcr-for-the-assessment-of-microchimerism-in-cellular-therapies
#9
David Kliman, Gloria Castellano-Gonzalez, Barbara Withers, Janine Street, Elizabeth Tegg, Oksana Mirochnik, Joey Lai, Leighton Clancy, David Gottlieb, Emily Blyth
Current techniques to assess chimerism after hematopoietic stem cell transplantation (HSCT) are limited in both sensitivity and precision. These drawbacks are problematic in the context of cellular therapies which frequently result in microchimerism (donor chimerism <1%). We have developed a highly sensitive droplet digital PCR (ddPCR) assay using commercially available regents with good performance throughout the range of clinically relevant chimerism measurements, including microchimerism. We tested the assay using spiked samples of known donor:recipient ratios and in clinical samples from HSCT recipients and patients enrolled on clinical trials of microtransplantation and 3rd party virus specific T cells (VST)...
January 2, 2018: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/29303179/capillary-based-integrated-digital-pcr-in-picoliter-droplets
#10
Jinyu Chen, Zhaofeng Luo, Lin Li, Jinlong He, Luoquan Li, Jianwei Zhu, Ping Wu, Liqun He
The droplet digital polymerase chain reaction (ddPCR) is becoming more and more popular in diagnostic applications in academia and industry. In commercially available ddPCR systems, after they have been made by a generator, the droplets have to be transferred manually to modules for amplification and detection. In practice, some of the droplets (∼10%) are lost during manual transfer, leading to underestimation of the targets. In addition, the droplets are also at risk of cross-contamination during transfer...
January 5, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29300373/urine-cell-free-dna-is-a-biomarker-for-nephroblastomatosis-or-wilms-tumor-in-pik3ca-related-overgrowth-spectrum-pros
#11
Marta Biderman Waberski, Marjorie Lindhurst, Kim M Keppler-Noreuil, Julie C Sapp, Laura Baker, Karen W Gripp, Denise M Adams, Leslie G Biesecker
PurposeWe set out to facilitate the molecular diagnosis of patients with PIK3CA-related overgrowth spectrum (PROS), a heterogeneous somatic disorder characterized by variable presentations of segmental overgrowth, vascular malformations, skin lesions, and nephroblastomatosis, rare precursor lesions to Wilms tumor. Molecular diagnosis of PROS is challenging due to its mosaic nature, often requiring invasive biopsies.MethodsDigital droplet polymerase chain reaction (ddPCR) was used to analyze tissues including urine, saliva, buccal cells, and blood, from eight patients with PROS...
January 4, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29290998/detection-of-somatic-variants-and-egfr-mutations-in-cell-free-dna-from-non-small-cell-lung-cancer-patients-by-ultra-deep-sequencing-using-the-ion-ampliseq-cancer-hotspot-panel-and-droplet-digital-polymerase-chain-reaction
#12
Jae Sook Sung, Hyon Yong Chong, Nak-Jung Kwon, Hae Mi Kim, Jong Won Lee, Boyeon Kim, Saet Byeol Lee, Chang Won Park, Jung Yoon Choi, Won Jin Chang, Yoon Ji Choi, Sung Yong Lee, Eun Joo Kang, Kyong Hwa Park, Yeul Hong Kim
Highly sensitive genotyping assays can detect mutations in cell-free DNA (cfDNA) from cancer patients, reflecting the biology of each patient's cancer. Because circulating tumor DNA comprises a small, variable fraction of DNA circulating in the blood, sensitive parallel multiplexing tests are required to determine mutation profiles. We prospectively examined the clinical utility of ultra-deep sequencing analysis of cfDNA from 126 non-small cell lung cancer (NSCLC) patients using the Ion AmpliSeq Cancer Hotspot Panel v2 (ICP) and validated these findings with droplet digital polymerase chain reaction (ddPCR)...
December 5, 2017: Oncotarget
https://www.readbyqxmd.com/read/29290257/primary-resistance-to-osimertinib-due-to-sclc-transformation-issue-of-t790m-determination-on-liquid-re-biopsy
#13
R Minari, P Bordi, M Del Re, F Facchinetti, F Mazzoni, F Barbieri, A Camerini, C E Comin, L Gnetti, C Azzoni, R Nizzoli, B Bortesi, E Rofi, P Petreni, N Campanini, G Rossi, R Danesi, M Tiseo
OBJECTIVES: EGFR T790M mutation is the most common mechanism of resistance to first-/second-generation EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) and could be overcome by third-generation EGFR-TKIs, such as osimertinib. Liquid biopsy, a non-invasive technique used to test the presence of the resistant mutation, may help avoiding tissue re-biopsy. However, analysing only circulating-free DNA, information about other less frequent and coexisting resistance mechanisms may remain unrevealed...
January 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29251615/-the-association-of-the-mitochondrial-dna-orib-variants-with-metabolic-syndrome
#14
D A Skuratovskaia, J K Sofronova, P A Zatolokin, M A Vasilenko, L S Litvinova, I O Mazunin
Different genes are involved in the development of pathology and formation the metabolic syndrome (MS) phenotype. In the literature, there is a data connection to the site oriB polymorphisms of mitochondrial DNA (mtDNA), known as 16184-16193 polycytosine tract, with insulin resistance, type 2 diabetes (T2DM) and other metabolic abnormalities in different ethnic populations. It is supposed that for certain polymorphisms at this site decreases mtDNA copy number in the cells. In this study, we have identified different allelic variants of the mtDNA oriB site in MS patients (n=106) and healthy individuals (n=71) using capillary sequencing, and determined the amount of mtDNA copy blood leukocytes by droplet digital polymerase chain reaction (ddPCR)...
