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Alexandra S Whale, Gerwyn M Jones, Jernej Pavšič, Tanja Dreo, Nicholas Redshaw, Sema Akyurek, Muslum Akgoz, Carla Divieto, Maria PaolaSassi, Hua-Jun He, Kenneth D Cole, Young-Kyung Bae, Sang-Ryoul Park, Liesbet Deprez, Philippe Corbisier, Sonia Garrigou, Valérie Taly, Raquel Larios, Simon Cowen, Denise M O'Sullivan, Claire A Bushell, Heidi Goenaga-Infante, Carole A Foy, Alison J Woolford, Helen Parkes, Jim F Huggett, Alison S Devonshire
BACKGROUND: Genetic testing of tumor tissue and circulating cell-free DNA for somatic variants guides patient treatment of many cancers. Such measurements will be fundamental in the future support of precision medicine. However, there are currently no primary reference measurement procedures available for nucleic acid quantification that would support translation of tests for circulating tumor DNA into routine use. METHODS: We assessed the accuracy of digital PCR (dPCR) for copy number quantification of a frequently occurring single-nucleotide variant in colorectal cancer ( KRAS c...
June 14, 2018: Clinical Chemistry
Wanxia Gai, Lu Ji, W K Jacky Lam, Kun Sun, Peiyong Jiang, Anthony W H Chan, John Wong, Paul B S Lai, Simon S M Ng, Brigette B Y Ma, Grace L H Wong, Vincent W S Wong, Henry L Y Chan, Rossa W K Chiu, Y M Dennis Lo, K C Allen Chan
BACKGROUND: Measurement of DNA derived from different tissues in the circulating DNA pool can provide important information regarding the presence of many pathological conditions. However, existing methods involving genome-wide bisulfite sequencing are relatively expensive and may present challenges for large-scale analysis. METHODS: Through identifying differentially methylated regions in the liver and colon compared with other tissues, we identified 2 markers and developed corresponding droplet digital PCR assays...
June 14, 2018: Clinical Chemistry
Emmanouil Papasavvas, Steven M Lada, Jocelin Joseph, Xiangfan Yin, Qin Liu, Livio Azzoni, Karam Mounzer, Jay R Kostman, Douglas Richman, Luis J Montaner
OBJECTIVE: The impact of short-term analytical antiretroviral therapy (ART) interruptions on the levels of cellular HIV and of residual activation after subsequent ART-mediated plasma HIV viral load re-suppression remains under active investigation. DESIGN: Peripheral blood mononuclear cells (PBMC) from 23 ART-suppressed, chronically HIV-1-infected subjects were evaluated at the initiation of an analytical treatment interruption (ATI), during ATI, and following plasma re-suppression of HIV with ART...
June 11, 2018: AIDS
Shingo Sakashita, Aya Shiba-Ishii, Yoshihiko Murata, Ryutaro Sekimoto, Yuko Minami, Yukio Sato, Masayuki Noguchi
EGFR T790M mutation is a crucial gene alteration causing EGFR TKI resistance. However, the implication of T790M mutation is still unknown for the stepwise progression of EGFR TKI naïve lung adenocarcinoma. In this study, we studied site-related EGFR T790M mutation analysis in EGFR TKI naïve lung adenocarcinomas harboring double EGFR mutation (L858R and T790M or Exon 19 deletion (Del.19) and T790M) by droplet digital (dd) PCR method. We examined three resected lung adenocarcinoma cases harboring EGFR double mutation including T790M...
May 21, 2018: Pathology, Research and Practice
Sibylle Hurschler Lichtsteiner, Werner Wicki, Péter Falmann
As recent studies and theoretical assumptions suggest that the quality of texts composed by children and adolescents is affected by their transcription skills, this experimental field trial aims at investigating the impact of combined handwriting/spelling training on fluency, spelling and text quality among normally developing 3rd graders (N = 175). In addition to the combined handwriting/spelling training group, the sample includes two other intervention groups, a handwriting training group and a spelling training group as well as a reading fluency training control group...
