Read by QxMD icon Read

Copy number

Sapna M Amin, Alexandra M Haugh, Christina Y Lee, Bin Zhang, Jeffrey A Bubley, Emily A Merkel, Anna Elisa Verzì, Pedram Gerami
Recent studies have identified translocations involving the kinase domains of ALK, NTRK1, BRAF, RET, and ROS in spitzoid neoplasms. Subsequent studies have also characterized morphologic features corresponding to ALK and NTRK1 translocations. In this study, we sought to further compare morphologic features across a range of 49 genetically defined spitzoid neoplasms with ALK, NTRK1, BRAF, or RET fusions to determine discriminating features. We also compared them with a group of 22 spitzoid neoplasms, which were confirmed to be negative for fusions in ALK, NTRK1, BRAF, and RET...
October 21, 2016: American Journal of Surgical Pathology
Moussa Biaye, Ewa Zbydniewska, Thierry Mélin, Dominique Deresmes, Guillaume Copie, Fabrizio Cleri, Neralagatta Sangeetha, Nicolas Decorde, Benoit Viallet, Jérémie Grisolia, Laurence Ressier, Heinrich Diesinger
Nanoparticle assemblies with thiol-terminated alkyl chains are studied by conducting atomic force microscopy (c-AFM) regarding their use as strain gauges for touch-sensitive panels. Current-force spectroscopy is used as a characterization tool complementary to the macroscopic setup since it allows a bias to be applied to a limited number of junctions, overcoming the Coulomb blockade energy and focusing on the contact electromechanics and the transport mechanism across the ligand. First, transition voltage spectroscopy is applied with varying force to target the underlying tunneling mechanism by observing whether the transition between the ohmic and exponential current-voltage behavior is force-dependent...
October 24, 2016: Nanotechnology
Joaquim Carreras, Yara Yukie Kikuti, Sílvia Beà, Masashi Miyaoka, Shinichiro Hiraiwa, Haruka Ikoma, Ryoko Nagao, David Martin-Garcia, Itziar Salaverria, Ai Sato, Ichiki Akifumi, Giovanna Roncador, Juan F Garcia, Kiyoshi Ando, Elias Campo, Naoya Nakamura
AIMS AND METHODS: We aimed to define the clinicopathological characteristics of 29 primary sinonasal diffuse large B-cell lymphoma (DLBCL(sn) ) in a series of 240 DLBCL(all ()(NOS)()) including DLBCL(sn) training set (n=11) and validation set (n=18), and DLBCL(non-sn) (n=211). RESULTS: In the training set 82% had non-GCB phenotype and 18% were EBER(+) . The genomic profile showed gains((+)) of 1q21.3q31.2 (55%), 10q24.1 (46%), 11q14.1 (46%) and 18q12.1q23 (46%); losses((-)) of 6q26q27 (55%) and 9p21...
October 24, 2016: Histopathology
Clyde Manuel, Matthew Moore, Lee-Ann Jaykus
AIMS: Human norovirus is a major public health burden and is resistant to numerous sanitizers and disinfectants. In this study, we tested the efficacy of an antimicrobial product containing a blend of silver ions and citric acid (silver dihydrogen citrate; SDC) against GI.6 and GII.4 HuNoV. METHODS AND RESULTS: Pure(®) hard surface disinfectant (Pure Bioscience, El Cajon, CA) was evaluated using ASTM International virucidal suspension and stainless steel carrier assays...
