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copy number variations

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https://www.readbyqxmd.com/read/28426752/somatic-copy-number-alterations-in-gastric-adenocarcinomas-among-asian-and-western-patients
#1
Steven E Schumacher, Byoung Yong Shim, Giovanni Corso, Min-Hee Ryu, Yoon-Koo Kang, Franco Roviello, Gordon Saksena, Shouyong Peng, Ramesh A Shivdasani, Adam J Bass, Rameen Beroukhim
Gastric cancer, a leading worldwide cause of cancer mortality, shows high geographic and ethnic variation in incidence rates, which are highest in East Asia. The anatomic locations and clinical behavior also differ by geography, leading to the controversial idea that Eastern and Western forms of the disease are distinct. In view of these differences, we investigated whether gastric cancers from Eastern and Western patients show distinct genomic profiles. We used high-density profiling of somatic copy-number aberrations to analyze the largest collection to date of gastric adenocarcinomas and utilized genotyping data to rigorously annotate ethnic status...
2017: PloS One
https://www.readbyqxmd.com/read/28424544/association-of-genetic-variations-in-the-mitochondrial-dna-control-region-with-presbycusis
#2
Masoumeh Falah, Mohammad Farhadi, Seyed Kamran Kamrava, Saeid Mahmoudian, Ahmad Daneshi, Maryam Balali, Alimohamad Asghari, Massoud Houshmand
BACKGROUND: The prominent role of mitochondria in the generation of reactive oxygen species, cell death, and energy production contributes to the importance of this organelle in the intracellular mechanism underlying the progression of the common sensory disorder of the elderly, presbycusis. Reduced mitochondrial DNA (mtDNA) gene expression and coding region variation have frequently been reported as being associated with the development of presbycusis. The mtDNA control region regulates gene expression and replication of the genome of this organelle...
2017: Clinical Interventions in Aging
https://www.readbyqxmd.com/read/28424525/genome-wide-detection-of-copy-number-variation-in-chinese-indigenous-sheep-using-an-ovine-high-density-600%C3%A2-k-snp-array
#3
Qing Ma, Xuexue Liu, Jianfei Pan, Lina Ma, Yuehui Ma, Xiaohong He, Qianjun Zhao, Yabin Pu, Yingkang Li, Lin Jiang
Copy number variants (CNVs) represent a form of genomic structural variation underlying phenotypic diversity. In this study, we used the Illumina Ovine SNP 600 K BeadChip array for genome-wide detection of CNVs in 48 Chinese Tan sheep. A total of 1,296 CNV regions (CNVRs), ranging from 1.2 kb to 2.3 Mb in length, were detected, representing approximately 4.7% of the entire ovine genome (Oar_v3.1). We combined our findings with five existing CNVR reports to generate a composite genome-wide dataset of 4,321 CNVRs, which revealed 556 (43%) novel CNVRs...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423314/cyanobacteria-maintain-constant-protein-concentration-despite-genome-copy-number-variation
#4
Xiao-Yu Zheng, Erin K O'Shea
The cyanobacterium Synechococcus elongatus PCC 7942 has multiple copies of its single chromosome, and the copy number varies in individual cells, providing an ideal system to study the effect of genome copy-number variation on cell size and gene expression. Using single-cell fluorescence imaging, we found that protein concentration remained constant across individual cells regardless of genome copy number. Cell volume and the total protein amount from a single gene were both positively, linearly correlated with genome copy number, suggesting that changes in cell volume play an important role in buffering genome copy-number variance...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28422718/validation-and-optimization-of-the-ion-torrent-s5-xl-sequencer-and-oncomine-workflow-for-brca1-and-brca2-genetic-testing
#5
Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung-Tae Lee, Jong Rak Choi, Kyung-A Lee
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA)...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422522/molecular-genetic-characterization-of-a-chinese-family-with-severe-split-hand-foot-malformation
#6
Lihua Cao, Wei Yang, Shusen Wang, Chen Chen, Xue Zhang, Yang Luo
AIMS: Split hand/foot malformation (SHFM) is a congenital limb malformation characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM is a genetically heterogeneous disease; the aim of this study was to identify pathogenic variations in a Chinese family with SHFM. MATERIALS AND METHODS: Haplotype analyses with microsatellite markers covering the five SHFM loci were performed to localize the causative locus...
