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https://www.readbyqxmd.com/read/28938747/prevalence-of-endocrine-and-genetic-abnormalities-in-boys-evaluated-systematically-for-a-disorder-of-sex-development
#1
R Nixon, V Cerqueira, A Kyriakou, A Lucas-Herald, J McNeilly, M McMillan, A I Purvis, E S Tobias, R McGowan, S F Ahmed
STUDY QUESTION: What is the likelihood of identifying genetic or endocrine abnormalities in a group of boys with 46, XY who present to a specialist clinic with a suspected disorder of sex development (DSD)? SUMMARY ANSWER: An endocrine abnormality of the gonadal axis may be present in a quarter of cases and copy number variants (CNVs) or single gene variants may be present in about half of the cases. WHAT IS KNOWN ALREADY: Evaluation of 46, XY DSD requires a combination of endocrine and genetic tests but the prevalence of these abnormalities in a sufficiently large group of boys presenting to one specialist multidisciplinary service is unclear...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938622/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#2
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938580/diagnostic-significance-of-urinary-long-non-coding-pca3-rna-in-prostate-cancer
#3
Tao Wang, Xiangyun Qu, Jiajia Jiang, Peng Gao, Dingding Zhao, Xueqi Lian, Xiaohua Li
Prostate cancer antigen 3(PCA3) is a long non-coding RNA, which was found increased expression in CaP patients than healthy individual. In this study, the individual nucleic acid of PCA3 and PSA was recombinant expressed as a reference reagent, and a quantitative RT-PCR with TaqMan assay was developed to examine the copies of PCA3 and PSA gene in urine. The results showed that the area under the receiver operating characteristic curve (AUROC) was 0.717, 0.444 and 0.916 for the number of PCA3 copy, PSA copy and for the score of PCA3/PSA RNA, respectively...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938536/integrating-omics-data-and-protein-interaction-networks-to-prioritize-driver-genes-in-cancer
#4
Tiejun Zhang, Di Zhang
Although numerous approaches have been proposed to discern driver from passenger, identification of driver genes remains a critical challenge in the cancer genomics field. Driver genes with low mutated frequency tend to be filtered in cancer research. In addition, the accumulation of different omics data necessitates the development of algorithmic frameworks for nominating putative driver genes. In this study, we presented a novel framework to identify driver genes through integrating multi-omics data such as somatic mutation, gene expression, and copy number alterations...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938089/drug-discovery-and-chemical-biology-of-cancer-epigenetics
#5
REVIEW
Scott Ribich, Darren Harvey, Robert A Copeland
Comprehensive whole-exome sequencing, DNA copy-number determination, and transcriptomic analyses of diverse cancers have greatly expanded our understanding of the biology of many tumor types. In addition to mutations in the common cell-of-origin specific driver mutations, these studies have also revealed a large number of loss-of-function and gain-of-function mutations in chromatin-modifying proteins (CMPs). This has revealed that epigenetic dysregulation is a common feature of most pediatric and adult cancers...
September 21, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28937367/associations-between-epidermal-growth-factor-receptor-and-topoisomerase-ii-alpha-gene-copy-number-variations-human-papillomavirus-positivity-and-cytologic-analysis-in-cervical-cell-lesions
#6
Işın Kaya, Oya Nermin Sivrikoz, Özdal Etlik, Abdülkadir Gök
BACKGROUND: Cervical cancer is the second most common gynecologic cancer worldwide. Human papillomavirus (HPV) infection is a leading etiological factor in cervical carcinoma.The aim of this study was to compare HPV positivity, EGFR and TOP2A gene copy number variations and cervical cytologic findings. MATERIALS AND METHODS: The study group comprised 100 female volunteers between 21-64 years old. Cytologic analysis was performed using the liquid-based cytology technique...
July 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/28936979/advances-of-selectable-marker-genes-in-plastid-genetic-engineering
#7
Yong He, An Luo, Lian-Sheng Mu, Qiang Chen, Yan Zhang, Kai-Wun Yeh, Zhi-Hong Tian
Plastid genetic engineering is a safer, more precise, and more efficient transgene expression system than the nuclear genetic transformation system. It has been widely used in basic research and biotechnology applications as the next-generation transgenic technology in plants. Similar to nuclear genetic transformation, selection markers are needed in plastid genetic engineering to identify 'true' transformants and acquire homoplasmy. Because of the high copy number of plastids, maternal inheritance of the plastid genome, and the long process of homogenization of transplastomic plants, the selection markers for plastid genetic engineering are different from those used in the nuclear transformation system...
