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https://www.readbyqxmd.com/read/28089353/cerebrospinal-fluid-mitochondrial-dna-in-the-alzheimer-s-disease-continuum
#1
Laura Cervera-Carles, Daniel Alcolea, Ainara Estanga, Mirian Ecay-Torres, Andrea Izagirre, Montserrat Clerigué, Maite García-Sebastián, Jorge Villanúa, Clàudia Escalas, Rafael Blesa, Pablo Martínez-Lage, Alberto Lleó, Juan Fortea, Jordi Clarimón
Low levels of cell-free mitochondrial DNA (mtDNA) in the cerebrospinal fluid (CSF) of Alzheimer's disease (AD) patients have been identified and proposed as a novel biomarker for the disease. The lack of validation studies of previous results prompted us to replicate this finding in a comprehensive series of patients and controls. We applied droplet digital polymerase chain reaction in CSF specimens from 124 patients representing the AD spectrum and 140 neurologically healthy controls. The following preanalytical and analytical parameters were evaluated: the effect of freeze-thaw cycles on mtDNA, the linearity of mtDNA load across serial dilutions, and the mtDNA levels in the diagnostic groups...
December 22, 2016: Neurobiology of Aging
https://www.readbyqxmd.com/read/28088212/ultrasensitive-detection-of-oncogenic-human-papillomavirus-in-oropharyngeal-tissue-swabs
#2
Andre Isaac, Morris Kostiuk, Han Zhang, Cameron Lindsay, Fawaz Makki, Daniel A O'Connell, Jeffrey R Harris, David W J Cote, Hadi Seikaly, Vincent L Biron
BACKGROUND: The incidence of oropharyngeal squamous cell carcinoma (OPSCC) caused by oncogenic human papillomavirus (HPV) is rising worldwide. HPV-OPSCC is commonly diagnosed by RT-qPCR of HPV E6 and E7 oncoproteins or by p16 immunohistochemistry (IHC). Droplet digital PCR (ddPCR) has been recently reported as an ultra-sensitive and highly precise method of nucleic acid quantification for biomarker analysis. To validate the use of a minimally invasive assay for detection of oncogenic HPV based on oropharyngeal swabs using ddPCR...
January 14, 2017: Journal of Otolaryngology—Head & Neck Surgery
https://www.readbyqxmd.com/read/28081181/aronia-melanocarpa-extract-ameliorates-hepatic-lipid-metabolism-through-ppar%C3%AE-2-downregulation
#3
Chung-Hwa Park, Jung-Hee Kim, Eun Byul Lee, Wonhee Hur, Oh-Joo Kwon, Hyoung-Jin Park, Seung Kew Yoon
Nonalcoholic fatty liver disease (NAFLD) is a hepatic manifestation of metabolic syndrome. Studies have demonstrated that anthocyanin-rich foods may improve hyperlipidemia and ameliorate hepatic steatosis. Here, effects of Aronia melanocarpa (AM), known to be rich of anthocyanins, on hepatic lipid metabolism and adipogenic genes were determined. AM was treated to C57BL/6N mice fed with high fat diet (HFD) or to FL83B cells treated with free fatty acid (FFA). Changes in levels of lipids, enzymes and hormones were observed, and expressions of adipogenic genes involved in hepatic lipid metabolism were detected by PCR, Western blotting and luciferase assay...
2017: PloS One
https://www.readbyqxmd.com/read/28079102/corrigendum-ultra-sensitive-droplet-digital-pcr-for-detecting-a-low-prevalence-somatic-gnaq-mutation-in-sturge-weber-syndrome
#4
Yuri Uchiyama, Mitsuko Nakashima, Satoshi Watanabe, Masakazu Miyajima, Masataka Taguri, Satoko Miyatake, Noriko Miyake, Hirotomo Saitsu, Hiroyuki Mishima, Akira Kinoshita, Hajime Arai, Ko-Ichiro Yoshiura, Naomichi Matsumoto
No abstract text is available yet for this article.
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28077562/sensitive-and-inexpensive-digital-dna-analysis-by-microfluidic-enrichment-of-rolling-circle-amplified-single-molecules
#5
Malte Kühnemund, Iván Hernández-Neuta, Mohd Istiaq Sharif, Matteo Cornaglia, Martin A M Gijs, Mats Nilsson
Single molecule quantification assays provide the ultimate sensitivity and precision for molecular analysis. However, most digital analysis techniques, i.e. droplet PCR, require sophisticated and expensive instrumentation for molecule compartmentalization, amplification and analysis. Rolling circle amplification (RCA) provides a simpler means for digital analysis. Nevertheless, the sensitivity of RCA assays has until now been limited by inefficient detection methods. We have developed a simple microfluidic strategy for enrichment of RCA products into a single field of view of a low magnification fluorescent sensor, enabling ultra-sensitive digital quantification of nucleic acids over a dynamic range from 1...
