keyword
MENU ▼
Read by QxMD icon Read
search

droplet pcr

keyword
https://www.readbyqxmd.com/read/29352043/prognostic-implications-of-multiplex-detection-of-kras-mutations-in-cell-free-dna-from-patients-with-pancreatic-ductal-adenocarcinoma
#1
Min Kyeong Kim, Sang Myung Woo, Boram Park, Kyong-Ah Yoon, Yun-Hee Kim, Jungnam Joo, Woo Jin Lee, Sung-Sik Han, Sang-Jae Park, Sun-Young Kong
BACKGROUND: Cell-free DNA (cfDNA) is known to provide potential biomarkers for predicting clinical outcome, but its value in pancreatic ductal adenocarcinoma (PDAC) has not been fully evaluated. The aim of this study was to evaluate the clinical applicability of quantitative analysis of multiplex KRAS mutations in cell-free DNA from patients with PDAC. METHODS: A total of 106 patients with PDAC were enrolled in this prospective study. The concentration and fraction of KRAS mutations were determined through multiplex detection of KRAS mutations in plasma samples by use of a droplet digital PCR kit (Bio-Rad)...
January 19, 2018: Clinical Chemistry
https://www.readbyqxmd.com/read/29351293/fibroblast-growth-factor-receptor-1-amplification-in-laryngeal-squamous-cell-carcinoma
#2
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/29350029/a-microwell-array-method-for-rapid-generation-of-uniform-agarose-droplets-and-beads-for-single-molecule-analysis
#3
Xingrui Li, Dongfeng Zhang, Huimin Zhang, Zhichao Guan, Yanling Song, Ruochen Liu, Zhi Zhu, Chaoyong James Yang
Compartmentalization of aqueous samples in uniform emulsion droplets has proven to be a useful tool for many chemical, biological, and biomedical applications. Herein, we introduce an array-based emulsification method for rapid and easy generation of monodisperse agarose-in-oil droplets in a PDMS microwell array. The microwells are filled with agarose solution, and subsequent addition of hot oil results in immediate formation of agarose droplets due to the surface-tension of the liquid solution. Because droplet size is determined solely by the array unit dimensions, uniform droplets with pre-selectable diameters ranging from 20 µm to 100 µm can be produced with relative standard deviations less than 3...
January 19, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29346025/linkage-of-metabolic-defects-to-activated-pik3ca-alleles-in-endothelial-cells-derived-from-lymphatic-malformation
#4
Kathryn Glaser, Peter Dickie, Derek Neilson, Alexander Osborn, Belinda Hsi Dickie
BACKGROUND: Lymphatic endothelial cells (LECs) derived from lymphatic malformations (LMs) bear activated PIK3CA alleles yet display an inflammatory gene expression profile. A basis for the inflammatory phenotype was sought by screening for coexisting somatic mutations. METHODS AND RESULTS: Fourteen independent LEC populations bearing activated PIK3CA alleles were isolated from LM. These were characterized by the expression of growth and inflammatory genes (VEGFC, IL-6, COX-2, IL-8, HO-1, E-SEL) by qRT-PCR...
January 18, 2018: Lymphatic Research and Biology
https://www.readbyqxmd.com/read/29344656/liraglutide-suppresses-proliferation-and-induces-adipogenic-differentiation-of-3t3-l1-cells-via-the-hippo-yap-signaling-pathway
#5
Yongmei Li, Jianying Du, Endong Zhu, Juanjuan Zhang, Jie Han, Wei Zhao, Bei Sun, Derun Tian
Liraglutide, as a glucagon-like peptide‑1 analogue, is used to treat type 2 diabetes mellitus and obesity. Previous findings have demonstrated the effects of liraglutide on adipogenesis; however, the underlying mechanism involved in this process remains to be elucidated. In the present study, to certify the effect of liraglutide on adipogenesis and explore the possible underlying mechanism involved in this process, preadipocyte 3T3‑L1 cells were cultured in adipocyte‑inducing medium and treated with liraglutide...
