keyword
MENU ▼
Read by QxMD icon Read
search

Copy number

keyword
https://www.readbyqxmd.com/read/28088185/igc-an-integrated-analysis-package-of-gene-expression-and-copy-number-alteration
#1
Yi-Pin Lai, Liang-Bo Wang, Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y Chuang
BACKGROUND: With the advancement in high-throughput technologies, researchers can simultaneously investigate gene expression and copy number alteration (CNA) data from individual patients at a lower cost. Traditional analysis methods analyze each type of data individually and integrate their results using Venn diagrams. Challenges arise, however, when the results are irreproducible and inconsistent across multiple platforms. To address these issues, one possible approach is to concurrently analyze both gene expression profiling and CNAs in the same individual...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28087982/the-impact-of-ces1-genotypes-on-the-pharmacokinetics-of-methylphenidate-in-healthy-danish-subjects
#2
Claus Stage, Gesche Jürgens, Louise Schow Guski, Ragnar Thomsen, Ditte Bjerre, Laura Ferrero-Miliani, Yassine Kamal Lyauk, Henrik Berg Rasmussen, Kim Dalhoff
AIM: This study investigated the influence of CES1 variations, including the SNP rs71647871 (G143E) and variation in copy number, on the pharmacokinetics of a single oral dose of 10 mg methylphenidate. METHODS: CES1 genotype was obtained from 200 healthy Danish Caucasian volunteers. Based on the genotype, 44 (19 males and 25 females) were invited to participate in an open, prospective trial involving six predefined genotypes: three groups with two, three, and four CES1 copies, respectively; a group of carriers of the CES1 143E allele; a group of individuals homozygous for CES1A1c (CES1VAR); and a group having three CES1 copies, in which the duplication, CES1A2, had increased transcriptional activity...
January 14, 2017: British Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28087780/oncogenes-without-a-neighboring-tumor-suppressor-gene-are-more-prone-to-amplification
#3
William K K Wu, Xiangchun Li, Xiansong Wang, Rudin Z W Dai, Alfred S L Cheng, Maggie H T Wang, Thomas Kwong, Tai C Chow, Jun Yu, Matthew T V Chan, Sunny H Wong
Focal copy number gains or losses are important genomic hallmarks of cancer. The genomic distribution of oncogenes and tumor-suppressor genes (TSG) in relation to focal copy number aberrations is unclear. Our analysis revealed that the mean distance of TSGs from oncogenes was significantly shorter than that of non-cancer genes, suggesting that oncogenes and TSGs tend to be in close physical proximity in the human genome. Such relationship was conserved in mouse and drosophila. Pan-cancer analysis using data from The Cancer Genome Atlas indicated that oncogenes without a nearby TSG are more prone to amplification...
January 12, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28087734/increased-mitophagy-in-the-skeletal-muscle-of-spinal-and-bulbar-muscular-atrophy-patients
#4
Doriana Borgia, Adriana Malena, Marco Spinazzi, Maria Andrea Desbats, Leonardo Salviati, Aaron P Russell, Giovanni Miotto, Laura Tosatto, Elena Pegoraro, Gianni Sorarù, Maria Pennuto, Lodovica Vergani
Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular disorder caused by polyglutamine expansion in the androgen receptor (AR) and characterized by the loss of lower motor neurons. Here we investigated pathological processes occurring in muscle biopsy specimens derived from SBMA patients and, as controls, age-matched healthy subjects and patients suffering from amyotrophic lateral sclerosis (ALS) and neurogenic atrophy. We detected atrophic fibers in the muscle of SBMA, ALS and neurogenic atrophy patients...
January 13, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28087673/rdna-stability-is-supported-by-many-buffer-genes-introduction-to-the-yeast-rdna-stability-database
#5
Takehiko Kobayashi, Mariko Sasaki
The ribosomal RNA gene (rDNA) is the most abundant gene in yeast and other eukaryotic organisms. Due to its heavy transcription, repetitive structure and programmed replication fork pauses, the rDNA is one of the most unstable regions in the genome. Thus, the rDNA is the best region to study the mechanisms responsible for maintaining genome integrity. Recently, we screened a library of ∼4,800 budding yeast gene knockout strains to identify mutants defective in the maintenance of rDNA stability. The results of this screen are summarized in the Yeast rDNA Stability Database, in which the stability and copy number of rDNA in each mutant are presented...