2018: Reading and Writing
Kazutaka Takeshita, Hideyuki Tamaki, Tsubasa Ohbayashi, Xian-Ying Meng, Teruo Sone, Yasuo Mitani, Charlotte Peeters, Yoshitomo Kikuchi, Peter Vandamme
A Gram-negative, aerobic, rod-shaped, non-spore-forming, motile bacterium, designated strain RPE64T , was isolated from the gut symbiotic organ of the bean bug Riptortus pedestris, collected in Tsukuba, Japan, in 2007. 16S rRNA gene sequencing showed that this strain belongs to the Burkholderia glathei clade, exhibiting the highest sequence similarity to Burkholderia peredens LMG 29314T (100 %), Burkholderia turbans LMG 29316T (99.52 %) and Burkholderia ptereochthonis LMG 29326T (99.04 %). Phylogenomic analyses based on 107 single-copy core genes and Genome blast Distance Phylogeny confirmed B...
June 4, 2018: International Journal of Systematic and Evolutionary Microbiology
G Maltese, S V Tan, E Bruno, A Brackenridge, S Thomas
BACKGROUND: Hereditary Neuropathy with liability to Pressure Palsies (HNPP) is an autosomal dominant neuropathy, associated with deletion of the Peripheral Myelin Protein-22 (PMP-22) gene, causing recurrent painless palsies with age of onset between 10 and 30 years old. Only a few cases of Type 2 Diabetes and HNPP have been described and the coexistence of HNPP and Type 1 diabetes has never been reported. CASE REPORT: A 54-year old man with a history of Type 1 diabetes, managed with continuous subcutaneous insulin infusion (CSII), presented with deterioration of long-standing motor and sensory symptoms, previously attributed to golfer's elbow, diabetic neuropathy and spinal degenerative disease...
June 4, 2018: Diabetic Medicine: a Journal of the British Diabetic Association
Manish Kohli, Jian Li, Meijun Du, David W Hillman, Scott M Dehm, Winston Tan, Rachel Carlson, Michael B Campion, Liguo Wang, Liewei Wang, Huijuan Zhang, Peng Zhang, Deepak Kilari, Chiang-Ching Huang, Liang Wang
BACKGROUND: The prognostic significance of plasma cell-free DNA (cfDNA) androgen receptor amplification (ARamp) in metastatic castration-resistant prostate cancer (mCRPC) compared with circulating tumor cell (CTC) counts is not known. METHODS: As part of correlative aims of a prospective study in mCRPC, concurrent and serial collections of plasma and CTCs were performed. Specimen collections were performed at baseline after progression on androgen deprivation therapy and then 12 weeks later...
June 1, 2018: Prostate Cancer and Prostatic Diseases
Roelof Dirk Coertze, Cornelius Carlos Bezuidenhout
This study aimed to investigate the presence and diversity of AmpC β-lactamase and integrase genes among DNA (genomic and plasmid) from bacterial populations in selected aquatic systems. Following an enrichment step, DNA was isolated and subjected to polymerase chain reaction (PCR) and digital droplet PCR. The intI1 gene and AmpC β-lactamase genes were present in genomic and plasmid DNA from all sites in the Mooi, Crocodile and Marico Rivers, with the exception of intI1 in the Marico River. Digital droplet PCR demonstrated that copy numbers varied considerably (0...
May 2018: Water Science and Technology: a Journal of the International Association on Water Pollution Research
Dana Wai Yi Tsui, Muhammed Murtaza, Alvin Seng Cheong Wong, Oscar M Rueda, Christopher G Smith, Dineika Chandrananda, Ross A Soo, Hong Liang Lim, Boon Cher Goh, Carlos Caldas, Tim Forshew, Davina Gale, Wei Liu, James Morris, Francesco Marass, Tim Eisen, Tan Min Chin, Nitzan Rosenfeld
Tumour heterogeneity leads to the development of multiple resistance mechanisms during targeted therapies. Identifying the dominant driver(s) is critical for treatment decision. We studied the relative dynamics of multiple oncogenic drivers in longitudinal plasma of 50 EGFR -mutant non-small-cell lung cancer patients receiving gefitinib and hydroxychloroquine. We performed digital PCR and targeted sequencing on samples from all patients and shallow whole-genome sequencing on samples from three patients who underwent histological transformation to small-cell lung cancer...
