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https://www.readbyqxmd.com/read/28645444/npm1-for-mrd-droplet-like-it-s-hot
#1
Gerald B W Wertheim, Adam Bagg
This commentary highlights the article by Mencia-Trinchant et al that describes a novel digital PCR assay for sensitive detection of minimal residual disease in NPM1 mutated acute myeloid leukemia.
July 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28640831/ribosomal-dna-copy-number-loss-and-sequence-variation-in-cancer
#2
Baoshan Xu, Hua Li, John M Perry, Vijay Pratap Singh, Jay Unruh, Zulin Yu, Musinu Zakari, William McDowell, Linheng Li, Jennifer L Gerton
Ribosomal DNA is one of the most variable regions in the human genome with respect to copy number. Despite the importance of rDNA for cellular function, we know virtually nothing about what governs its copy number, stability, and sequence in the mammalian genome due to challenges associated with mapping and analysis. We applied computational and droplet digital PCR approaches to measure rDNA copy number in normal and cancer states in human and mouse genomes. We find that copy number and sequence can change in cancer genomes...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28637527/rodents-goats-and-dogs-their-potential-roles-in-the-transmission-of-schistosomiasis-in-china
#3
Clare F VAN Dorssen, Catherine A Gordon, Yuesheng Li, Gail M Williams, Yuanyuan Wang, Zhenhua Luo, Geoffrey N Gobert, Hong You, Donald P McManus, Darren J Gray
Schistosomiasis in China has been substantially reduced due to an effective control programme employing various measures including bovine and human chemotherapy, and the removal of bovines from endemic areas. To fulfil elimination targets, it will be necessary to identify other possible reservoir hosts for Schistosoma japonicum and include them in future control efforts. This study determined the infection prevalence of S. japonicum in rodents (0-9·21%), dogs (0-18·37%) and goats (6·9-46·4%) from the Dongting Lake area of Hunan province, using a combination of traditional coproparasitological techniques (miracidial hatching technique and Kato-Katz thick smear technique) and molecular methods [quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR)]...
June 22, 2017: Parasitology
https://www.readbyqxmd.com/read/28636544/analysis-of-esr1-and-pik3ca-mutations-in-plasma-cell-free-dna-from-er-positive-breast-cancer-patients
#4
Takashi Takeshita, Yutaka Yamamoto, Mutsuko Yamamoto-Ibusuki, Mai Tomiguchi, Aiko Sueta, Keiichi Murakami, Yoko Omoto, Hirotaka Iwase
BACKGROUND: The measurement of ESR1 and PIK3CA mutations in plasma cell-free DNA (cfDNA) has been studied as a non-invasive method to quickly assess and monitor endocrine therapy (ET) resistant metastatic breast cancer (MBC) patients. METHODS: The subjects of this retrospective study were a total of 185 plasma samples from 86 estrogen receptor-positive BC patients, of which 151 plasma samples were from 69 MBC patients and 34 plasma samples were from 17 primary BC (PBC) patients...
June 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28629339/droplet-digital-pcr-for-detection-and-quantification-of-circulating-tumor-dna-in-plasma-of-head-and-neck-cancer-patients
#5
Joost H van Ginkel, Manon M H Huibers, Robert J J van Es, Remco de Bree, Stefan M Willems
BACKGROUND: During posttreatment surveillance of head and neck cancer patients, imaging is insufficiently accurate for the early detection of relapsing disease. Free circulating tumor DNA (ctDNA) may serve as a novel biomarker for monitoring tumor burden during posttreatment surveillance of these patients. In this exploratory study, we investigated whether low level ctDNA in plasma of head and neck cancer patients can be detected using Droplet Digital PCR (ddPCR). METHODS: TP53 mutations were determined in surgically resected primary tumor samples from six patients with high stage (II-IV), moderate to poorly differentiated head and neck squamous cell carcinoma (HNSCC)...
June 19, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28626778/single-cell-based-vector-tracing-in-patients-with-ada-scid-treated-with-stem-cell-gene-therapy
#6
Yuka Igarashi, Toru Uchiyama, Tomoko Minegishi, Sirirat Takahashi, Nobuyuki Watanabe, Toshinao Kawai, Masafumi Yamada, Tadashi Ariga, Masafumi Onodera
Clinical improvement in stem cell gene therapy (SCGT) for primary immunodeficiencies depends on the engraftment levels of genetically corrected cells, and tracing the transgene in each hematopoietic lineage is therefore extremely important in evaluating the efficacy of SCGT. We established a single cell-based droplet digital PCR (sc-ddPCR) method consisting of the encapsulation of a single cell into each droplet, followed by emulsion PCR with primers and probes specific for the transgene. A fluorescent signal in a droplet indicates the presence of a single cell carrying the target gene in its genome, and this system can clearly determine the ratio of transgene-positive cells in the entire population at the genomic level...
