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https://www.readbyqxmd.com/read/28930282/esophageal-cancer-genomic-and-molecular-characterization-stem-cell-compartment-and-clonal-evolution
#1
REVIEW
Ugo Testa, Germana Castelli, Elvira Pelosi
Esophageal cancer (EC) is the eighth most common cancer and is the sixth leading cause of death worldwide. The incidence of histologic subtypes of EC, esophageal adenocarcinoma (EAC) and esophageal squamous carcinoma (ESCC), display considerable geographic variation. EAC arises from metaplastic Barrett's esophagus (BE) in the context of chronic inflammation secondary to exposure to acid and bile. The main risk factors for developing ESCC are cigarette smoking and alcohol consumption. The main somatic genetic abnormalities showed a different genetic landscape in EAC compared to ESCC...
September 14, 2017: Medicines (Basel, Switzerland)
https://www.readbyqxmd.com/read/28929030/genomic-analysis-of-p-elements-in-natural-populations-of-drosophila-melanogaster
#2
Casey M Bergman, Shunhua Han, Michael G Nelson, Vladyslav Bondarenko, Iryna Kozeretska
The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations...
2017: PeerJ
https://www.readbyqxmd.com/read/28927463/towards-precision-medicine-discovering-novel-gynecological-cancer-biomarkers-and-pathways-using-linked-data
#3
Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
BACKGROUND: Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, these datasets are published from the isolated and different sequencing facilities. Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories, the automation of data linkage, the volume of the data, efficient querying mechanism, and information rich intuitive visualisation...
September 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28926134/early-genetic-aberrations-in-patients-with-sporadic-colorectal-cancer
#4
Brooke R Druliner, Xiaoyang Ruan, Hugues Sicotte, Daniel O'Brien, Hongfang Liu, Jean-Pierre A Kocher, Lisa Boardman
Chromosome instability (CIN) is widely observed in both sporadic and hereditary colorectal cancer (CRC). Defects in APC and WNT signaling are primarily associated with CIN in hereditary CRC, but the genetic causes for CIN in sporadic CRC remain elusive. Using high-density SNP array and exome data from The Cancer Genome Atlas, we characterized loss of heterozygosity (LOH) and copy number variation (CNV) in the peripheral blood, normal colon and corresponding tumor tissue in 15 CRC patients with proficient mismatch repair (MMR) and 24 CRC patients with deficient MMR...
September 19, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28924535/benign-pathogenic-and-copy-number-variations-of-unknown-clinical-significance-in-patients-with-congenital-malformations-and-developmental-delay
#5
M Mihaylova, R Staneva, D Toncheva, M Pancheva, S Hadjidekova
The high frequency (3.0-5.0%) of congenital anomalies (CA) and intellectual disabilities (IDs), make them a serious problem, responsible for a high percentage (33.0%) of neonatal mortality. The genetic cause remains unclear in 40.0% of cases. Recently, molecular karyotyping has become the most powerful method for detection of pathogenic imbalances in patients with multiple CAs and IDs. This method is with high resolution and gives us the opportunity to investigate and identify candidate genes that could explain the genotype-phenotype correlations...
June 30, 2017: Balkan Journal of Medical Genetics: BJMG
https://www.readbyqxmd.com/read/28923607/the-role-of-ctx-and-rs1-satellite-phages-genomic-arrangement-in-vibrio-cholera-toxin-production-in-two-recent-cholera-outbreaks-2012-and-2013-in-ir-iran
#6
Niloofar Rezaie, Bita Bakhshi, Shahin-Najar Peerayeh
The objective of the present study was to investigate the genomic arrangement of CTX/RS1 prophages in 30 Vibrio cholerae strains obtained from 2 consecutive years of cholera outbreak and to compare the role of different CTX/RS1 arrangements in cholera toxin expression among the El Tor strains. Profile A with TLC-RS1-CTX-RTX arrangement was observed in 46.7% of the isolates with RS1 phage locating adjacent to TLC element. About 50% of the isolates showed Profile B with TLC-CTX-RS1-RTX arrangement and one single isolate (3...
September 16, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28917637/diversity-of-copy-number-variation-in-a-worldwide-population-of-sheep
#7
Liu Yang, Lingyang Xu, Yang Zhou, Mei Liu, Lei Wang, James W Kijas, Hongping Zhang, Li Li, George E Liu
Copy number variation (CNV) represents a major source of genomic variation. We investigated the diversity of CNV distribution using SNP array data collected from a comprehensive collection of geographically dispersed sheep breeds. We identified 24,558 putative CNVs, which can be merged into 619 CNV regions, spanning 197Mb of total length and corresponding to ~6.9% of the sheep genome. Our results reveal a population differentiation in CNV between different geographical areas, including Africa, America, Asia, Southwestern Asia, Central Europe, Northern Europe and Southwestern Europe...