January 10, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28073896/patient-specific-circulating-tumor-dna-detection-during-neoadjuvant-chemotherapy-in-triple-negative-breast-cancer
#6
Francesca Riva, Francois-Clement Bidard, Alexandre Houy, Adrien Saliou, Jordan Madic, Aurore Rampanou, Caroline Hego, Maud Milder, Paul Cottu, Marie-Paule Sablin, Anne Vincent-Salomon, Olivier Lantz, Marc-Henri Stern, Charlotte Proudhon, Jean-Yves Pierga
BACKGROUND: In nonmetastatic triple-negative breast cancer (TNBC) patients, we investigated whether circulating tumor DNA (ctDNA) detection can reflect the tumor response to neoadjuvant chemotherapy (NCT) and detect minimal residual disease after surgery. METHODS: Ten milliliters of plasma were collected at 4 time points: before NCT; after 1 cycle; before surgery; after surgery. Customized droplet digital PCR (ddPCR) assays were used to track tumor protein p53 (TP53) mutations previously characterized in tumor tissue by massively parallel sequencing...
January 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28073294/circulating-tumor-cells-and-dna-for-real-time-egfr-detection-and-monitoring-of-non-small-cell-lung-cancer
#7
Jinfeng He, Wei Tan, Jingping Ma
AIM: We investigate the suitability of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in non-small-cell lung cancer management, which is challenging in conventional biopsies. MATERIALS & METHODS: We performed serial blood extraction from 120 patients of varying EGFR status. Molecular profiling was performed using droplet digital PCR and correlated to survival outcome. RESULTS: Overall, we observed 95% agreement using CTCs and ctDNA with conventional tissue biopsies, which indicated the disease's close correlation...
January 11, 2017: Future Oncology
https://www.readbyqxmd.com/read/28069289/liquid-biopsy-analysis-of-fgfr3-and-pik3ca-hotspot-mutations-for-disease-surveillance-in-bladder-cancer
#8
Emil Christensen, Karin Birkenkamp-Demtröder, Iver Nordentoft, Søren Høyer, Kirstin van der Keur, Kim van Kessel, Ellen Zwarthoff, Mads Agerbæk, Torben Falck Ørntoft, Jørgen Bjerggaard Jensen, Lars Dyrskjøt
BACKGROUND: Disease surveillance in patients with bladder cancer is important for early diagnosis of progression and metastasis and for optimised treatment. OBJECTIVE: To develop urine and plasma assays for disease surveillance for patients with FGFR3 and PIK3CA tumour mutations. DESIGN, SETTING, AND PARTICIPANTS: Droplet digital polymerase chain reaction (ddPCR) assays were developed and tumour DNA from two patient cohorts was screened for FGFR3 and PIK3CA hotspot mutations...
January 6, 2017: European Urology
https://www.readbyqxmd.com/read/28064476/chemoselective-coupling-preserves-the-substrate-integrity-of-surface-immobilized-oligonucleotides-for-emulsion-pcr-based-gene-library-construction
#9
Marie L Malone, Valerie J Cavett, Brian M Paegel
Combinatorial bead libraries figure prominently in next-generation sequencing and are also important tools for in vitro evolution. The most common methodology for generating such bead libraries, emulsion PCR (emPCR), enzymatically extends bead-immobilized oligonucleotide PCR primers in emulsion droplets containing a single progenitor library member. Primers are almost always immobilized on beads via noncovalent biotin-streptavidin binding. Here, we describe covalent bead functionalization with primers (∼10(6) primers/2...
January 9, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28061461/estimation-of-cell-free-circulating-egfr-mutation-concentration-predicts-outcomes-in-nsclc-patients-treated-with-egfr-tkis
#10
Yan-Juan Zhu, Hai-Bo Zhang, Yi-Hong Liu, Fu-Li Zhang, Ya-Zhen Zhu, Yong Li, Jian-Ping Bai, Li-Rong Liu, Yan-Chun Qu, Xin Qu, Xian Chen, Yan Li, Guang-Juan Zheng
Detection of circulating tumor DNA using droplet digital polymerase chain reaction (ddPCR) is a highly-sensitive, minimally invasive alternative to serial biopsies for assessment and management of cancer. We used ddPCR to assess the utility of measuring plasma concentrations of common epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, and T790M) in 57 non-small cell lung cancer (NSCLC) patients treated with EGFR tyrosine kinase inhibitors (EGFR-TKIs). High baseline plasma EGFR mutation (pEGFRmut) concentrations were associated with shorter progression-free survival (8...