September 15, 2017: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/28625643/sequential-liquid-biopsies-reveal-dynamic-alterations-of-egfr-driver-mutations-and-indicate-egfr-amplification-as-a-new-mechanism-of-resistance-to-osimertinib-in-nsclc
#7
Franciele H Knebel, Fabiana Bettoni, Andrea K Shimada, Manoel Cruz, João Victor Alessi, Marcelo V Negrão, Luiz Fernando L Reis, Artur Katz, Anamaria A Camargo
Osimertinib is an EGFR-T790M-specific TKI, which has demonstrated impressive response rates in NSCLC, after failure to first-line anti-EGFR TKIs. However, acquired resistance to osimertinib is also observed and the molecular mechanisms of resistance are not yet fully understood. Monitoring and managing NSCLC patients who progressed on osimertinib is, therefore, emerging as an important clinical challenge. Sequential liquid biopsies were used to monitor a patient with EGFR-exon19del positive NSCLC, who received erlotinib and progressed through the acquisition of the EGFR-T790M mutation...
June 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28623522/h3-k27m-mutations-are-extremely-rare-in-posterior-fossa-group-a-ependymoma
#8
Scott Ryall, Miguel Guzman, Samer K Elbabaa, Betty Luu, Stephen C Mack, Michal Zapotocky, Michael D Taylor, Cynthia Hawkins, Vijay Ramaswamy
BACKGROUND: Mutations in the tail of histone H3 (K27M) are frequently found in pediatric midline high-grade glioma's but have rarely been reported in other malignancies. Recently, recurrent somatic nucleotide variants in histone H3 (H3 K27M) have been reported in group A posterior fossa ependymoma (EPN_PFA), an entity previously described to have no recurrent mutations. However, the true incidence of H3 K27M mutations in EPN_PFA is unknown. METHODS: In order to discern the frequency of K27M mutations in histone H3 in EPN_PFA, we analyzed 151 EPN_PFA previously profiled with genome-wide methylation arrays using a validated droplet digital PCR assay...
June 16, 2017: Child's Nervous System: ChNS: Official Journal of the International Society for Pediatric Neurosurgery
https://www.readbyqxmd.com/read/28619387/evaluation-of-ameliorative-ability-of-silibinin-against-zidovudine-and-isoniazid-induced-hepatotoxicity-and-hyperlipidaemia-in-rats-role-of-silibinin-in-phase-i-and-ii-drug-metabolism
#9
Raghu Ramanathan, Karthikeyan Sivanesan
HIV/AIDS patients have suppressed immune system, making them vulnerable to many opportunistic infections including tuberculosis (TB). The patients who are co-infected with TB undergo combined regimens with anti-retroviral drugs such as zidovudine (AZT) and anti-tubercular drug such as isoniazid (INH) for therapy leading to hepatotoxicty. Silibinin (SBN), extracted from Silybum marianum commonly called as "Milk thistle" is used against several drugs-induced hepatotoxicity. The present study evaluates the ameliorative effect of SBN against AZT alone, INH alone, and INH + AZT-induced toxic insults to liver of rats...
June 13, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28615231/single-nucleotide-polymorphism-leading-to-false-allelic-fraction-by-droplet-digital-pcr
#10
Eric S Christenson, William B Dalton, David Chu, Ian Waters, Karen Cravero, Daniel J Zabransky, Amy DeZern, Ben Ho Park
BACKGROUND: Molecular-based diagnostics have great utility for cancer detection. We have used droplet digital PCR (ddPCR) as a platform for identifying mutations in circulating plasma tumor DNA (ptDNA). We present the unexpected finding of a spurious mutant allele fraction that was discovered to be artifactual because of the presence of a single-nucleotide polymorphism (SNP) in a patient sample. DESIGN AND METHODS: Probe and primer combinations for the K700 and V701 loci of the SF3B1 spliceosome gene were designed for ddPCR to identify the percentage of mutant and wild-type alleles...