November 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29214759/clinical-implications-of-quantitative-jak2-v617f-analysis-using-droplet-digital-pcr-in-myeloproliferative-neoplasms
#15
Eunyoung Lee, Kyoung Joo Lee, Hyein Park, Jin Young Chung, Mi Na Lee, Myung Hee Chang, Jongha Yoo, Hyewon Lee, Sun Young Kong, Hyeon Seok Eom
BACKGROUND: JAK2 V617F is the most common mutation in myeloproliferative neoplasms (MPNs) and is a major diagnostic criterion. Mutation quantification is useful for classifying patients with MPN into subgroups and for prognostic prediction. Droplet digital PCR (ddPCR) can provide accurate and reproducible quantitative analysis of DNA. This study was designed to verify the correlation of ddPCR with pyrosequencing results in the diagnosis of MPN and to investigate clinical implications of the mutational burden...
March 2018: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/29212777/detection-and-monitoring-of-circulating-tumor-dna-in-adrenocortical-carcinoma
#16
Simon Garinet, Juliette Nectoux, Mario Neou, Eric Pasmant, Anne Jouinot, Mathilde Sibony, Lucie Orhant, Juliana Pipoli da Fonseca, Karine Hecale-Perlemoine, Leopoldine Bricaire, Lionel Groussin, Olivier Soubrane, Bertrand Dousset, Rossella Libé, Franck Letourneur, Jerome Bertherat, Guillaume Assié
Adrenocortical carcinomas (ACC) are aggressive tumors with limited prognostic and follow-up biomarkers. Circulating tumor DNA (ctDNA) is an emerging biomarker, now used for several cancer types. This study aimed to reliably detect and quantify ctDNA in ACC patients; to identify parameters impacting detection of ctDNA. A prospective monocentric study conducted in Cochin Hospital and Cochin Institute, Paris, France. Eleven ACC patients were included with either primary tumor or relapse or metastases from 2015 to 2016...
December 6, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29210102/the-use-of-droplet-digital-pcr-in-liquid-biopsies-a-highly-sensitive-technique-for-myd88-p-l265p-detection-in-cerebrospinal-fluid
#17
Laura S Hiemcke-Jiwa, Monique C Minnema, Joyce H Radersma-van Loon, N Mehdi Jiwa, Mirthe de Boer, Roos J Leguit, Roel A de Weger, Manon M H Huibers
The gold standard for diagnosis of central nervous system lymphomas still regards a stereotactic brain biopsy, with the risk of major complications for the patient. As tumor cells can be detected in cerebrospinal fluid (CSF), CSF analysis can be used as an alternative. In this respect, mutation analysis in CSF can be of added value to other diagnostic parameters such a cytomorphology and clonality analysis. A well-known example of targeted mutation analysis entails MYD88 p.(L265P) detection, which is present in the majority of Bing Neel syndrome and primary central nervous system lymphoma (PCNSL) patients...
December 6, 2017: Hematological Oncology
https://www.readbyqxmd.com/read/29209860/identification-of-inhibitory-compounds-against-singapore-grouper-iridovirus-infection-by-cell-viability-based-screening-assay-and-droplet-digital-pcr
#18
Kuntong Jia, Yongming Yuan, Wei Liu, Lan Liu, Qiwei Qin, Meisheng Yi
Singapore grouper iridovirus (SGIV) is one of the major causative agents of fish diseases and has caused significant economic losses in the aquaculture industry. There is currently no commercial vaccine or effective antiviral treatment against SGIV infection. Annually, an increasing number of small molecule compounds from various sources have been produced, and many are proved to be potential inhibitors against viruses. Here, a high-throughput in vitro cell viability-based screening assay was developed to identify antiviral compounds against SGIV using the luminescent-based CellTiter-Glo reagent in cultured grouper spleen cells by quantificational measurement of the cytopathic effects induced by SGIV infection...
December 5, 2017: Marine Biotechnology
https://www.readbyqxmd.com/read/29197654/exploring-viral-reservoir-the-combining-approach-of-cell-sorting-and-droplet-digital-pcr
#19
REVIEW
Lara Gibellini, Simone Pecorini, Sara De Biasi, Marcello Pinti, Elena Bianchini, Anna De Gaetano, Margherita Digaetano, Rosalberta Pullano, Domenico Lo Tartaro, Anna Iannone, Cristina Mussini, Andrea Cossarizza, Milena Nasi
Combined antiretroviral therapy (cART) blocks different steps of HIV replication and maintains plasma viral RNA at undetectable levels. The virus can remain in long-living cells and create a reservoir where HIV can restart replicating after cART discontinuation. A persistent viral production triggers and maintains a persistent immune activation, which is a well-known feature of chronic HIV infection, and contributes either to precocious aging, or to the increased incidence of morbidity and mortality of HIV positive patients...
November 29, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29173762/quantification-of-plasma-egfr-mutations-in-patients-with-lung-cancers-comparison-of-the-performance-of-arms-plus-and-droplet-digital-pcr
#20
Lin Wang, Qiaomei Guo, Wenjun Yu, Lihua Qiao, Mingna Zhao, Chenzi Zhang, Xiaomeng Hu, Guohua Yang, Liwen Xiong, Jiatao Lou
OBJECTIVES: EGFR mutation is a key factor to predict EGFR-TKI efficacy. However, a significant number of advanced patients do not have sufficient tumor specimens for molecular testing. Also, there is a lack of quantitative assay to analyze the mutant abundance. This study aims to evaluate the detection efficiency and clinical feasibility of a new platform, namely ARMS-Plus, for the detection and quantification of EGFR mutations in plasma. MATERIALS AND METHODS: The detection limit of ARMS-Plus was assessed by detecting spiked mutant plasmids which were serially diluted with normal human genomic DNA...
December 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
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