January 16, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29340107/a-comparison-of-arms-plus-and-droplet-digital-pcr-for-detecting-egfr-activating-mutations-in-plasma
#6
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
#7
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
#8
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/29333205/high-aspect-ratio-induced-spontaneous-generation-of-monodisperse-picolitre-droplets-for-digital-pcr
#9
Xiaonan Xu, Haojun Yuan, Ruyuan Song, Miao Yu, Ho Yin Chung, Youmin Hou, Yuhe Shang, Hongbo Zhou, Shuhuai Yao
Droplet microfluidics, which involves micrometer-sized emulsion droplets on a microfabricated platform, has been demonstrated as a unique system for many biological and chemical applications. Robust and scalable generation of monodisperse droplets at high throughput is of fundamental importance for droplet microfluidics. Classic designs for droplet generation employ shear fluid dynamics to induce the breakup of droplets in a two-phase flow and the droplet size is sensitive to flow rate fluctuations, often resulting in polydispersity...
January 2018: Biomicrofluidics
https://www.readbyqxmd.com/read/29330836/pathogenesis-of-non-alcoholic-fatty-liver-disease-mediated-by-yap
#10
Ping Chen, Qihui Luo, Chao Huang, Qi Gao, Like Li, Jingfei Chen, Bing Chen, Wentao Liu, Wen Zeng, Zhengli Chen
OBJECTIVE: This study aimed to investigate the mechanism of the interaction between Yes-associated protein (YAP) and transforming growth factor-β (TGF-β)/Smad signaling pathways in the development of non-alcoholic fatty liver disease (NAFLD). METHODS: Serum samples of monkeys with biopsy-proven NAFLD and healthy normal monkeys were used to measure fasting plasma glucose (FPG), low-density lipoprotein (LDL), high-density lipoprotein (HDL), triglyceride (TG) and albumin (ALB) with the BECKMAN CX5 PRO...
January 12, 2018: Hepatology International
https://www.readbyqxmd.com/read/29327201/allele-specific-biased-expression-of-the-cntn6-gene-in-ips-cell-derived-neurons-from-a-patient-with-intellectual-disability-and-3p26-3-microduplication-involving-the-cntn6-gene
#11
Maria M Gridina, Natalia M Matveeva, Veniamin S Fishman, Aleksei G Menzorov, Helen A Kizilova, Nikolay A Beregovoy, Igor I Kovrigin, Inna E Pristyazhnyuk, Igor P Oscorbin, Maxim L Filipenko, Anna A Kashevarova, Nikolay A Skryabin, Tatyana V Nikitina, Elena A Sazhenova, Ludmila P Nazarenko, Igor N Lebedev, Oleg L Serov
Copy number variations (CNVs) of the human CNTN6 gene caused by megabase-scale microdeletions or microduplications in the 3p26.3 region are often the cause of neurodevelopmental disorders, including intellectual disability and developmental delay. Surprisingly, patients with different copy numbers of this gene display notable overlapping of neuropsychiatric symptoms. The complexity of the study of human neuropathologies is associated with the inaccessibility of brain material. This problem can be overcome through the use of reprogramming technologies that permit the generation of induced pluripotent stem (iPS) cells from fibroblasts and their subsequent in vitro differentiation into neurons...
January 11, 2018: Molecular Neurobiology
https://www.readbyqxmd.com/read/29327010/dna-methylation-assay-using-droplet-based-dna-melting-curve-analysis
#12
F-W Liu, H-F Liao, S-P Lin, Y-W Lu
DNA methylation is an epigenetic regulation of gene expression, which has drawn great attention in biomedical research due to its association with various diseases. A robust, inexpensive platform to detect and quantify the methylation status in a specific genomic region is necessary. In this study, an on-chip analytical technique of cytosine methylation with droplets in a microchannel is proposed. Genomic DNA samples are encapsulated into a series of droplets and transported through a detection region, where a stable temperature gradient is created...
