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https://www.readbyqxmd.com/read/28718531/next-generation-sequencing-for-patients-with-non-obstructive-azoospermia-implications-for-significant-roles-of-monogenic-oligogenic-mutations
#1
S Nakamura, M Miyado, K Saito, M Katsumi, A Nakamura, Y Kobori, Y Tanaka, H Ishikawa, A Yoshida, H Okada, K Hata, K Nakabayashi, K Okamura, H Ogata, Y Matsubara, T Ogata, H Nakai, M Fukami
Azoospermia affects up to 1% of adult men. Non-obstructive azoospermia is a multifactorial disorder whose molecular basis remains largely unknown. To date, mutations in several genes and multiple submicroscopic copy-number variations (CNVs) have been identified in patients with non-obstructive azoospermia. The aim of this study was to clarify the contribution of nucleotide substitutions in known causative genes and submicroscopic CNVs in the genome to the development of non-obstructive azoospermia. To this end, we conducted sequence analysis of 25 known disease-associated genes using next-generation sequencing and genome-wide copy-number analysis using array-based comparative genomic hybridization...
July 2017: Andrology
https://www.readbyqxmd.com/read/28716697/copy-number-variations-of-the-il-22-gene-are-associated-with-ankylosing-spondylitis-a-case-control-study-in-chinese-han-population
#2
Xu Zhang, Xiaona Li, Renfang Han, Mengya Chen, Yaping Yuan, Xingxing Hu, Mengmeng Wang, Rui Li, Xiao Yang, Qing Xia, Yubo Ma, Jiajia Yang, Jingjing Tong, Shengqian Xu, Jianhua Xu, Zongwen Shuai, Faming Pan
IL-22 provides a new insight into the mechanisms of autoimmunity, and copy number variations (CNVs) are associated with autoimmune diseases. This study aims to explore the association of IL-22 gene CNVs with ankylosing spondylitis (AS) susceptibility. The copy numbers of IL-22 gene (2 fragments: IL-22_1, IL-22_2) were examined by AccuCopy(TM) methods in a cohort of 649 AS patients and 628 controls. Association of IL-22 CNVs and AS susceptibility was analyzed, and AS risk was estimated by Odds Ratio (ORs) and 95% confidence intervals (CIs), and the Benjamini-Hochberg method was applied to regulate the false discovery rate (FDR)...
July 14, 2017: Human Immunology
https://www.readbyqxmd.com/read/28716534/mutations-in-tyrobp-are-not-a-common-cause-of-dementia-in-a-turkish-cohort
#3
Lee Darwent, Susana Carmona, Ebba Lohmann, Gamze Guven, Celia Kun-Rodrigues, Basar Bilgic, Hasmet Hanagasi, Hakan Gurvit, Nihan Erginel-Unaltuna, Meltem Pak, John Hardy, Andrew Singleton, Jose Brás, Rita Guerreiro
Mutations in TYROBP and TREM2 have been shown to cause polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy. Recently, variants in TREM2 were also associated with frontotemporal dementia and Alzheimer's disease. Given the functional proximity between these 2 genes, we investigated the genetic variation of TYROBP in a Turkish cohort of 103 dementia patients. No mutations or copy number variants predicted to be pathogenic were identified. These results indicate that mutations in TYROBP are not a common cause of dementia in this Turkish cohort...
June 28, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28715081/molecular-constraints-on-resistance-tolerance-tradeoffs
#4
J Miles Mesa, Daniel R Scholes, Jack Juvik, Ken N Paige
Plants have numerous mechanisms to cope with the negative effects of herbivory, including plant resistance, structural and chemical traits that reduce damage, and plant tolerance, the ability to compensate for tissues lost. It has been argued that resistance and tolerance represent alternate strategies and thus there should be a tradeoff between resistance and tolerance. However, resistance and tolerance are controlled via the same molecular pathway, the oxidative pentose phosphate pathway and the process of endoreduplication...