June 14, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28614778/the-human-immunodeficiency-virus-hiv1-protease-inhibitor-sanquinavir-activates-autophagy-and-removes-lipids-deposited-in-lipid-droplets
#11
A Polus, M Bociaga-Jasik, U Czech, J Goralska, U Cialowicz, M Chojnacka, M Polus, K Jurowski, A Dembinska-Kiec
Reduction in mortality and increased average life span of the human immunodeficiency virus (HIV)-infected patients treated with antiretroviral therapy (ART) are associated with the risk of unwanted effects, such as insulin resistance and dyslipidemia with cardiovascular complications. Antiretroviral therapy may also be associated with lipodystrophy characterized as peripheral lipoatrophy with central fat accumulation. Understanding the molecular mechanisms of lipodystrophy caused by ART is important for therapeutic strategy and the prediction of side-effects...
April 2017: Journal of Physiology and Pharmacology: An Official Journal of the Polish Physiological Society
https://www.readbyqxmd.com/read/28602964/droplet-digital-pcr-improved-the-egfr-mutation-diagnosis-with-pleural-fluid-samples-in-non-small-cell-lung-cancer-patients
#12
Xiaoyan Li, Yi Liu, Weiwei Shi, Huayan Xu, Haixu Hu, Zhengwei Dong, Guanshan Zhu, Yun Sun, Bing Liu, Hongjun Gao, Chuanhao Tang, Xiaoqing Liu
BACKGROUND: Droplet digital polymerase chain reaction (ddPCR) is a promising method for analyzing minor amounts of nucleic acid. However, its application has not been reported in pleural fluid, which is an ideal sample source for epidermal growth factor receptor (EGFR) mutation analysis in non-small-cell lung cancer (NSCLC) patients. METHODS: The extracted DNA from supernatants of pleural fluid was selected from our sample bank and re-analyzed by our previously established ddPCR assay...
June 8, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28601386/detection-of-alk-and-kras-mutations-in-circulating-tumor-dna-of-patients-with-advanced-alk-positive-nsclc-with-disease-progression-during-crizotinib-treatment
#13
Paola Bordi, Marcello Tiseo, Eleonora Rofi, Iacopo Petrini, Giuliana Restante, Romano Danesi, Marzia Del Re
BACKGROUND: In patients with anaplastic lymphoma kinase (ALK)-positive non-small-cell lung cancer (NSCLC), disease progression occurs after a median of 9 to 10 months of crizotinib treatment. Several mechanisms of resistance have been identified and include ALK mutations and amplification or the activation of bypassing signaling pathways. Rebiopsy in NSCLC patients represents a critical issue and the analysis of circulating cell-free DNA (cfDNA) has a promising role for the identification of resistance mechanisms...
May 18, 2017: Clinical Lung Cancer
https://www.readbyqxmd.com/read/28599456/dynamic-monitoring-of-egfr-mutations-in-circulating-cell-free-dna-for-egfr-mutant-metastatic-patients-with-lung-cancer-early-detection-of-drug-resistance-and-prognostic-significance
#14
Jianjiao Ni, Linqian Weng, Yi Liu, Zhao Sun, Chunmei Bai, Yingyi Wang
Detecting genetic mutations in circulating cell-free DNA (cfDNA) is a promising approach of liquid biopsy. Between June 2014 and May 2015, 168 plasma samples were collected monthly from 20 patients with metastatic lung adenocarcinoma with epidermal growth factor receptor (EGFR) mutation receiving gefitinib therapy. Clinically relevant EGFR mutations, including exon 19 deletion, L858R and T790M, were quantified using droplet digital polymerase chain reaction. In baseline samples, 19 (95.0%) patients had the same mutation with the matched tumors, and pretreatment T790M mutations were also detected in 3 (15...
June 2017: Oncology Letters
https://www.readbyqxmd.com/read/28598079/-effects-of-different-concentrations-of-glucose-on-the-osteogenic-differentiation-of-orofacial-bone-mesenchymal-stem-cells
#15
Yang Chen, Yun Hu, Lan Yang, Jie Zhou, Yu-Ying Tang, Lei-Lei Zheng
OBJECTIVES: To determine the effects of different concentrations of glucose on the proliferation and osteogenic differentiation of orofacial bonemesenchymal stem cells (OFMSCs). METHODS: OFMSCs were primarily cultured and identified in vitro to undergo osteogenic/adipogenic/chondrogenic differentiation. The cells were exposed to osteogenic medium containing different levels of glucose: 5.5,11,16.5,25,44 mmol/L. The cell activity and proliferation index were measured using a cell counting kit (CCK)-8 and flow cytometry...