October 24, 2016: Journal of Applied Microbiology
Fara Brasó-Maristany, Simone Filosto, Steven Catchpole, Rebecca Marlow, Jelmar Quist, Erika Francesch-Domenech, Darren A Plumb, Leila Zakka, Patrycja Gazinska, Gianmaria Liccardi, Pascal Meier, Albert Gris-Oliver, Maggie Chon U Cheang, Anna Perdrix-Rosell, Manar Shafat, Elodie Noël, Nirmesh Patel, Kristen McEachern, Maurizio Scaltriti, Pau Castel, Farzana Noor, Richard Buus, Sumi Mathew, Johnathan Watkins, Violeta Serra, Pierfrancesco Marra, Anita Grigoriadis, Andrew N Tutt
Triple-negative breast cancers (TNBCs) have poor prognosis and lack targeted therapies. Here we identified increased copy number and expression of the PIM1 proto-oncogene in genomic data sets of patients with TNBC. TNBC cells, but not nonmalignant mammary epithelial cells, were dependent on PIM1 for proliferation and protection from apoptosis. PIM1 knockdown reduced expression of the anti-apoptotic factor BCL2, and dynamic BH3 profiling of apoptotic priming revealed that PIM1 prevents mitochondrial-mediated apoptosis in TNBC cell lines...
October 24, 2016: Nature Medicine
Jerome A Staal, Yanxin Pei, Brian R Rood
Brain tumors are the leading cause of cancer-related deaths in children, and medulloblastoma is the most prevalent malignant childhood/pediatric brain tumor. Providing effective treatment for these cancers, with minimal damage to the still-developing brain, remains one of the greatest challenges faced by clinicians. Understanding the diverse events driving tumor formation, maintenance, progression, and recurrence is necessary for identifying novel targeted therapeutics and improving survival of patients with this disease...
October 19, 2016: International Journal of Molecular Sciences
B N Keel, J W Keele, W M Snelling
Copy number variations (CNVs) are large insertions, deletions or duplications in the genome that vary between members of a species and are known to affect a wide variety of phenotypic traits. In this study, we identified CNVs in a population of bulls using low coverage next-generation sequence data. First, in order to determine a suitable strategy for CNV detection in our data, we compared the performance of three distinct CNV detection algorithms on benchmark CNV datasets and concluded that using the multiple sample read depth approach was the best method for identifying CNVs in our sequences...
October 24, 2016: Animal Genetics
Liwen Hu, Xinyue Yao, Yi Shen
Accumulating epidemiological evidence indicates that the quantitative changes in human mitochondrial DNA (mtDNA) copy number could affect the genetic susceptibility of malignancies in a tumor-specific manner, but the results are still elusive. To provide a more precise estimation on the association between mtDNA copy number and risk of diverse malignancies, a meta-analysis was conducted by calculating the pooled odds ratios (OR) and the 95% confidence intervals (95% CI). A total of 36 case-control studies involving 11,847 cases and 15,438 controls were finally included in the meta-analysis...
October 24, 2016: Scientific Reports
Kenta Tezuka, Madoka Kuramitsu, Kazu Okuma, Kiyoko Nojima, Kumiko Araki, Naoya Shinohara, Chieko Matsumoto, Masahiro Satake, Tomohiko Takasaki, Masayuki Saijo, Ichiro Kurane, Isao Hamaguchi
BACKGROUND: Dengue fever is caused by four related RNA viruses of the genus Flavivirus, dengue virus (DENV)-1, -2, -3, and -4, which are transmitted to humans by mosquitoes. Although DENV is not endemic in Japan, an autochthonous dengue outbreak occurred in 2014. Several transfusion-transmitted cases have also been reported after the use of blood and plasma products in DENV-endemic countries. The aim of this study was to develop a novel multiplex reverse transcription-polymerase chain reaction (RT-PCR) assay for DENV blood screening...
October 23, 2016: Transfusion
Chen Chi, Rasif Ajwad, Qin Kuang, Pingzhao Hu
Many cancers have been linked to copy number variations (CNVs) in the genomic DNA. Although there are existing methods to analyze CNVs from individual samples, cancer-causing genes are more frequently discovered in regions where CNVs are common among tumor samples, also known as recurrent CNVs. Integrating multiple samples and locating recurrent CNV regions remain a challenge, both computationally and conceptually. We propose a new graph-based algorithm for identifying recurrent CNVs using the maximal clique detection technique...