July 17, 2017: Ecology
https://www.readbyqxmd.com/read/28714986/genome-wide-reconstruction-of-complex-structural-variants-using-read-clouds
#5
Noah Spies, Ziming Weng, Alex Bishara, Jennifer McDaniel, David Catoe, Justin M Zook, Marc Salit, Robert B West, Serafim Batzoglou, Arend Sidow
In read cloud approaches, microfluidic partitioning of long genomic DNA fragments and barcoding of shorter fragments derived from these fragments retains long-range information in short sequencing reads. This combination of short reads with long-range information represents a powerful alternative to single-molecule long-read sequencing. We develop Genome-wide Reconstruction of Complex Structural Variants (GROC-SVs) for SV detection and assembly from read cloud data and apply this method to Illumina-sequenced 10x Genomics sarcoma and breast cancer data sets...
July 17, 2017: Nature Methods
https://www.readbyqxmd.com/read/28706735/the-importance-of-copy-number-variation-in-congenital-heart-disease
#6
Gregory Costain, Candice K Silversides, Anne S Bassett
Congenital heart disease (CHD) is the most common class of major malformations in humans. The historical association with large chromosomal abnormalities foreshadowed the role of submicroscopic rare copy number variations (CNVs) as important genetic causes of CHD. Recent studies have provided robust evidence for these structural variants as genome-wide contributors to all forms of CHD, including CHD that appears isolated without extra-cardiac features. Overall, a CNV-related molecular diagnosis can be made in up to one in eight patients with CHD...
September 14, 2016: NPJ Genomic Medicine
https://www.readbyqxmd.com/read/28705883/assessing-genome-wide-copy-number-variation-in-the-han-chinese-population
#7
Jianqi Lu, Haiyi Lou, Ruiqing Fu, Dongsheng Lu, Feng Zhang, Zhendong Wu, Xi Zhang, Changhua Li, Baijun Fang, Fangfang Pu, Jingning Wei, Qian Wei, Chao Zhang, Xiaoji Wang, Yan Lu, Shi Yan, Yajun Yang, Li Jin, Shuhua Xu
BACKGROUND: Copy number variation (CNV) is a valuable source of genetic diversity in the human genome and a well-recognised cause of various genetic diseases. However, CNVs have been considerably under-represented in population-based studies, particularly the Han Chinese which is the largest ethnic group in the world. OBJECTIVES: To build a representative CNV map for the Han Chinese population. METHODS: We conducted a genome-wide CNV study involving 451 male Han Chinese samples from 11 geographical regions encompassing 28 dialect groups, representing a less-biased panel compared with the currently available data...
July 13, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28704682/mutagenic-potential-of-hypoxanthine-in-live-human-cells
#8
Stephen DeVito, Jordan Woodrick, Linze Song, Rabindra Roy
Hypoxanthine (Hx) is a major DNA lesion generated by deamination of adenine during chronic inflammatory conditions, which is an underlying cause of various diseases including cancer of colon, liver, pancreas, bladder and stomach. There is evidence that deamination of DNA bases induces mutations, but no study has directly linked Hx accumulation to mutagenesis and strand-specific mutations yet in human cells. Using a site-specific mutagenesis approach, we report the first direct evidence of mutation potential and pattern of Hx in live human cells...
June 28, 2017: Mutation Research
https://www.readbyqxmd.com/read/28700469/microarray-analysis-of-copy-number-variations-and-gene-expression-profiles-in-prostate-cancer
#9
Yuping Han, Xuefei Jin, Hongyan Li, Kaichen Wang, Ji Gao, Lide Song, Yanting Lv
BACKGROUND: This study aimed to identify potential prostate cancer (PC)-related variations in gene expression profiles. METHODS: Microarray data from the GSE21032 dataset that contained the whole-transcript and exon-level expression profile (GSE21034) and Agilent 244K array-comparative genomic hybridization data (GSE21035) were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and copy-number variations (CNVs) were identified between PC and normal tissue samples...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28700439/genital-rhabdomyoma-of-the-lower-female-genital-tract-a-study-of-12-cases-with-molecular-cytogenetic-findings
#10
J Kenneth Schoolmeester, Deyin Xing, Gary L Keeney, William R Sukov
Of the subtypes of extracardiac rhabdomyoma, genital rhabdomyoma is most uncommon and is occasionally classified as fetal rhabdomyoma due to morphologic similarities. In contrast to other forms of rhabdomyoma, the genetic alterations of genital rhabdomyoma are unknown. The clinical and pathologic findings in 12 cases were reviewed and 2 cases were processed for whole genome copy number analysis by single nucleotide polymorphism microarray. Twelve patients ranged in age from 43 to 65 yr (mean: 50.2 yr). Nine tumors arose in the vagina and 3 in the cervix, with their greatest dimension spanning 0...