September 2016: Sichuan da Xue Xue Bao. Yi Xue Ban, Journal of Sichuan University. Medical Science Edition
https://www.readbyqxmd.com/read/28590119/parallel-evaluation-of-melting-temperatures-of-dnas-in-the-arrayed-droplets-through-the-fluorescence-from-dna-intercalators
#16
Yuzuru Shimazaki, Junko Tanaka, Yoshinobu Kohara, Masao Kamahori, Takeshi Sakamoto
Parallel evaluation of melting temperatures (Tm's) of DNA molecules in multiple floating droplets (20 μm in diameter) was demonstrated. The Tm values were evaluated from the melting curves which were observed through the fluorescence from the DNA intercalators. The Tm values measured in the droplets corresponded well to those measured in the bulk, indicating the validity of the measurement. The parallel evaluation of Tm's was realized by observing melting curves of DNAs in the different droplets at the same time using the "droplet guide", which guided and fixed the floating droplets to the designated points in the observing plane...
June 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28589341/highly-sensitive-and-reliable-detection-of-egfr-exon-19-deletions-by-droplet-digital-polymerase-chain-reaction
#17
Natalya Oskina, Igor Oscorbin, Evgeniy Khrapov, Ulyana Boyarskikh, Dmitriy Subbotin, Irina Demidova, Evgeny Imyanitov, Maxim Filipenko
BACKGROUND: Analysis of EGFR mutations is becoming a routine clinical practice but the optimal EGFR mutation testing method is still to be determined. METHODS: We determined the nucleotide sequence of deletions located in exon 19 of the EGFR gene in lung tumor samples of patients residing in different regions of Russia (153 tumor DNA specimens), using Sanger sequencing. We developed a droplet digital polymerase chain reaction assay capable of detecting all common EGFR deletions in exon 19...
June 6, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28587748/liquid-biopsy-of-pik3ca-mutations-in-cervical-cancer-in-hong-kong-chinese-women
#18
Tony K H Chung, Tak Hong Cheung, So Fan Yim, Mei Yun Yu, Rossa W K Chiu, Keith W K Lo, Ida P C Lee, Raymond R Y Wong, Kitty K M Lau, Vivian W Wang, Michael J Worley, Kevin M Elias, Stephen J Fiascone, David I Smith, Ross S Berkowitz, Yick Fu Wong
INTRODUCTION: Cervical cancer is the fourth most common female cancer worldwide. The prognosis for women with advanced-stage or recurrent cervical cancer remains poor and response to treatment is variable. Standardized management protocols leave little room for individualization. We report on a novel blood-based liquid biopsy for specific PIK3CA mutations as a clinically useful biomarker in patients with invasive cervical cancer. METHODS: One hundred seventeen Hong Kong Chinese women with primary invasive cervical cancer and their pre-treatment plasma samples were investigated...
June 3, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28585566/analysis-of-line-1-elements-in-dna-from-postmortem-brains-of-individuals-with-schizophrenia
#19
Glenn A Doyle, Richard C Crist, Emre T Karatas, Matthew J Hammond, Adam D Ewing, Thomas N Ferraro, Chang-Gyu Hahn, Wade H Berrettini
Whereas some rare genetic variants convey high risk for schizophrenia (SZ), common alleles conveying even moderate risk remain elusive. Long interspersed element-1s (L1) are mobile retrotransposons comprising ~17% of the human genome. L1 retrotransposition can cause somatic mosaicism during neurodevelopment by insertional mutagenesis. We hypothesized that, compared to controls, patients diagnosed with schizophrenia (PDS) may have increased numbers of deleterious L1 insertions, perhaps occurring de novo, in brain-expressed genes of dorsolateral prefrontal cortex (DLPFC) neurons...
June 6, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28580707/a-classifier-integrating-plasma-biomarkers-and-radiological-characteristics-for-distinguishing-malignant-from-benign-pulmonary-nodules
#20
Yanli Lin, Qixin Leng, Zhengran Jiang, Maria A Guarnera, Yun Zhou, Xueqi Chen, Heping Wang, Wenxian Zhou, Ling Cai, HongBin Fang, Jie Li, Hairong Jin, Linghui Wang, Shaoqiong Yi, Wei Lu, David Evers, Carol B Fowle, Yun Su, Feng Jiang
Lung cancer is primarily caused by cigarette smoking and the leading cancer killer in the USA and across the world. Early detection of lung cancer by low-dose CT (LDCT) can reduce the mortality. However, LDCT dramatically increases the number of indeterminate pulmonary nodules (PNs), leading to overdiagnosis. Having a definitive preoperative diagnosis of malignant PNs is clinically important. Using microarray and droplet digital PCR to directly profile plasma miRNA expressions of 135 patients with PNs, we identified 11 plasma miRNAs that displayed a significant difference between patients with malignant versus benign PNs...
June 4, 2017: International Journal of Cancer. Journal International du Cancer
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