January 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060130/intracardiac-low-grade-sarcoma-following-treatment-for-ewing-sarcoma
#11
Michael V Ortiz, Heather Magnan, Emily K Slotkin, Srikanth R Ambati, Alexander J Chou, Leonard H Wexler, Paul A Meyers, Michael F Walsh, Todd Heaton, Leonard N Girardi, Suzanne L Wolden, Anita P Price, Jennifer A Kennedy, Ahmet Zehir, Meera Hameed, Michael F Berger, Alex Kentsis, Neerav Shukla
A 16-year-old male was diagnosed with Ewing sarcoma of the ribcage with pulmonary metastases. Six months after completion of scheduled therapy, he was found to have a new intracardiac mass, presumed recurrent Ewing sarcoma. EWSR1 fusion was not detected by droplet digital polymerase chain reaction from blood plasma. After no improvement with salvage chemotherapy, he underwent surgical resection that identified a low-grade spindle cell sarcoma. Despite the near-synchronous presentation of 2 unrelated sarcomas, extensive genomic analyses did not reveal any unifying somatic or germline mutations nor any apparent cancer predisposition...
January 5, 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28059126/an-exploratory-study-of-predisposing-genetic-factors-for-digeorge-velocardiofacial-syndrome
#12
Laia Vergés, Francesca Vidal, Esther Geán, Alexandra Alemany-Schmidt, Maria Oliver-Bonet, Joan Blanco
DiGeorge/velocardiofacial syndrome (DGS/VCFS) is a disorder caused by a 22q11.2 deletion mediated by non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs). We have evaluated the role of LCR22 genomic architecture and PRDM9 variants as DGS/VCFS predisposing factors. We applied FISH using fosmid probes on chromatin fibers to analyze the number of tandem repeat blocks in LCR22 in two DGS/VCFS fathers-of-origin with proven 22q11.2 NAHR susceptibility. Results revealed copy number variations (CNVs) of L9 and K3 fosmids in these individuals compared to controls...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28058543/genomic-profiling-of-canine-mast-cell-tumors-identifies-dna-copy-number-aberrations-associated-with-kit-mutations-and-high-histological-grade
#13
Hiroyuki Mochizuki, Rachael Thomas, Scott Moroff, Matthew Breen
Mast cell tumor (MCT) is the most common skin malignancy of domestic dogs and presents with a widely variable clinical behavior. Although activating KIT mutations are present in approximately 20% of canine MCTs, molecular etiology is largely unknown for the majority of this cancer. Characterization of genomic alterations in canine MCTs may identify genomic regions and/or genes responsible for their development and progression, facilitating the discovery of new therapeutic targets and improved clinical management of this heterogeneous cancer...
January 5, 2017: Chromosome Research
https://www.readbyqxmd.com/read/28052016/total-dna-input-is-a-crucial-determinant-of-the-sensitivity-of-plasma-cell-free-dna-egfr-mutation-detection-using-droplet-digital-pcr
#14
Yu Zhang, Yan Xu, Wei Zhong, Jing Zhao, Minjiang Chen, Li Zhang, Longyun Li, Mengzhao Wang
We evaluated the use of droplet digital PCR (ddPCR) to detect plasma cell-free DNA (cfDNA) epidermal growth factor receptor (EGFR) mutations in advanced non-small cell lung cancer (NSCLC) patients. Compared with tumor-tissue-based detection, the sensitivity of ddPCR for detecting plasma cfDNA tyrosine kinase inhibitor (TKI)-sensitizing EGFR mutations was 61.3%, the specificity was 96.7%, and the consistency rate was 81.4% (κ=0.605, 95% confidence interval: 0.501-0.706, p <0.0001). The sensitivity declined from 82...
December 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/28046096/early-antiretroviral-therapy-is-associated-with-lower-hiv-dna-molecular-diversity-and-lower-inflammation-in-cerebrospinal-fluid-but-does-not-prevent-the-establishment-of-compartmentalized-hiv-dna-populations
#15
Michelli F Oliveira, Antoine Chaillon, Masato Nakazawa, Milenka Vargas, Scott L Letendre, Matthew C Strain, Ronald J Ellis, Sheldon Morris, Susan J Little, Davey M Smith, Sara Gianella
Even when antiretroviral therapy (ART) is started early after infection, HIV DNA might persist in the central nervous system (CNS), possibly contributing to inflammation, brain damage and neurocognitive impairment. Paired blood and cerebrospinal fluid (CSF) were collected from 16 HIV-infected individuals on suppressive ART: 9 participants started ART <4 months of the estimated date of infection (EDI) ("early ART"), and 7 participants started ART >14 months after EDI ("late ART"). For each participant, neurocognitive functioning was measured by Global Deficit Score (GDS)...