May 30, 2018: EMBO Molecular Medicine
M J A Weerts, E C Timmermans, A van de Stolpe, R H A M Vossen, S Y Anvar, J A Foekens, S Sleijfer, J W M Martens
The use of blood-circulating cell-free DNA (cfDNA) as a "liquid biopsy" in oncology is being explored for its potential as a cancer biomarker. Mitochondria contain their own circular genomic entity (mitochondrial DNA, mtDNA), up to even thousands of copies per cell. The mutation rate of mtDNA is several orders of magnitude higher than that of the nuclear DNA. Tumor-specific variants have been identified in tumors along the entire mtDNA, and their number varies among and within tumors. The high mtDNA copy number per cell and the high mtDNA mutation rate make it worthwhile to explore the potential of tumor-specific cf-mtDNA variants as cancer marker in the blood of cancer patients...
May 26, 2018: Neoplasia: An International Journal for Oncology Research
Ronald Klein, Kristine E Lee, Lorraine Danforth, Michael Y Tsai, Ronald E Gangnon, Stacy E Meuer, Tien Y Wong, Carol Y Cheung, Barbara E K Klein
PURPOSE: To examine the relationships of retinal vessel geometric characteristics (RVGCs) to the incidence and progression of diabetic retinopathy (DR). DESIGN: Observational, prospective cohort study. PARTICIPANTS: Nine hundred ninety-six persons with type 1 diabetes mellitus (T1DM) and 1370 persons with type 2 diabetes mellitus (T2DM) seen at a baseline examination who were eligible for follow-up examinations at subsequent 5-year intervals...
May 17, 2018: Ophthalmology
Irene Gullo, Patrícia Oliveira, Maria Athelogou, Gilza Gonçalves, Marta L Pinto, Joana Carvalho, Ana Valente, Hugo Pinheiro, Sara Andrade, Gabriela M Almeida, Ralf Huss, Kakoli Das, Patrick Tan, José C Machado, Carla Oliveira, Fátima Carneiro
BACKGROUND: Gastric cancer with lymphoid stroma (GCLS) is characterized by prominent stromal infiltration of T-lymphocytes. The aim of this study was to investigate GCLS biology through analysis of clinicopathological features, EBV infection, microsatellite instability (MSI), immune gene-expression profiling and PD-L1 status in neoplastic cells and tumor immune microenvironment. METHODS: Twenty-four GCLSs were analyzed by RNA in situ hybridization for EBV (EBER), PCR/fragment analysis for MSI, immunohistochemistry (PD-L1, cytokeratin, CD3, CD8), co-immunofluorescence (CK/PD-L1, CD68/PD-L1), NanoString gene-expression assay for immune-related genes and PD-L1 copy number alterations...
May 19, 2018: Gastric Cancer
Vijayanandraj Selvaraj, Yogita Maheshwari, Subhas Hajeri, Jianchi Chen, Thomas Greg McCollum, Raymond Yokomi
Huanglongbing (HLB, citrus greening) is a devastating citrus disease affecting citrus production worldwide. It is associated with the bacterium "Candidatus Liberibacter asiaticus" (CLas) and is vectored by the Asian citrus psyllid (ACP). Currently, diagnosis of CLas in regulatory samples is based on real-time quantitative polymerase chain reaction (qPCR) using 16S rRNA gene specific primers/probe. The detection of CLas using qPCR is challenging due to low pathogen titer and uneven distribution in infected plants and exacerbated by sampling issues and presence of inhibitors...
2018: PloS One
Deepani D Fernando, Simone L Reynolds, Martha Zakrzewski, Ehtesham Mofiz, Anthony T Papenfuss, Deborah Holt, Katja Fischer
BACKGROUND: Scabies is worldwide one of the most common, yet neglected, parasitic skin infections, affecting a wide range of mammals including humans. Limited treatment options and evidence of emerging mite resistance against the currently used drugs drive our research to explore new therapeutic candidates. Previously, we discovered a multicopy family of genes encoding cysteine proteases with their catalytic sites inactivated by mutation (SMIPP-Cs). This protein family is unique in parasitic scabies mites and is absent in related non-burrowing mites...
