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https://www.readbyqxmd.com/read/29667179/characteristics-of-genomic-alterations-of-lung-adenocarcinoma-in-young-never-smokers
#1
Wenxin Luo, Panwen Tian, Yue Wang, Heng Xu, Lu Chen, Chao Tang, Yang Shu, Shouyue Zhang, Zhoufeng Wang, Jun Zhang, Li Zhang, Lili Jiang, Lunxu Liu, Guowei Che, Chenglin Guo, Hong Zhang, Jiali Wang, Weimin Li
Non-small cell lung cancer (NSCLC) has been recognized as a highly heterogeneous disease with phenotypic and genotypic diversity in each subgroup. While never-smoker patients with NSCLC have been well studied through next generation sequencing, we have yet to recognize the potentially unique molecular features of young never-smoker patients with NSCLC. In this study, we conducted whole genome sequencing (WGS) to characterize the genomic alterations of 36 never-smoker Chinese patients, who were diagnosed with lung adenocarcinoma (LUAD) at 45 years or younger...
April 18, 2018: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/29666320/y-chromosome-polymorphisms-of-the-domestic-bactrian-camel-in-china
#2
Huiling Chen, Zhanjun Ren, Jiping Zhao, Chengdong Zhang, Xuejiao Yang
Single-nucleotide polymorphisms (SNPs), microsatellites and copy number variation (CNV) were studied on the Y chromosome to understand the paternal origin and phylogenetic relationships for resource protection, rational development and utilization of the domestic Bactrian camel in China. Our sample set consisted of 94 Chinese domestic Bactrian camels from four regions (Inner Mongolia, Gansu, Qinghai and Xinjiang), we screened 29 Y-chromosome-specific loci for SNPs, analysed 40 bovine-derived microsatellite loci and measured CNVs of HSFY and SRY through Sanger sequencing, automated fluorescence-based microsatellite analysis and quantitative real-time PCR, respectively...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29665866/mitochondrial-dna-copy-number-variation-leukocyte-telomere-length-and-breast-cancer-risk-in-the-european-prospective-investigation-into-cancer-and-nutrition-epic-study
#3
Daniele Campa, Myrto Barrdahl, Aurelia Santoro, Gianluca Severi, Laura Baglietto, Hanane Omichessan, Rosario Tumino, H B As Bueno-de-Mesquita, Petra H Peeters, Elisabete Weiderpass, Maria-Dolores Chirlaque, Miguel Rodríguez-Barranco, Antonio Agudo, Marc Gunter, Laure Dossus, Vittorio Krogh, Giuseppe Matullo, Antonia Trichopoulou, Ruth C Travis, Federico Canzian, Rudolf Kaaks
BACKGROUND: Leukocyte telomere length (LTL) and mitochondrial genome (mtDNA) copy number and deletions have been proposed as risk markers for various cancer types, including breast cancer (BC). METHODS: To gain a more comprehensive picture on how these markers can modulate BC risk, alone or in conjunction, we performed simultaneous measurements of LTL and mtDNA copy number in up to 570 BC cases and 538 controls from the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort...
April 17, 2018: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/29658457/-association-between-copy-number-variations-and-risk-of-overweight-obesity-among-han-uyghur-and-kazak-children
#4
Abidan Ainiwaer, Adalibieke Adalibieke, Bing-Xue Huang, Y E Yekejiergeli, Ya-Lan Dou, Jie Wu, Jiang-Hong Dai
OBJECTIVE: To study the association between the prevalence of overweight/obesity and copy number variations (CNVs) among Han, Uyghur, and Kazak children in Xinjiang, China. METHODS: The kindergartens in Ili, Altay, and Karamay in Xinjiang were selected as research sites, and stratified cluster sampling was used to select the children aged 3-7 years. Body height and body weight were measured, and exfoliated buccal mucosa cells were collected. CNVplex® was used to measure the CNVs of FTO_1, IRX3_1, IRX3_2, MC4R_1, and MC4R_2...
April 2018: Zhongguo Dang Dai Er Ke za Zhi, Chinese Journal of Contemporary Pediatrics
https://www.readbyqxmd.com/read/29656515/comparative-cyp-omic-analysis-between-the-ddt-susceptible-and-resistant-drosophila-melanogaster-strains-91-c-and-91-r
#5
Keon Mook Seong, Brad S Coates, May R Berenbaum, John M Clark, Barry R Pittendrigh
BACKGROUND: Cytochrome P450 monooxygenases (P450s) are involved in the biosynthesis of endogenous intracellular compounds and the metabolism of xenobiotics, including chemical insecticides. We investigated the structural and expression level variance across all P450 genes with respect to the evolution of insecticide resistance under multigenerational DDT selection. RESULTS: RNA-seq and reverse transcriptase quantitative PCR indicated that the transcript levels of seven P450 genes were significantly up-regulated and three P450 genes were down-regulated in the DDT-resistant strain 91-R, as compared to the control strain 91-C...