September 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28936814/-the-role-of-molecular-karyotyping-in-the-genetic-etiology-of-autism
#8
Burcu Özbaran, Bilçağ Akgün, Duygu Kaçamak, Sezen Köse, Ayşenur Kavasoğlu, Hüseyin Onay
OBJECTIVE: The aim of this study was to investigate the deletions and duplications with a molecular karyotyping technique and to elucidate the etiology of autism. METHOD: A total of 31 patients (20 boys and 11 girls) between 4 to 18 years old with normal chromosomal analysis and no Fragile X mutation were diagnosed in the Ege University Child and Adolescent Psychiatry Clinic with autism (according to DSM-IV-TR criteria) and were enrolled in the study. Symptom severity of the patients was evaluated with a Childhood Autism Rating Scale...
2017: Türk Psikiyatri Dergisi, Turkish Journal of Psychiatry
https://www.readbyqxmd.com/read/28936174/the-effect-of-velvet-antler-proteins-on-cardiac-microvascular-endothelial-cells-challenged-with-ischemia-hypoxia
#9
Xiang Xiao, Shuqiang Xu, Lin Li, Min Mao, Jinping Wang, Yanjun Li, Ziwei Wang, Fei Ye, Li Huang
Velvet antler (VA) is a precious traditional Chinese medicine that is capable of repeated regeneration. Based on the Chinese medicine theory of coordination the heart and kidneys, VA has been employed to treat heart diseases, including ischemic heart disease, heart failure, and arrhythmia. We examined the effects of VA proteins on primary cardiac microvascular endothelial cells (CMECs) that were subjected to ischemia-hypoxia (IH) to investigate their effects on and mechanism of action in the treatment of ischemic heart disease...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28935972/chromosomal-microarray-analysis-in-a-cohort-of-underrepresented-population-identifies-serinc2-as-a-novel-candidate-gene-for-autism-spectrum-disorder
#10
Areerat Hnoonual, Weerin Thammachote, Thipwimol Tim-Aroon, Kitiwan Rojnueangnit, Tippawan Hansakunachai, Tasanawat Sombuntham, Rawiwan Roongpraiwan, Juthamas Worachotekamjorn, Jariya Chuthapisith, Suthat Fucharoen, Duangrurdee Wattanasirichaigoon, Nichara Ruangdaraganon, Pornprot Limprasert, Natini Jinawath
Chromosomal microarray (CMA) is now recognized as the first-tier genetic test for detection of copy number variations (CNVs) in patients with autism spectrum disorder (ASD). The aims of this study were to identify known and novel ASD associated-CNVs and to evaluate the diagnostic yield of CMA in Thai patients with ASD. The Infinium CytoSNP-850K BeadChip was used to detect CNVs in 114 Thai patients comprised of 68 retrospective ASD patients (group 1) with the use of CMA as a second line test and 46 prospective ASD and developmental delay patients (group 2) with the use of CMA as the first-tier test...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935813/asxl3-is-a-novel-pluripotency-factor-in-human-respiratory-epithelial-cells-and-a-potential-therapeutic-target-in-small-cell-lung-cancer
#11
Vivek Shukla, Mahadev Rao, Hongen Zhang, Jeanette Beers, Darawalee Wangsa, Danny Wangsa, Floryne O Buishand, Yonghong Wang, Zhiya Yu, Holly Stevenson, Emily Reardon, Kaitlin C McLoughlin, Andrew Kaufman, Eden Payabyab, Julie A Hong, Mary Zhang, Sean R Davis, Daniel C Edelman, Guokai Chen, Markku Miettinen, Nicholas Restfo, Thomas Ried, Paul S Meltzer, David S Schrump
In this study, we generated induced pluripotent stem cells (iPSC) from normal human small airway epithelial cells (SAEC) to investigate epigenetic mechanisms of stemness and pluripotency in lung cancers. We documented key hallmarks of reprogramming in lung iPSC (Lu-iPSC) that coincided with modulation of more than 15,000 genes relative to parental SAEC. Of particular novelty, we identified the PRC2-associated protein, ASXL3 which was markedly upregulated in Lu-iPSC and small cell lung cancer (SCLC) lines and clinical specimens...