April 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28422133/gene-set-analysis-shows-association-between-fmrp-targets-and-autism-spectrum-disorder
#7
Arija Jansen, Gwen C Dieleman, August B Smit, Matthijs Verhage, Frank C Verhulst, Tinca J C Polderman, Danielle Posthuma
Autism spectrum disorder (ASD) is a heterogeneous group of disorders characterized by problems with social interaction, communication, and repetitive and restricted behavior. Despite its high heritability and the substantial progress made in elucidating genetic associations, the corresponding biological mechanisms are largely unknown. Our objective is to investigate the contribution of common genetic variation to biological pathways functionally involved in ASD. We conducted gene-set analyses to identify ASD-associated functional biological pathways using the statistical tools MAGMA and INRICH...
April 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28421090/comparative-genomics-and-phylogenomics-of-east-asian-tulips-amana-liliaceae
#8
Pan Li, Rui-Sen Lu, Wu-Qin Xu, Tetsuo Ohi-Toma, Min-Qi Cai, Ying-Xiong Qiu, Kenneth M Cameron, Cheng-Xin Fu
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28420428/significant-heterogeneity-in-wolbachia-copy-number-within-and-between-populations-of-onchocerca-volvulus
#9
Samuel Armoo, Stephen R Doyle, Mike Y Osei-Atweneboana, Warwick N Grant
BACKGROUND: Wolbachia are intracellular bacteria found in arthropods and several filarial nematode species. The filarial Wolbachia have been proposed to be involved in the immunopathology associated with onchocerciasis. Higher Wolbachia-to-nematode ratios have been reported in the savannah-ecotype compared to the forest-ecotype, and have been interpreted as consistent with a correlation between Wolbachia density and disease severity. However, factors such as geographic stratification and ivermectin drug exposure can lead to significant genetic heterogeneity in the nematode host populations, so we investigated whether Wolbachia copy number variation is also associated with these underlying factors...
April 18, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28420389/assessment-of-copy-number-variation-in-genes-related-to-drug-resistance-in-plasmodium-vivax-and-plasmodium-falciparum-isolates-from-the-brazilian-amazon-and-a-systematic-review-of-the-literature
#10
Gabriel Luíz Costa, Lara Cotta Amaral, Cor Jesus Fernandes Fontes, Luzia Helena Carvalho, Cristiana Ferreira Alves de Brito, Taís Nóbrega de Sousa
BACKGROUND: Parasite resistance to anti-malarials represents a great obstacle for malaria elimination. The majority of studies have investigated the association between single-nucleotide polymorphisms (SNPs) and drug resistance; however, it is becoming clear that the copy number variation (CNV) is also associated with this parasite phenotype. To provide a baseline for molecular surveillance of anti-malarial drug resistance in the Brazilian Amazon, the present study characterized the genetic profile of both markers in the most common genes associated with drug resistance in Plasmodium falciparum and Plasmodium vivax isolates...
April 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28420343/on-the-association-analysis-of-cnv-data-a-fast-and-robust-family-based-association-method
#11
Meiling Liu, Sanghoon Moon, Longfei Wang, Sulgi Kim, Yeon-Jung Kim, Mi Yeong Hwang, Young Jin Kim, Robert C Elston, Bong-Jo Kim, Sungho Won
BACKGROUND: Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical methods for CNV association analysis can be categorized into two different strategies. First, the copy number is estimated by maximum likelihood and association of the expected copy number with the phenotype is tested. Second, the observed probe intensity measurements can be directly used to detect association of CNV with the phenotypes of interest...