January 12, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28087598/bayesian-network-inference-modeling-identifies-trib1-as-a-novel-regulator-of-cell-cycle-progression-and-survival-in-cancer-cells
#6
Rina Gendelman, Heming Xing, Olga K Mirzoeva, Preeti Sarde, Christina Curtis, Heidi Feiler, Paul McDonagh, Joe W Gray, Iya Khalil, W Michael Korn
Molecular networks governing cellular responses to targeted therapies are complex dynamic systems with non-intuitive behaviors. Here we applied a novel computational strategy to infer probabilistic causal relationships between network components based on gene expression. We constructed a model comprised of an ensemble of networks using multidimensional data from cell line models of cell cycle arrest caused by inhibition of MEK1/2. Through simulation of reverse-engineered Bayesian network modeling, we generated predictions of G1-S transition...
January 13, 2017: Cancer Research
https://www.readbyqxmd.com/read/28087349/combination-of-multiple-ligation-dependent-probe-amplification-and-illumina-miseq-amplicon-sequencing-for-tsc1-tsc2-gene-analyses-in-patients-with-tuberous-sclerosis-complex
#7
Nur Farrah Dila Ismail, Abdul Qawee Rani, Nik Mohd Ariff Nik Abdul Malik, Chia Boon Hock, Siti Nabilahuda Mohd Azlan, Salmi Abdul Razak, Wee Teik Keng, Lock Hock Ngu, Abdul Rashid Silawati, Nor AzniYahya, Narazah Mohd Yusoff, Teguh Haryo Sasongko, Zabidi Azhar Mohd Hussin
Tuberous sclerosis complex (TSC) is an autosomal dominant neurocutaneous disorder characterized by tumor growth in multiple organs and caused by mutations in either TSC1 or TSC2 genes. Because of their relatively large genomic sizes, absence of hotspots, and common type of mutations, mutation detection in TSC1 and TSC2 genes has been challenging. We devised a combination of multiple ligation-dependent probe amplification (MLPA) and amplicon sequencing (AS) to simplify the detection strategy, yet we come up with reasonably high detection rate...
January 10, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28086915/comparative-study-in-infertile-couples-with-and-without-chlamydia-trachomatis-genital-infection
#8
Yuanchang Zhu, Biao Yin, Tonghua Wu, Lijun Ye, Chunmei Chen, Yong Zeng, Yaou Zhang
BACKGROUND: Chlamydia, caused by the bacterium Chlamydia trachomatis(C. trachomatis), is the most common sexually transmitted disease. The incidence is not clear due to the asymptomatic nature of early stage of infections. The incidence of Chlamydia has not been fully investigated in the Chinese Han population. Since chronic infection with can C. trachomatis can lead to infertility in males and females, it is important to determine the impact of infection on clinical outcomes. The aim of this study is to explore the epidemiology of C...
January 13, 2017: Reproductive Health
https://www.readbyqxmd.com/read/28081277/comparative-genomic-hybridization-analysis-of-rice-dwarf-mutants-induced-by-gamma-irradiation
#9
J E Hwang, S-H Kim, I J Jung, S M Han, J-W Ahn, S-J Kwon, S H Kim, S-Y Kang, D S Kim, J-B Kim
Comparative genomic hybridization (CGH) is a powerful tool used to analyze changes in copy number, polymorphisms, and structural variations in the genome. Gene copy number variation (CNV) is a common form of natural diversity in the genome, which can create new genes and alter gene structure. Thus, CNVs may influence phenotypic variation and gene expression. In this study, to detect CNVs, we irradiated rice seeds with gamma rays (300 Gy) and selected two dwarf mutagenized plants, GA-III-189 and -1052, in the M3 generation...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28080987/ploidy-dynamics-and-evolvability-in-fungi
#10
REVIEW
Noa Blutraich Wertheimer, Neil Stone, Judith Berman
Rapid responses to acute stresses are essential for stress survival and are critical to the ability of fungal pathogens to adapt to new environments or hosts. The rapid emergence of drug resistance is used as a model for how fungi adapt and survive stress conditions that inhibit the growth of progenitor cells. Aneuploidy and loss of heterozygosity (LOH), which are large-scale genome shifts involving whole chromosomes or chromosome arms, occur at higher frequency than point mutations and have the potential to mediate stress survival...