2016: Cancer Informatics
Matthew M Dougherty, Eric R Larson, Mark A Renshaw, Crysta A Gantz, Scott P Egan, Daniel M Erickson, David M Lodge
Early detection is invaluable for the cost-effective control and eradication of invasive species, yet many traditional sampling techniques are ineffective at the low population abundances found at the onset of the invasion process. Environmental DNA (eDNA) is a promising and sensitive tool for early detection of some invasive species, but its efficacy has not yet been evaluated for many taxonomic groups and habitat types.We evaluated the ability of eDNA to detect the invasive rusty crayfish Orconectes rusticus and to reflect patterns of its relative abundance, in upper Midwest, USA, inland lakes...
June 2016: Journal of Applied Ecology
Ken M Kunisaki, Dennis E Niewoehner, Gary Collins, Bitten Aagaard, Nafisah B Atako, Elzbieta Bakowska, Amanda Clarke, Giulio Maria Corbelli, Ernest Ekong, Sean Emery, Elizabeth B Finley, Eric Florence, Rosa M Infante, Cissy M Kityo, Juan Sierra Madero, Daniel E Nixon, Ellen Tedaldi, Jørgen Vestbo, Robin Wood, John E Connett
BACKGROUND: Observational data have been conflicted regarding the potential role of HIV antiretroviral therapy (ART) as a causative factor for, or protective factor against, COPD. We therefore aimed to investigate the effect of immediate versus deferred ART on decline in lung function in HIV-positive individuals. METHODS: We did a nested substudy within the randomised, controlled Strategic Timing of Antiretroviral Treatment (START) trial at 80 sites in multiple settings in 20 high-income and low-to-middle-income countries...
October 20, 2016: Lancet Respiratory Medicine
Monica Dalva, Khadija El Jellas, Solrun J Steine, Bente B Johansson, Monika Ringdal, Janniche Torsvik, Heike Immervoll, Dag Hoem, Felix Laemmerhirt, Peter Simon, Markus M Lerch, Stefan Johansson, Pål R Njølstad, Frank U Weiss, Karianne Fjeld, Anders Molven
BACKGROUND/OBJECTIVES: We have recently described copy number variants (CNVs) of the human carboxyl-ester lipase (CEL) gene, including a recombined deletion allele (CEL-HYB) that is a genetic risk factor for chronic pancreatitis. Associations with pancreatic disease have also been reported for the variable number of tandem repeat (VNTR) region located in CEL exon 11. Here, we examined if CEL CNVs and VNTR length polymorphisms affect the risk for developing pancreatic cancer. METHODS: CEL CNVs and VNTR were genotyped in a German family with non-alcoholic chronic pancreatitis and pancreatic cancer, in 265 German and 197 Norwegian patients diagnosed with pancreatic adenocarcinoma, and in 882 controls...
October 11, 2016: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
Kimberley M Kendall, Elliott Rees, Valentina Escott-Price, Mark Einon, Rhys Thomas, Jonathan Hewitt, Michael C O'Donovan, Michael J Owen, James T R Walters, George Kirov
BACKGROUND: The UK Biobank is a unique resource for biomedical research, with extensive phenotypic and genetic data on half a million adults from the general population. We aimed to examine the effect of neurodevelopmental copy number variants (CNVs) on the cognitive performance of participants. METHODS: We used Affymetrix Power Tools and PennCNV-Affy software to analyze Affymetrix microarrays of the first 152,728 genotyped individuals. We annotated a list of 93 CNVs and compared their frequencies with control datasets...
August 18, 2016: Biological Psychiatry
Laila Y AlAyadhi, Jamil A Hashmi, Muhammad Iqbal, Alia M Albalawi, Mohammad I Samman, Nadra E Elamin, Shahid Bashir, Sulman Basit
Single nucleotide polymorphisms (SNP) - based genotyping using microarray platform is now frequently used to detect copy number variants (CNVs) in the human genome. Here, we report CNVs identified using Illumina HumanOmni 2.5 M oligonucleotide microarrays in 11 multiplex families with autism spectrum disorder (ASD) referred to Autism Research and Treatment Center (ART) and Madinah Maternity and Children Hospital (MMCH). Of the 11 families, 22 patients with ASD (all males) and their parents, were recruited for the present study...