July 11, 2017: International Journal of Gynecological Pathology
https://www.readbyqxmd.com/read/28698882/excnvss-a-noise-robust-method-for-copy-number-variation-detection-in-whole-exome-sequencing-data
#11
Jinhwa Kong, Jaemoon Shin, Jungim Won, Keonbae Lee, Unjoo Lee, Jeehee Yoon
Copy number variations (CNVs) are structural variants associated with human diseases. Recent studies verified that disease-related genes are based on the extraction of rare de novo and transmitted CNVs from exome sequencing data. The need for more efficient and accurate methods has increased, which still remains a challenging problem due to coverage biases, as well as the sparse, small-sized, and noncontinuous nature of exome sequencing. In this study, we developed a new CNV detection method, ExCNVSS, based on read coverage depth evaluation and scale-space filtering to resolve these problems...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28697800/segcorr-a-statistical-procedure-for-the-detection-of-genomic-regions-of-correlated-expression
#12
Eleni Ioanna Delatola, Emilie Lebarbier, Tristan Mary-Huard, François Radvanyi, Stéphane Robin, Jennifer Wong
BACKGROUND: Detecting local correlations in expression between neighboring genes along the genome has proved to be an effective strategy to identify possible causes of transcriptional deregulation in cancer. It has been successfully used to illustrate the role of mechanisms such as copy number variation (CNV) or epigenetic alterations as factors that may significantly alter expression in large chromosomal regions (gene silencing or gene activation). RESULTS: The identification of correlated regions requires segmenting the gene expression correlation matrix into regions of homogeneously correlated genes and assessing whether the observed local correlation is significantly higher than the background chromosomal correlation...
July 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28696556/1d-genome-sequencing-on-the-oxford-nanopore-minion
#13
Sara Goodwin, Robert Wappel, W Richard McCombie
Today's short-read sequencing instruments can generate read lengths between 50 bp and 700 bp depending on the specific instrument. These high-throughput sequencing approaches have revolutionized genomic science, allowing hundreds of thousands of full genomes to be sequenced, and have become indispensable tools for many researchers. With greater insight has come the revelation that many genomes are much more complicated than originally thought and include many rearrangements and copy-number variations. Unfortunately, short-read sequencing technologies are not well suited for identifying many of these types of events...
July 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28696413/genome-wide-meta-analysis-of-copy-number-variations-with-alcohol-dependence
#14
A Sulovari, Z Liu, Z Zhu, D Li
Genetic association studies and meta-analyses of alcohol dependence (AD) have reported AD-associated single nucleotide polymorphisms (SNPs). These SNPs collectively account for a small portion of estimated heritability in AD. Recent genome-wide copy number variation (CNV) studies have identified CNVs associated with AD and substance dependence, suggesting that a portion of the missing heritability is explained by CNV. We applied PennCNV and QuantiSNP CNV calling algorithms to identify consensus CNVs in five AD cohorts of European and African origins...
July 11, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28695677/combined-genetic-analyses-can-achieve-efficient-diagnostic-yields-for-subjects-with-alagille-syndrome-and-incomplete-alagille-syndrome
#15
Kei Ohashi, Takao Togawa, Tokio Sugiura, Koichi Ito, Takeshi Endo, Kohei Aoyama, Yutaka Negishi, Toyoichiro Kudo, Reiko Ito, Shinji Saitoh
AIM: We evaluated combined genetic analyses with targeted next-generation sequencing (NGS), multiplex ligation probe amplification (MLPA) of Jagged1 (JAG1) genes and microarray comparative genomic hybridisation (CGH) in subjects with Alagille syndrome, incomplete clinical features of Alagille syndrome and biliary atresia. METHODS: Subjects recruited from April 2013 to December 2015 underwent a targeted NGS analysis, including JAG1 and Notch homolog 2 (NOTCH2). If no mutations were detected in JAG1 or NOTCH2, or if copy number variations were suggested by the NGS analysis, we performed an MLPA analysis of JAG1...