May 16, 2018: Parasites & Vectors
Alvin Ho-Kwan Cheung, Chit Chow, Jinglin Zhang, Yuhang Zhou, Tingting Huang, Kayla Ching-Kei Ng, Terry Cho-Tsun Or, Yoyo Yao Yao, Yujuan Dong, Jackie Mei-Wah Fung, Lei Xiong, Aden Ka-Yin Chan, Wai-Ming Raymond Lung, Wei Kang, Ka-Fai To
Cancer cells are defined genetically by the mutations they harbor, commonly single nucleotide substitutions. Therapeutic approaches which specifically target cancer cells by recognizing these defining genetic aberrations are expected to exhibit minimal side-effects. However, current protein-based targeted therapy is greatly limited by the range of genes that can be targeted, as well as by acquired resistance. We hypothesized that a therapeutic oligonucleotide-based strategy may address this need of specific cancer targeting...
May 10, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
Havell Markus, Tania Contente-Cuomo, Maria Farooq, Winnie S Liang, Mitesh J Borad, Shivan Sivakumar, Simon Gollins, Nhan L Tran, Harshil D Dhruv, Michael E Berens, Alan Bryce, Aleksandar Sekulic, Antoni Ribas, Jeffrey M Trent, Patricia M LoRusso, Muhammed Murtaza
Pre-analytical factors can significantly affect circulating cell-free DNA (cfDNA) analysis. However, there are few robust methods to rapidly assess sample quality and the impact of pre-analytical processing. To address this gap and to evaluate effects of DNA extraction methods and blood collection tubes on cfDNA yield and fragment size, we developed a multiplexed droplet digital PCR (ddPCR) assay with 5 short and 4 long amplicons targeting single copy genomic loci. Using this assay, we compared 7 cfDNA extraction kits and found cfDNA yield and fragment size vary significantly...
May 9, 2018: Scientific Reports
Annika Antonsson, Lani Knight, Benedict J Panizza, Sandro V Porceddu, Sarah Emmett, David C Whiteman
CONCLUSIONS: We did not identify any strong associations between HPV-16 viral load and any of the clinical or lifestyle factors. OBJECTIVE: The epidemiology of oropharyngeal SCC is changing, with an increasing proportion of HPV-positive cases seen in the last decade. It is known that a high viral load is linked to the development of cervical cancer, the relation between viral load and oropharyngeal SCC is less clear. We sought to determine HPV-16 viral load in HPV-positive oropharyngeal SCCs using highly sensitive digital PCR and to identify clinical and lifestyle factors associated with viral load...
May 9, 2018: Acta Oto-laryngologica
Frédéric Auvré, Julien Coutier, Michèle T Martin, Nicolas O Fortunel
Genetic and epigenetic characterization of the large cellular diversity observed within tissues is essential to understanding the molecular networks that ensure the regulation of homeostasis, repair, and regeneration, but also pathophysiological processes. Skin is composed of multiple cell lineages and is therefore fully concerned by this complexity. Even within one particular lineage, such as epidermal keratinocytes, different immaturity statuses or differentiation stages are represented, which are still incompletely characterized...
May 8, 2018: Methods in Molecular Biology
Shun-Ichiro Kageyama, Keiji Nihei, Katsuyuki Karasawa, Takeshi Sawada, Fumiaki Koizumi, Shigeo Yamaguchi, Shunsuke Kato, Hidehiro Hojo, Atsuhi Motegi, Katsuya Tsuchihara, Tetsuo Akimoto
We investigated the plasma levels of tumor-specific cell-free DNA (cfDNA) in 17 stage I-II (early) and IV (advanced) non-small cell lung cancer (NSCLC) patients who underwent radiotherapy. Digital polymerase chain reaction (PCR) and targeted sequencing showed that total and tumor-specific cfDNA levels increased in response to radiotherapy in both early- and advanced-stage NSCLC patients. We detected high copy numbers of epidermal growth factor receptor mutations (L858R and T790M) in the cfDNA samples from stage IV NSCLC patients who underwent stereotactic body radiation therapy to treat brain metastasis related to tyrosine kinase inhibitor (TKI) treatment failure...
April 10, 2018: Oncotarget
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