September 13, 2017: Genomics
https://www.readbyqxmd.com/read/28917518/genome-stability-of-programmed-stem-cell-products
#8
REVIEW
Ulrich Martin
Inherited and acquired genomic abnormalities are known to cause genetic diseases and contribute to cancer formation. Recent studies demonstrated a substantial mutational load in mouse and human embryonic and induced pluripotent stem cells (ESCs and iPSCs). Single nucleotide variants, copy number variations, and larger chromosomal abnormalities may influence the differentiation capacity of pluripotent stem cells and the functionality of their derivatives in disease modelling and drug screening, and are considered a serious risk for cellular therapies based on ESC or iPSC derivatives...
September 13, 2017: Advanced Drug Delivery Reviews
https://www.readbyqxmd.com/read/28915599/copy-number-variations-of-circulating-cell-free-dna-in-urothelial-carcinoma-of-the-bladder-patients-treated-with-radical-cystectomy-a-prospective-study
#9
Armin Soave, Felix K-H Chun, Timo Hillebrand, Michael Rink, Lars Weisbach, Bettina Steinbach, Margit Fisch, Klaus Pantel, Heidi Schwarzenbach
The aim of the present study was to establish a rapid profiling method using multiplex ligation-dependent probe amplification (MLPA) and characterize copy number variations (CNV) in circulating, cell-free DNA (cfDNA) in 85 urothelial carcinoma of the bladder (UCB) patients treated with radical cystectomy (RC). MLPA was tested for the use of cfDNA extracted from serum and plasma by various commercial extraction kits. Eighteen probes served as reference to control denaturation, ligation and amplification efficiency...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28914499/copy-number-variants-of-ras-mapk-pathway-genes-in-patients-with-isolated-cryptorchidism
#10
F Rodríguez, C Vallejos, F Giraudo, N Unanue, M I Hernández, P Godoy, S Célis, R Martín-Arenas, M Palomares-Bralo, K E Heath, M T López, F Cassorla
Cryptorchidism is the most common congenital disorder in boys, but the cause for most cases remains unknown. Patients with Noonan Syndrome are characterized by a typical face, growth retardation, congenital heart defects, learning disabilities and cryptorchidism. Copy number variations of Ras/MAPK pathway genes are unusual in patients with several clinical features of Noonan Syndrome; however, they have not been studied in patients with only one feature of this condition, such as cryptorchidism. Our aim was to determine whether patients with isolated cryptorchidism exhibit Ras/MAPK pathway gene copy number variations (CNVs)...
September 2017: Andrology
https://www.readbyqxmd.com/read/28914414/novel-insights-in-biopurification-system-for-dissipation-of-a-pesticide-mixture-in-repeated-applications
#11
Maria Cristina Diez, Bárbara Leiva, Felipe Gallardo
A biopurification system based on the adsorption and degradation capacity of a biomixture to degrade a mixture of pesticides (atrazine, chlorpyrifos, iprodione; 50 mg kg(-1) each) in repeated applications (0, 30, and 60 days) was evaluated. Tanks of 1 m(3) packed with a biomixture (ρ 0.29 g mL(-1)) with and without vegetal cover were used. The biomixture contained soil, peat, and wheat straw in a proportion 1:1:2 by volume, respectively. Pesticide concentrations, biological activities (urease, phenoloxidase, and dehydrogenase), and microbial community changes (DGGE and qPCR) were evaluated periodically...
September 15, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28914264/comprehensive-use-of-extended-exome-analysis-improves-diagnostic-yield-in-rare-disease-a-retrospective-survey-in-1-059-cases
#12
Gaber Bergant, Ales Maver, Luca Lovrecic, Goran Čuturilo, Alenka Hodzic, Borut Peterlin
PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28913947/extreme-chromosome-17-copy-number-instability-is-a-prognostic-factor-in-patients-with-gastroesophageal-adenocarcinoma-a-retrospective-cohort-study
#13
Jacqueline E Birkness, Neal G Spada, Caitlyn Miller, James D Luketich, Katie S Nason, Weijing Sun, Jon M Davison
Gastric and esophageal cancers frequently show genomic instability and aneuploidy. Chromosomal copy number instability (CIN) is a form of genomic instability that exerts pleiotropic effects on cellular biology and is a source of genetic heterogeneity in a population of cells. CIN results in cell-to-cell variation in chromosome copy number which can be detected and quantified by fluorescence in situ hybridization (FISH). CIN is a biomarker associated with differential response to a number of chemotherapy compounds...
September 14, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/28912957/characteristics-of-rare-and-private-deletions-identified-in-phenotypically-normal-individuals
#14
Keiko Shimojima, Toshiyuki Yamamoto
Genomic copy number variations (CNVs) identified through chromosomal microarray testing must be validated to confirm whether they are pathogenically and functionally relevant to their respective clinical features. Although larger deletions have a higher probability to be pathogenic, this is not always true. Phenotypically normal individuals showed five CNV deletions larger than 1.5 Mb. The genes related to autosomal dominant trait were absent within these CNV deletions.