July 11, 2017: Acta Paediatrica
https://www.readbyqxmd.com/read/28693295/germline-dna-copy-number-variations-as-potential-prognostic-markers-for-non-muscle-invasive-bladder-cancer-progression
#16
Yoshiaki Yamamoto, Yutaka Suehiro, Atomu Suzuki, Ryosuke Nawata, Yoshihisa Kawai, Ryo Inoue, Hiroshi Hirata, Hiroaki Matsumoto, Takahiro Yamasaki, Kohsuke Sasaki, Hideyasu Matsuyama
Accumulating evidence has suggested that germline DNA copy number variations (CNVs) affect various disorders, including human malignancies. However, the significance of CNVs in non-muscle invasive bladder cancer (NMIBC) remains unclear. The purpose of the present study was to identify the role of CNVs in NMIBC. Array comparative genomic hybridization (CGH) analysis was performed to search for candidate CNVs associated with NMIBC susceptibility. Quantitative polymerase chain reaction was carried out to evaluate CNVs associated with patient outcome in 189 NMIBC cases...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28692986/heavy-tailed-noise-suppression-and-derivative-wavelet-scalogram-for-detecting-dna-copy-number-aberrations
#17
Nha Nguyen, An Vo, Haibin Sun, Heng Huang
Most existing array comparative genomic hybridization (array CGH) data processing methods and evaluation models assumed that the probability density function of noise in array CGH is a Gaussian distribution. However, in practice such noise distribution is peaky and heavy-tailed. A more accurate and sufficient model of noise in array CGH data is necessary and beneficial to the detection of DNA copy number variations. We analyze the real array CGH data from different platforms and show that the distribution of noise in array CGH data is fitted very well by generalized Gaussian distribution (GGD)...
July 6, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28691711/generation-and-comparison-of-crispr-cas9-and-cre-mediated-genetically-engineered-mouse-models-of-sarcoma
#18
Jianguo Huang, Mark Chen, Melodi Javid Whitley, Hsuan-Cheng Kuo, Eric S Xu, Andrea Walens, Yvonne M Mowery, David Van Mater, William C Eward, Diana M Cardona, Lixia Luo, Yan Ma, Omar M Lopez, Christopher E Nelson, Jacqueline N Robinson-Hamm, Anupama Reddy, Sandeep S Dave, Charles A Gersbach, Rebecca D Dodd, David G Kirsch
Genetically engineered mouse models that employ site-specific recombinase technology are important tools for cancer research but can be costly and time-consuming. The CRISPR-Cas9 system has been adapted to generate autochthonous tumours in mice, but how these tumours compare to tumours generated by conventional recombinase technology remains to be fully explored. Here we use CRISPR-Cas9 to generate multiple subtypes of primary sarcomas efficiently in wild type and genetically engineered mice. These data demonstrate that CRISPR-Cas9 can be used to generate multiple subtypes of soft tissue sarcomas in mice...
July 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28690986/next-generation-sequencing-and-array-based-comparative-genomic-hybridization-for-molecular-diagnosis-of-pediatric-endocrine-disorders
#19
REVIEW
Maki Fukami, Mami Miyado
Next-generation sequencing (NGS) and array-based comparative genomic hybridization (array CGH) have enabled us to perform high-throughput mutation screening and genome-wide copy number analysis, respectively. These methods can be used for molecular diagnosis of pediatric endocrine disorders. NGS has determined the frequency and phenotypic variation of mutations in several disease-associated genes. Furthermore, whole exome analysis using NGS has successfully identified several novel causative genes for endocrine disorders...
June 2017: Annals of Pediatric Endocrinology & Metabolism
https://www.readbyqxmd.com/read/28686586/quantifying-transcription-factor-dna-binding-in-single-cells-in-vivo-with-photoactivatable-fluorescence-correlation-spectroscopy
#20
Ziqing Winston Zhao, Melanie D White, Yanina D Alvarez, Jennifer Zenker, Stephanie Bissiere, Nicolas Plachta
Probing transcription factor (TF)-DNA interactions remains challenging in complex in vivo systems such as mammalian embryos, especially when TF copy numbers and fluorescence background are high. To address this difficulty, fluorescence correlation spectroscopy (FCS) can be combined with the use of photoactivatable fluorescent proteins to achieve selective photoactivation of a subset of tagged TF molecules. This approach, termed paFCS, enables FCS measurements within single cell nuclei inside live embryos, and obtains autocorrelation data of a quality previously only attainable in simpler in vitro cell culture systems...
July 2017: Nature Protocols
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