September 21, 2017: Cancer Research
https://www.readbyqxmd.com/read/28935600/identification-and-function-analysis-of-ras-related-nuclear-protein-from-macrobrachium-rosenbergii-involved-in-spiroplasma-eriocheiris-infection
#12
Mingxiao Ning, Yunji Xiu, Meijun Yuan, Jingxiu Bi, Min Liu, Panpan Wei, Yuye Yan, Wei Gu, Wen Wang, Qingguo Meng
A ras-related nuclear protein (Ran) protein was obtained from Macrobrachium rosenbergii, named MrRan. Phylogenetic analysis results showed that MrRan was clustered in one group together with other crustaceans. Tissue distribution analysis revealed that MrRan was expressed mainly in gill, intestine and stomach, and expressed weakly in muscle. The MrRan expression levels in gill and hemocyte of prawns were significantly up-regulated after challenged by Spiroplasma eriocheiris. The copy number of S. eriocheiris in MrRan dsRNA injection group was significantly less than control groups during infection...
September 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28935545/integrated-molecular-analysis-of-tamoxifen-resistant-invasive-lobular-breast-cancer-cells-identifies-mapk-and-grm-mglur-signaling-as-therapeutic-vulnerabilities
#13
REVIEW
Hillary Stires, Mary M Heckler, Xiaoyong Fu, Zhao Li, Catherine S Grasso, Michael J Quist, Joseph A Lewis, Uwe Klimach, Alan Zwart, Akanksha Mahajan, Balázs Győrffy, Luciane R Cavalli, Rebecca B Riggins
Invasive lobular breast cancer (ILC) is an understudied malignancy with distinct clinical, pathological, and molecular features that distinguish it from the more common invasive ductal carcinoma (IDC). Mounting evidence suggests that estrogen receptor-alpha positive (ER+) ILC has a poor response to Tamoxifen (TAM), but the mechanistic drivers of this are undefined. In the current work, we comprehensively characterize the SUM44/LCCTam ILC cell model system through integrated analysis of gene expression, copy number, and mutation, with the goal of identifying actionable alterations relevant to clinical ILC that can be co-targeted along with ER to improve treatment outcomes...
September 18, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28935259/module-based-systematic-construction-of-plasmids-for-episomal-gene-expression-in-fission-yeast
#14
Keita Kiriya, Hayato Tsuyuzaki, Masamitsu Sato
The fission yeast Schizosaccharomyces pombe is a powerful model organism for cell biology and molecular biology, as genetic manipulation is easily achieved. Introduction of exogenous genes cloned in episomal plasmids into yeast cells can be done through well-established transformation methods. For expression of genes in S. pombe cells, the multi-copy plasmid pREP1 and its derivatives, including pREP41 and pREP81, have been widely used as vectors. Although recent advancement of technology brought a number of useful genetic elements such as new promoters, selection marker genes and fluorescent protein tags, introduction of those elements into conventional pREP1 requires a large commitment of both time and effort because cloning procedures need to be repeated until the final products are constructed...
September 18, 2017: Gene
https://www.readbyqxmd.com/read/28934986/identification-of-novel-candidate-disease-genes-from-de-novo-exonic-copy-number-variants
#15
Tomasz Gambin, Bo Yuan, Weimin Bi, Pengfei Liu, Jill A Rosenfeld, Zeynep Coban-Akdemir, Amber N Pursley, Sandesh C S Nagamani, Ronit Marom, Sailaja Golla, Lauren Dengle, Heather G Petrie, Reuben Matalon, Lisa Emrick, Monica B Proud, Diane Treadwell-Deering, Hsiao-Tuan Chao, Hannele Koillinen, Chester Brown, Nora Urraca, Roya Mostafavi, Saunder Bernes, Elizabeth R Roeder, Kimberly M Nugent, Patricia I Bader, Gary Bellus, Michael Cummings, Hope Northrup, Myla Ashfaq, Rachel Westman, Robert Wildin, Anita E Beck, LaDonna Immken, Lindsay Elton, Shaun Varghese, Edward Buchanan, Laurence Faivre, Mathilde Lefebvre, Christian P Schaaf, Magdalena Walkiewicz, Yaping Yang, Sung-Hae L Kang, Seema R Lalani, Carlos A Bacino, Arthur L Beaudet, Amy M Breman, Janice L Smith, Sau Wai Cheung, James R Lupski, Ankita Patel, Chad A Shaw, Paweł Stankiewicz
BACKGROUND: Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS: We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017...