December 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28080109/the-dynamic-range-of-response-set-activation-during-action-sequencing
#11
Lawrence P Behmer, Matthew J C Crump
We show that theories of response scheduling for sequential action can be discriminated on the basis of their predictions for the dynamic range of response set activation during sequencing, which refers to the momentary span of activation states for completed and to-be-completed actions in a response set. In particular, theories allow that future actions in a plan are partially activated, but differ with respect to the width of the range, which refers to the number of future actions that are partially activated...
January 12, 2017: Journal of Experimental Psychology. Human Perception and Performance
https://www.readbyqxmd.com/read/28079792/amplification-of-her2-and-top2a-and-deletion-of-top2a-genes-in-a-series-of-taiwanese-breast-cancer
#12
Jim-Ray Chen, Hui-Ping Chien, Kuo-Su Chen, Cheng-Cheng Hwang, Huang-Yang Chen, Kun-Yan Yeh, Tsan-Yu Hsieh, Liang-Che Chang, Yuan-Chun Hsu, Ren-Jie Lu, Chung-Ching Hua
BACKGROUND: The prognostic relevance of topoisomerase II alpha (TOP2A) copy number change remains not well established. This study is aimed to investigate the frequency and pattern of TOP2A aberrations; to correlate TOP2A alterations with human epidermal growth factor receptor 2 (HER2) status and clinicopathological parameters, and further to explore prognostic value of TOP2A and HER2 status in breast cancer in Taiwan. METHODS: We analyzed tissue samples from 311 invasive carcinomas in tissue microarrays for TOP2A and HER2 status by fluorescent in situ hybridization...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28079598/interobserver-agreement-in-endometrial-carcinoma-histotype-diagnosis-varies-depending-on-the-cancer-genome-atlas-tcga-based-molecular-subgroup
#13
Lien N Hoang, Mary A Kinloch, Joyce M Leo, Katherine Grondin, Cheng-Han Lee, Carol Ewanowich, Martin Köbel, Angela Cheng, Aline Talhouk, Melissa McConechy, David G Huntsman, Jessica N McAlpine, Robert A Soslow, C Blake Gilks
The Cancer Genome Atlas recently identified a genomic-based molecular classification of endometrial carcinomas, with 4 molecular categories: (1) ultramutated (polymerase epsilon [POLE] mutated), (2) hypermutated (microsatellite instability), (3) copy number abnormalities-low, and (4) copy number abnormalities-high. Two studies have since proposed models to classify endometrial carcinomas into 4 molecular subgroups, modeled after The Cancer Genome Atlas, using simplified and more clinically applicable surrogate methodologies...
February 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28079130/association-of-nsv823469-copy-number-loss-with-decreased-risk-of-chronic-obstructive-pulmonary-disease-and-pulmonary-function-in-chinese
#14
Xiaoliang Chen, Xiaoxiao Lu, Jiansong Chen, Di Wu, Fuman Qiu, Huali Xiong, Zihua Pan, Lei Yang, Binyao Yang, Chenli Xie, Yifeng Zhou, Dongsheng Huang, Yumin Zhou, Jiachun Lu
It is highly possible that copy number variations (CNVs) in susceptible regions have effects on chronic obstructive pulmonary disease (COPD) development, while long noncoding RNA (lncRNAs) have been shown to cause COPD. We hypothesized that the common CNV, named nsv823469 located on 6p22.1, and covering lncRNAs (major histocompatibility complex, class I, A (HLA-A) and HLA complex group 4B (HCG4B)) has an effect on COPD risk. This association was assessed through a two-stage case-control study, and was further confirmed with COPD and pulmonary function-based family analyses, respectively...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#15
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078827/fam83-family-oncogenes-are-broadly-involved-in-human-cancers-an-integrative-multi-omics-approach
#16
Antoine M Snijders, Sun-Young Lee, Bo Hang, Wenshan Hao, Mina J Bissell, Jian-Hua Mao
The development of novel targeted therapies for cancer treatment requires identification of reliable targets. FAM83 ('family with sequence similarity 83') family members A, B, and D were shown recently to have oncogenic potential. However, the overall oncogenic abilities of FAM83 family genes remain largely unknown. Here, we used a systematic and integrative genomics approach to investigate oncogenic properties of the entire FAM83 family members. We assessed transcriptional expression patterns of eight FAM83 family genes (FAM83A-H) across tumor types, the relationship between their expression and changes in DNA copy number, and the association with patient survival...