2017: Human Genome Variation
https://www.readbyqxmd.com/read/28911203/mutations-of-conserved-non-coding-elements-of-pitx2-in-patients-with-ocular-dysgenesis-and-developmental-glaucoma
#15
Meredith E Protas, Eric Weh, Tim Footz, Jay Kasberger, Scott C Baraban, Alex V Levin, L Jay Katz, Robert Ritch, Michael A Walter, Elena V Semina, Douglas B Gould
Mutations in FOXC1 and PITX2 constitute the most common causes of ocular anterior segment dysgenesis (ASD), and confer a high risk for secondary glaucoma. The genetic causes underlying ASD in approximately half of patients remain unknown, despite many of them being screened by whole exome sequencing. Here, we performed whole genome sequencing on DNA from two affected individuals from a family with dominantly inherited ASD and glaucoma to identify a 748-kb deletion in a gene desert that contains conserved putative PITX2 regulatory elements...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28911002/intratumor-heterogeneity-predicts-metastasis-of-triple-negative-breast-cancer
#16
Fang Yang, Yucai Wang, Quan Li, Lulu Cao, Zijia Sun, Juan Jin, Hehui Fang, Aiyu Zhu, Yan Li, Wenwen Zhang, Yanru Wang, Hui Xie, Jan-Åke Gustafsson, Shui Wang, Xiaoxiang Guan
Even with the identical clinicopathological features, the ability for metastasis is vastly different among triple-negative breast cancer (TNBC) patients. Intratumor heterogeneity (ITH), which is common in breast cancer, may be a key mechanism leading to the tumor progression. In this study, we studied whether a quantitative genetic definition of ITH can predict clinical outcomes in patients with TNBC. We quantified ITH by calculating Shannon index, a measure of diversity in a population, based on Myc, epidermal growth factor receptor/centromeric probe 7 (EGFR/CEP7) and cyclin D1/centromeric probe 11 (CCND1/CEP11) copy number variations (CNVs) in 300 cells at three different locations of a tumor...
September 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28910969/polymorphisms-of-immunoglobulin-receptors-and-the-effects-on-clinical-outcome-in-cancer-immunotherapy-and-other-immune-diseases-a-general-review
#17
Tomonori Kaifu, Akira Nakamura
Receptors for the Fc domain of immunoglobulins [Fc receptors (FcRs)] are essential for the maintenance of antibody-mediated immune responses. FcRs consist of activating- and inhibitory-type receptors that regulate adequate thresholds for various immune cells. In particular, polymorphisms and/or gene copy-number variations of FcRs for IgG (FcγRs) are closely associated with the development of inflammatory disorders, including autoimmune diseases. Recent evidence has implicated polymorphisms of FcRs in the efficacy of monoclonal antibody (mAb)-mediated therapy...
July 1, 2017: International Immunology
https://www.readbyqxmd.com/read/28910957/-effects-of-cell-cycle-regulatory-genes-on-breast-cancer-neo-adjuvant-chemotherapy-by-m-fish
#18
C Y Li, W Su, S Zhang, Y H Hu, J J Liu, J Zhang
Objective: The dysregulation of cell cycle could influence cell proliferation, differentiation and response to medicine. The purpose of this study is to explore the correlation between cell cycle regulatory genes and breast cancer neo-adjuvant chemotherapy (NAC) in patients with local advanced breast cancer, and thus to find some predictors of NAC to provide guidance for clinical treatment. Methods: Ninety five cases of local advanced breast cancer were collected, which were treated with NAC of TAC (Taxanes/Anthracycline/Cyclophosphamide) regimen...
September 12, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/28904201/heterogeneity-of-the-epstein-barr-virus-major-internal-repeat-reveals-evolutionary-mechanisms-of-ebv-and-a-functional-defect-in-the-prototype-ebv-strain-b95-8
#19
Mohammed Ba Abdullah, Richard Palermo, Anne Palser, Nicholas E Grayson, Paul Kellam, Samantha Correia, Agnieszka Szymula, Rob White
Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified both through co-evolution with its host, and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging, because of the large number and length of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat of EBV (IR1 or BamW repeats) from over 70 strains...
September 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28902850/copy-number-variation-analysis-in-cytochromes-and-glutathione-s-transferases-may-predict-efficacy-of-tyrosine-kinase-inhibitors-in-chronic-myeloid-leukemia
#20
Alexander V Lavrov, Oksana A Ustaeva, Elmira P Adilgereeva, Svetlana A Smirnikhina, Ekaterina Y Chelysheva, Oleg A Shukhov, Yuriy V Shatokhin, Sergey V Mordanov, Anna G Turkina, Sergey I Kutsev
Chronic myeloid leukemia (CML) is a myeloproliferative disease characterized by the presence of BCR/ABL fusion gene in leukemic cells, which promotes uncontrolled cell proliferation. Up to 20% of CML patients show primary resistance or non-optimal response to tyrosine kinase inhibitor (TKI) therapy. We investigated the association between copy number variation (CNV) in glutathione S-transferases (GST) and cytochromes (CYP) and the response rate to TKI. We enrolled 47 patients with CML: 31 with an optimal response and 16 with failure at 6 months in accordance with European LeukemiaNet 2013 recommendations...
2017: PloS One
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