April 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28418179/copy-number-variation-increased-gene-expression-and-molecular-mechanisms-of-neurofascin-in-lung-cancer
#12
Johanna Samulin Erdem, Yke Jildouw Arnoldussen, Vidar Skaug, Aage Haugen, Shanbeh Zienolddiny
Metastasis and cell adhesion are key aspects of cancer progression. Neurofascin (NFASC) is a member of the immunoglobulin superfamily of adhesion molecules and, while studies on NFASC are inadequate, other members have been indicated pivotal roles in cancer progression and metastasis. This study aimed at increasing the knowledge on the involvement of adhesion molecules in lung cancer progression by studying the regulation and role of NFASC in non-small cell lung cancer (NSCLC). Here, copy number variations in the NFASC gene were analyzed in tumor and non-tumorous lung tissues of 204 NSCLC patients...
April 18, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28413933/primer-in-genetics-and-genomics-article-3-explaining-human-diversity-the-role-of-dna
#13
Catherine Y Read
Genetic variation lays the foundation for diversity and enables humans to adapt to changing environments. The order of the nucleotides adenine, guanine, cytosine, and thymine on the deoxyribonucleic acid (DNA) molecules of the nuclear chromosomes and mitochondrial DNA (mtDNA) plays an important role in normal cell division, tissue development, and reproduction but is susceptible to alteration from a large number of random, inherited, or environmental events. Variations can range from a change in a single nucleotide to duplication of entire chromosomes...
May 2017: Biological Research for Nursing
https://www.readbyqxmd.com/read/28410642/ipscore-a-resource-of-222-ipsc-lines-enabling-functional-characterization-of-genetic-variation-across-a-variety-of-cell-types
#14
Athanasia D Panopoulos, Matteo D'Antonio, Paola Benaglio, Roy Williams, Sherin I Hashem, Bernhard M Schuldt, Christopher DeBoever, Angelo D Arias, Melvin Garcia, Bradley C Nelson, Olivier Harismendy, David A Jakubosky, Margaret K R Donovan, William W Greenwald, KathyJean Farnam, Megan Cook, Victor Borja, Carl A Miller, Jonathan D Grinstein, Frauke Drees, Jonathan Okubo, Kenneth E Diffenderfer, Yuriko Hishida, Veronica Modesto, Carl T Dargitz, Rachel Feiring, Chang Zhao, Aitor Aguirre, Thomas J McGarry, Hiroko Matsui, He Li, Joaquin Reyna, Fangwen Rao, Daniel T O'Connor, Gene W Yeo, Sylvia M Evans, Neil C Chi, Kristen Jepsen, Naoki Nariai, Franz-Josef Müller, Lawrence S B Goldstein, Juan Carlos Izpisua Belmonte, Eric Adler, Jeanne F Loring, W Travis Berggren, Agnieszka D'Antonio-Chronowska, Erin N Smith, Kelly A Frazer
Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively...
April 11, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28410206/development-of-diagnostic-scar-markers-for-genomic-dna-amplifications-in-breast-carcinoma-by-dna-cloning-of-high-gc-ramp-pcr-fragments
#15
Shangyi Fu, Jingliang Cheng, Chunli Wei, Luquan Yang, Xiuli Xiao, Dianzheng Zhang, M David Stewart, Junjiang Fu
Cancer is genetically heterogeneous regarding to molecular genetic characteristics and pathogenic pathways. A wide spectrum of biomarkers, including DNA markers, is used in determining genomic instability, molecular subtype determination and disease prognosis, and estimating sensitivity to different drugs in clinical practice. In a previous study, we developed highly effective DNA markers using improved random amplified polymorphic DNA (RAPD) with high-GC primers, which is a valuable approach for the genetic authentication of medicinal plants...
March 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28409824/a-comparative-genomic-hybridization-approach-to-study-gene-copy-number-variations-among-chinese-hamster-cell-lines
#16
Nandita Vishwanathan, Arpan Bandyopadhyay, Hsu-Yuan Fu, Kathryn C Johnson, Nathan M Springer, Wei-Shou Hu
Chinese Hamster Ovary (CHO) cells are aneuploid in nature. The genome of recombinant protein producing CHO cell lines continuously undergoes changes in its structure and organization. We analyzed nine cell lines, including parental cell lines, using a comparative genomic hybridization (CGH) array focused on gene-containing regions. The comparison of CGH with copy-number estimates from sequencing data showed good correlation. Hierarchical clustering of the gene copy number variation data from CGH data revealed the lineage relationships between the cell lines...