September 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28934930/xcavator-accurate-detection-and-genotyping-of-copy-number-variants-from-second-and-third-generation-whole-genome-sequencing-experiments
#16
Alberto Magi, Tommaso Pippucci, Carlo Sidore
BACKGROUND: We developed a novel software package, XCAVATOR, for the identification of genomic regions involved in copy number variants/alterations (CNVs/CNAs) from short and long reads whole-genome sequencing experiments. RESULTS: By using simulated and real datasets we showed that our tool, based on read count approach, is capable to predict the boundaries and the absolute number of DNA copies CNVs/CNAs with high resolutions. To demonstrate the power of our software we applied it to the analysis Illumina and Pacific Bioscencies data and we compared its performance to other ten state of the art tools...
September 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28934561/epigenetic-mechanisms-regulating-adaptive-responses-to-targeted-kinase-inhibitors-in-cancer
#17
Steven P Angus, Jon S Zawistowski, Gary L Johnson
Although targeted inhibition of oncogenic kinase drivers has achieved remarkable patient responses in many cancers, the development of resistance has remained a significant challenge. Numerous mechanisms have been identified, including the acquisition of gatekeeper mutations, activating pathway mutations, and copy number loss or gain of the driver or alternate nodes. These changes have prompted the development of kinase inhibitors with increased selectivity, use of second-line therapeutics to overcome primary resistance, and combination treatment to forestall resistance...
September 15, 2017: Annual Review of Pharmacology and Toxicology
https://www.readbyqxmd.com/read/28934520/damage-of-inner-ear-sensory-hair-cells-via-mitochondrial-loss-in-a-murine-model-of-sleep-apnea-with-chronic-intermittent-hypoxia
#18
Young Joon Seo, Hyun Mi Ju, Sun Hee Lee, Sang Hyun Kwak, Min Jung Kang, Joo-Heon Yoon, Chang-Hoon Kim, Hyung-Ju Cho
Study Objectives: Investigating the exact pathophysiology of obstructive sleep apnea syndrome (OSAS)-induced hearing loss is critical. We sought to verify the hypothesis that a correlation exists between mitochondrial dysfunction in inner ear hair cells and the auditory dysfunction induced by chronic intermittent hypoxia (CIH) in a murine model of sleep apnea. Methods: C57BL/6J adult male mice were randomized to 4 weeks of CIH (n = 12) or normoxia (Sham) (n = 12)...
September 1, 2017: Sleep
https://www.readbyqxmd.com/read/28934307/amplification-of-the-egfr-gene-can-be-maintained-and-modulated-by-variation-of-egf-concentrations-in-in-vitro-models-of-glioblastoma-multiforme
#19
Doreen William, Poroshista Mokri, Nora Lamp, Michael Linnebacher, Carl Friedrich Classen, Andreas Erbersdobler, Björn Schneider
Glioblastoma multiforme (GBM) is the most common and lethal brain tumor in adults. It is known that amplification of the epidermal growth factor receptor gene (EGFR) occurs in approximately 40% of GBM, leading to enhanced activation of the EGFR signaling pathway and promoting tumor growth. Although GBM mutations are stably maintained in GBM in vitro models, rapid loss of EGFR gene amplification is a common observation during cell culture. To maintain EGFR amplification in vitro, heterotopic GBM xenografts with elevated EGFR copy number were cultured under varying serum conditions and EGF concentrations...
2017: PloS One
https://www.readbyqxmd.com/read/28934280/recurrent-deletions-of-the-x-chromosome-linked-cnv64-cnv67-and-cnv69-shows-geographic-differences-across-china-and-no-association-with-idiopathic-infertility-in-men
#20
Xiulan Ma, Martin Kuete, Xiuli Gu, Hui Zhou, Chengliang Xiong, Honggang Li
A recent study found that three recurrent deletions of X chromosome linked copy number variations (CNVs), CNV64, CNV67 and CNV69 were associated with idiopathic male infertility in Spanish and Italian populations, especially CNV67 resembling the azoospermia factor deletions. That merits further investigations among different populations. This study was conducted to examine the prevalence of the three CNVs deletions and their associations with idiopathic male infertility in Chinese Han population. The present study included a large population of 1550 Chinese Han subjects recruited between 2014 and 2016...
2017: PloS One
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