October 19, 2016: Neuroscience
German Demidov, Tamara Simakova, Julia Vnuchkova, Anton Bragin
BACKGROUND: Multiplex polymerase chain reaction (PCR) is a common enrichment technique for targeted massive parallel sequencing (MPS) protocols. MPS is widely used in biomedical research and clinical diagnostics as the fast and accurate tool for the detection of short genetic variations. However, identification of larger variations such as structure variants and copy number variations (CNV) is still being a challenge for targeted MPS. Some approaches and tools for structural variants detection were proposed, but they have limitations and often require datasets of certain type, size and expected number of amplicons affected by CNVs...
October 22, 2016: BMC Bioinformatics
Majid Zaki Dizaji, Seyed H Ghaffari, Elham Hosseini, Nasrin Alizadeh, Shahrbano Rostami, Majid Momeny, Kamran Alimoghaddam, Ardeshir Ghavamzadeh
AIM: Survivin, an inhibitor of apoptosis protein, is overexpressed in most cancers and is associated with chemotherapy resistance, increased tumor recurrence and shorter patient survival. Several survivin splice variants have been described, and none of their expressions have been defined in acute promyelocytic leukemia (APL). METHODS: Expression of the survivin gene isoforms (survivin, -2α, -2B, -ΔΕx3 and -3B) were analyzed in 50 peripheral blood and 19 bone marrow samples that were collected at different phases of the disease (diagnostic, remission and relapse) in APL patients treated with arsenic trioxide (ATO) as a front-line therapy...
October 22, 2016: Asia-Pacific Journal of Clinical Oncology
Haruyoshi Tanaka, Mitsuro Kanda, Dai Shimizu, Chie Tanaka, Daisuke Kobayashi, Masamichi Hayashi, Naoki Iwata, Suguru Yamada, Tsutomu Fujii, Goro Nakayama, Hiroyuki Sugimoto, Michitaka Fujiwara, Yukiko Niwa, Yasuhiro Kodera
BACKGROUND: Gastric cancer (GC) relapse can occur even if curative resection is achieved. Biomarkers predicting recurrence are needed to provide appropriate postoperative surveillance and perioperative therapeutic strategy. METHODS: A global expression profiling was performed using tissues from GC patients with synchronous liver-confined metastasis. Family with sequence similarity 46, member C (FAM46C), was identified as a candidate biomarker. mRNA expression analysis, direct nucleotide sequencing, bisulfite sequencing and copy number assays for FAM46C were performed with eleven GC cell lines...
October 21, 2016: Annals of Surgical Oncology
Liyan Song, Shu Yang, Hongjie Liu, Jing Xu
Little is known regarding how bacterial communities assemble at landfill, as well as how the environment shapes the composition of bacterial community. In this study, up to 42 refuse samples from a large-scale landfill in China were physicochemically and phylogenetically investigated. 16S ribosomal RNA (rRNA) gene-based Illumina MiSeq sequencing (nine samples) revealed that representatives of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes were dominant in the refuse samples, which was similar to a previous study on landfill leachate by using 454 pyrosequencing...
October 21, 2016: Applied Microbiology and Biotechnology
Auke B C Otten, Alphons P M Stassen, Michiel Adriaens, Mike Gerards, Richard G J Dohmen, Adriana J Timmer, Sabina J V Vanherle, Rick Kamps, Iris B W Boesten, Jo M Vanoevelen, Marc Muller, Bert Smeets
Of all pathogenic mitochondrial DNA (mtDNA) mutations in humans, ~25% is de novo, although the occurrence in oocytes has never been directly assessed. We used next generation sequencing to detect point mutations directly in the mtDNA of 3-15 individual mature oocytes and three somatic tissues from eight zebrafish females. Various statistical and biological filters allowed reliable detection of de novo variants with heteroplasmy ≥1.5%. In total, we detected 38 de novo base substitutions, but no insertions or deletions...
October 21, 2016: Genetics
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"