April 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28409725/genetic-landscape-of-sporadic-vestibular-schwannoma
#17
Aril Løge Håvik, Ove Bruland, Erling Myrseth, Hrvoje Miletic, Mads Aarhus, Per-Morten Knappskog, Morten Lund-Johansen
OBJECTIVE Vestibular schwannoma (VS) is a benign tumor with associated morbidities and reduced quality of life. Except for mutations in NF2, the genetic landscape of VS remains to be elucidated. Little is known about the effect of Gamma Knife radiosurgery (GKRS) on the VS genome. The aim of this study was to characterize mutations occurring in this tumor to identify new genes and signaling pathways important for the development of VS. In addition, the authors sought to evaluate whether GKRS resulted in an increase in the number of mutations...
April 14, 2017: Journal of Neurosurgery
https://www.readbyqxmd.com/read/28408773/can-mitochondria-dna-provide-a-novel-biomarker-for-evaluating-the-risk-and-prognosis-of-colorectal-cancer
#18
REVIEW
Han Shuwen, Yang Xi, Pan Yuefen
Colorectal cancer (CRC) was one of the most frequent cancers worldwide. Accurate risk and prognosis evaluation could obtain better quality of life and longer survival time for the patients. Current research hotspot was focus on the gene biomarker to evaluate the risk and prognosis. Mitochondrion contains its own DNA and regulates self-replicating so that it can be as a candidate biomarker for evaluating the risk and prognosis of colorectal cancer. But there were already huge controversies on this issue. The review was to summarize current viewpoints of the controversial issues and described our understanding from the four aspects including mtDNA copy number, mitochondrial displacement loop, mtDNA variation, and mtDNA microsatellite instability, wishing the summary of the mtDNA in colorectal cancer could provide a meaningful reference or a valuable direction in the future studies...
2017: Disease Markers
https://www.readbyqxmd.com/read/28408749/high-prevalence-of-tp53-mutations-is-associated-with-poor-survival-and-an-emt-signature-in-gliosarcoma-patients
#19
Sung-Yup Cho, Changho Park, Deukchae Na, Jee Yun Han, Jieun Lee, Ok-Kyoung Park, Chengsheng Zhang, Chang Ohk Sung, Hyo Eun Moon, Yona Kim, Jeong Hoon Kim, Jong Jae Kim, Shin Kwang Khang, Do-Hyun Nam, Jung Won Choi, Yeon-Lim Suh, Dong Gyu Kim, Sung Hye Park, Hyewon Youn, Kyuson Yun, Jong-Il Kim, Charles Lee, Sun Ha Paek, Hansoo Park
Gliosarcoma (GS) is a rare variant (2%) of glioblastoma (GBM) that poses clinical genomic challenges because of its poor prognosis and limited genomic information. To gain a comprehensive view of the genomic alterations in GS and to understand the molecular etiology of GS, we applied whole-exome sequencing analyses for 28 GS cases (6 blood-matched fresh-frozen tissues for the discovery set, 22 formalin-fixed paraffin-embedded tissues for the validation set) and copy-number variation microarrays for 5 blood-matched fresh-frozen tissues...
April 14, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/28408603/single-cell-whole-genome-analyses-by-linear-amplification-via-transposon-insertion-lianti
#20
Chongyi Chen, Dong Xing, Longzhi Tan, Heng Li, Guangyu Zhou, Lei Huang, X Sunney Xie
Single-cell genomics is important for biology and medicine. However, current whole-genome amplification (WGA) methods are limited by low accuracy of copy-number variation (CNV) detection and low amplification fidelity. Here we report an improved single-cell WGA method, Linear Amplification via Transposon Insertion (LIANTI), which outperforms existing methods, enabling micro-CNV detection with kilobase resolution. This allowed direct observation of stochastic firing of DNA replication origins, which differs from cell to cell...
April 14, 2017: Science
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