January 12, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29326285/prevalence-of-aflatoxin-associated-tp53r249s-mutation-in-hepatocellular-carcinoma-in-hispanics-in-south-texas
#13
Jingjing Jiao, Weibo Niu, Ying Wang, Keith Baggerly, Yuanqing Ye, Xifeng Wu, Dewitt Davenport, Jose Luis Almeda, Monica M Betancourt-Garcia, R Armour Forse, Heather L Stevenson, Gordon P Watt, Joseph B McCormick, Susan P Fisher-Hoch, Laura Beretta
We aimed to determine whether aflatoxin dietary exposure plays a role in the high incidence of hepatocellular carcinoma (HCC) observed among Hispanics in South Texas. We measured TP53R249S somatic mutation, hallmark of aflatoxin etiology in HCC, using droplet digital PCR and RFLP. TP53R249S mutation was detected in 3 of 41 HCC tumors from Hispanics in South Texas (7.3%). We also measured TP53R249S mutation in plasma cell-free DNA (cfDNA) from 218 HCC patients and 96 Hispanic subjects with advanced fibrosis or cirrhosis, from South Texas...
January 11, 2018: Cancer Prevention Research
https://www.readbyqxmd.com/read/29324546/applying-precision-medicine-to-ovarian-cancer-proof-of-principle-for-a-molecular-second-look
#14
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/29323170/droplet-digital-pcr-based-egfr-mutation-detection-with-an-internal-quality-control-index-to-determine-the-quality-of-dna
#15
Sung-Su Kim, Hyun-Jeung Choi, Jin Ju Kim, M Sun Kim, In-Seon Lee, Bohyun Byun, Lina Jia, Myung Ryurl Oh, Youngho Moon, Sarah Park, Joon-Seok Choi, Seoung Wan Chae, Byung-Ho Nam, Jin-Soo Kim, Jihun Kim, Byung Soh Min, Jae Seok Lee, Jae-Kyung Won, Soo Youn Cho, Yoon-La Choi, Young Kee Shin
In clinical translational research and molecular in vitro diagnostics, a major challenge in the detection of genetic mutations is overcoming artefactual results caused by the low-quality of formalin-fixed paraffin-embedded tissue (FFPET)-derived DNA (FFPET-DNA). Here, we propose the use of an 'internal quality control (iQC) index' as a criterion for judging the minimum quality of DNA for PCR-based analyses. In a pre-clinical study comparing the results from droplet digital PCR-based EGFR mutation test (ddEGFR test) and qPCR-based EGFR mutation test (cobas EGFR test), iQC index ≥ 0...
January 11, 2018: Scientific Reports
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
#16
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/29312652/tyrosine-kinase-inhibitor-sensitive-pdgfr%C3%AE-mutations-in-gist-two-cases-and-review-of-the-literature
#17
Pieter A Boonstra, Jourik A Gietema, Albert J H Suurmeijer, Matthew R Groves, Fernando de Assis Batista, Ed Schuuring, Anna K L Reyners
Gastrointestinal stromal tumors (GISTs) are rare mesenchymal malignancies of the gastrointestinal tract. Most GISTs harbor a c-KIT (80%) or a PDGFRα (10%) mutation that leads to constitutive activation of the tyrosine kinase receptor. Response to treatment with tyrosine kinase inhibitors (TKIs) is dependent on mutational status of the tumor. The most common mutation in PDGFRα, D842V, is known to be imatinib resistant. Almost all other PDGFRα mutations are imatinib sensitive. We describe two patients with a PDGFRα exon 18 mutated GIST responding to treatment with TKIs...
December 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29305255/comparative-analysis-of-gene-expression-in-maternal-peripheral-blood-and-monocytes-during-spontaneous-preterm-labor
#18
Alison G Paquette, Oksana Shynlova, Mark Kibschull, Nathan D Price, Stephen J Lye
BACKGROUND: Preterm birth is the leading cause of newborn death worldwide, and is associated with significant cognitive and physiological challenges in later life. There is a pressing need to define the mechanisms that initiate spontaneous preterm labor , and for development of novel clinical biomarkers to identify high-risk pregnancies. Most preterm birth studies utilize fetal tissues, and there is limited understanding of the transcriptional changes that occur in mothers undergoing spontaneous preterm labor...
January 2, 2018: American Journal of Obstetrics and Gynecology
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
#19
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
#20
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
keyword
keyword
96508
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"