October 26, 2016: Molecular Oncology
https://www.readbyqxmd.com/read/28078253/effects-of-eicosapentaenoic-acid-and-docosahexaenoic-acid-on-mitochondrial-dna-replication-and-pgc-1%C3%AE-gene-expression-in-c2c12-muscle-cells
#17
Mak-Soon Lee, Yoonjin Shin, Sohee Moon, Seunghae Kim, Yangha Kim
Mitochondrial biogenesis is a complex process requiring coordinated expression of nuclear and mitochondrial genomes. The peroxisome proliferator-activated receptor gamma co-activator 1-alpha (PGC-1α) is a key regulator of mitochondrial biogenesis, and it controls mitochondrial DNA (mtDNA) replication within diverse tissues, including muscle tissue. The aim of this study was to investigate the effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on mtDNA copy number and PGC-1α promoter activity in C2C12 muscle cells...
December 2016: Preventive Nutrition and Food Science
https://www.readbyqxmd.com/read/28077637/role-of-litopenaeus-vannamei-yin-yang-1-in-the-regulation-of-the-white-spot-syndrome-virus-immediate-early-gene-ie1
#18
Ping-Han Huang, Ting-Yi Huang, Pei-Si Cai, Li-Kwan Chang
: Yin Yang 1 (YY1) is a multifunctional zinc-finger transcription factor that regulates many key cellular processes. In this study, we report the cloning of YY1 from shrimp, Litopenaeus vannamei, (LvYY1). The study shows that LvYY1 is ubiquitously expressed in shrimp tissues, and knockdown of LvYY1 expression by dsRNA injection in WSSV-infected shrimp reduced both mRNA levels of the WSSV immediate-early gene, ie1, as well as overall copy numbers of the WSSV genome. The cumulative mortality of infected shrimp also declined with LvYY1 dsRNA injection...
January 11, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28077604/the-mitochondrial-dna-content-of-cumulus-granulosa-cells-is-linked-to-embryo-quality
#19
V Desquiret-Dumas, A Clément, V Seegers, L Boucret, V Ferré-L'Hotellier, P E Bouet, P Descamps, V Procaccio, P Reynier, P May-Panloup
STUDY QUESTION: Could the mitochondrial DNA (mtDNA) content of cumulus granulosa cells (CGCs) be related to oocyte competence? SUMMARY ANSWER: The quality of embryos obtained during IVF procedures appears to be linked to mtDNA copy numbers in the CGCs. WHAT IS KNOWN ALREADY: Oocyte quality is linked to oocyte mtDNA content in the human and other species, and the mtDNA copy number of the oocyte is related to that of the corresponding CGCs. Moreover, the quantification of CGC mtDNA has recently been proposed as a biomarker of embryo viability...
January 6, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28077389/enhanced-oxidative-capacity-of-ground-squirrel-brain-mitochondria-during-hibernation
#20
Mallory A Ballinger, Christine Schwartz, Matthew T Andrews
During hibernation, thirteen-lined ground squirrels (Ictidomys tridecemlineatus) regularly cycle between bouts of torpor and interbout arousal (IBA).  Most of the brain is electrically quiescent during torpor, but regains activity quickly upon arousal to IBA resulting in extreme oscillations in energy demand during hibernation.  We predicted increased functional capacity of brain mitochondria during hibernation compared to spring to accommodate the variable energy demands of hibernation.  To address this hypothesis, we examined mitochondrial bioenergetics in the ground squirrel brain across three time points: spring (SP), torpor (TOR), and IBA...
January 11, 2017: American Journal of Physiology. Regulatory, Integrative and Comparative Physiology
keyword
keyword
17289
1
2
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"