January 3, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28046094/analysis-of-genetic-variation-in-cyp450-genes-for-clinical-implementation
#16
Liuh Ling Goh, Chia Wei Lim, Wey Cheng Sim, Li Xian Toh, Khai Pang Leong
BACKGROUND: Genetic determinants of drug response remain stable throughout life and offer great promise to patient-tailored drug therapy. The adoption of pharmacogenetic (PGx) testing in patient care requires accurate, cost effective and rapid genotyping with clear guidance on the use of the results. Hence, we evaluated a 32 SNPs panel for implementing PGx testing in clinical laboratories. METHODS: We designed a 32-SNP panel for PGx testing in clinical laboratories...
2017: PloS One
https://www.readbyqxmd.com/read/28044294/droplet-based-microfluidics-digital-pcr-for-the-detection-of-kras-mutations
#17
Deniz Pekin, Valerie Taly
We demonstrate an accurate and sensitive quantification of mutated KRAS oncogene in genomic DNA, using droplet-based microfluidics and digital PCR.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28042001/relationship-between-ccr5-wt-%C3%AE-32-heterozygosity-and-hiv-1-reservoir-size-in-adolescents-and-young-adults-with-perinatally-acquired-hiv-1-infection
#18
Marta Martínez-Bonet, A González-Serna, Maria Isabel Clemente, Sara Morón-López, Laura Díaz, Marisa Navarro, Maria C Puertas, Manuel Leal, Ezequiel Ruiz-Mateos, Javier Martinez-Picado, Maria Angeles Muñoz Fernández
BACKGROUND: Several host factors contribute to HIV disease progression in the absence of combination antiretroviral therapy (cART). Among them, the CC-chemokine receptor 5 (CCR5) is known to be the main coreceptor used by HIV-1 to enter target cells during the early stages of an HIV-1 infection. OBJECTIVE: We evaluated the association of CCR5((WT/Δ32)) heterozygosity with HIV-1 reservoir size, lymphocyte differentiation, activation and immunosenescence in adolescents and young adults with perinatally acquired HIV-infection receiving cART...
December 29, 2016: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/28040796/role-of-rpl39-in-metaplastic-breast-cancer
#19
Bhuvanesh Dave, Daniel D Gonzalez, Zhi-Bin Liu, Xiaoxian Li, Helen Wong, Sergio Granados, Nadeer E Ezzedine, Douglas H Sieglaff, Joe E Ensor, Kathy D Miller, Milan Radovich, Agda KarinaEtrovic, Steven S Gross, Olivier Elemento, Gordon B Mills, Michael Z Gilcrease, Jenny C Chang
BACKGROUND: Metaplastic breast cancer is one of the most therapeutically challenging forms of breast cancer because of its highly heterogeneous and chemoresistant nature. We have previously demonstrated that ribosomal protein L39 (RPL39) and its gain-of-function mutation A14V have oncogenic activity in triple-negative breast cancer and this activity may be mediated through inducible nitric oxide synthase (iNOS). The function of RPL39 and A14V in other breast cancer subtypes is currently unknown...
June 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/28039535/use-of-droplet-digital-pcr-for-quantitative-and-automatic-analysis-of-the-her2-status-in-breast-cancer-patients
#20
Kazutaka Otsuji, Takeshi Sasaki, Atsushi Tanaka, Akiko Kunita, Masako Ikemura, Keisuke Matsusaka, Keiichiro Tada, Masashi Fukayama, Yasuyuki Seto
PURPOSE: Digital polymerase chain reaction (dPCR) has been used to yield an absolute measure of nucleic acid concentrations. Recently, a new method referred to as droplet digital PCR (ddPCR) has gained attention as a more precise and less subjective assay to quantify DNA amplification. We demonstrated the usefulness of ddPCR to determine HER2 gene amplification of breast cancer. METHODS: In this study, we used ddPCR to measure the HER2 gene copy number in clinical formalin-fixed paraffin-embedded samples of 41 primary breast cancer patients...
December 30, 2016: Breast Cancer Research and Treatment
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