April 15, 2018: Pest Management Science
https://www.readbyqxmd.com/read/29655801/analysis-of-intragenic-ush2a-copy-number-variation-unveils-broad-spectrum-of-unique-and-recurrent-variants
#6
Christina A Austin-Tse, Diana L Mandelker, Andrea M Oza, Heather Mason-Suares, Heidi L Rehm, Sami S Amr
Given that all forms of Usher syndrome (USH) present with hearing loss in advance of retinal disease, the syndromic nature of the disorder is rarely appreciated when critical management decisions are being made. As a result, molecular diagnostics are crucial in guiding the management of USH patients. While 11 genes have been associated with USH, the USH2A gene is one of the largest contributors. Approximately 20% of suspected USH probands that undergo USH2A sequencing at our laboratory receive an inconclusive result due to the identification of a monoallelic disease-causing variant in USH2A...
April 12, 2018: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29653001/-genetic-analysis-of-two-fetuses-with-congenital-heart-defects-and-3q-microdeletion
#7
Wei Long, Jiandong Gu, Jun Ouyang, Saiyu Jia, Bin Zhang, Jianbin Liu, Bin Yu
OBJECTIVE: To determine the nature of genomic copy number variations (CNVs) in two fetuses with congenital heart defects (CHD) and explore the correlation between 3q microdeletions and CHD. METHODS: Genomic DNA was extracted from fetal umbilical cord tissue, and chromosome copy number variations were detected by low coverage whole genome sequencing. RESULTS: Both fetuses had microdeletions of the long arm of chromosome 3. Fetus 1 had ventricular septal defect, cleft lip and palate, and a 1...
April 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29650813/-the-cutting-edge-of-sarcoma-genomics
#8
Katsuhito Takahashi
Sarcoma is well-known rare cancer with few therapeutic options. Recent comprehensive genomic analyses of adult soft tissue sarcoma revealed few somatic mutations and massive copy number variations(CNVs)by the specific chromosomes. Those features are quite different from the genomics of carcinoma such as lung and colon cancers in which driver and passenger mutations play a central role in the pathogenesis. Furthermore, it has been demonstrated that substantial population of sarcoma patients has pathological germline variants of cancer predisposition genes...
April 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
https://www.readbyqxmd.com/read/29649218/global-characterization-of-copy-number-variants-in-epilepsy-patients-from-whole-genome-sequencing
#9
Jean Monlong, Simon L Girard, Caroline Meloche, Maxime Cadieux-Dion, Danielle M Andrade, Ron G Lafreniere, Micheline Gravel, Dan Spiegelman, Alexandre Dionne-Laporte, Cyrus Boelman, Fadi F Hamdan, Jacques L Michaud, Guy Rouleau, Berge A Minassian, Guillaume Bourque, Patrick Cossette
Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs...
April 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29643504/genome-evolution-across-1-011-saccharomyces-cerevisiae-isolates
#10
Jackson Peter, Matteo De Chiara, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, Benjamin Barre, Kelle Freel, Agnès Llored, Corinne Cruaud, Karine Labadie, Jean-Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Patrick Wincker, Gianni Liti, Joseph Schacherer
Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole-genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species-wide phenotypic landscape of this yeast. Genomic analyses support a single 'out-of-China' origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29643403/toxicity-of-enrofloxacin-copper-and-their-interactions-on-soil-microbial-populations-and-ammonia-oxidizing-archaea-and-bacteria
#11
Ziyan Wei, Jinhua Wang, Lusheng Zhu, Jun Wang, Guodong Zhu
Enrofloxacin (EFX) is one of the most frequently used broad-spectrum veterinary drugs, and copper (Cu) is a heavy metal that could easily bind to certain antibiotic molecules. Hence EFX and Cu were chosen as representatives of antibiotics and heavy metals to explore the abundance and variation of soil microbial populations with a plate-counting technique, as well as the copy numbers of amoA gene in ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) by quantitative PCR methods in Argosols samples...
April 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29642851/tracing-the-evolution-of-the-heterotrimeric-g-protein-%C3%AE-subunit-in-metazoa
#12
A D Lokits, H Indrischek, J Meiler, H E Hamm, P F Stadler
BACKGROUND: Heterotrimeric G proteins are fundamental signaling proteins composed of three subunits, Gα and a Gβγ dimer. The role of Gα as a molecular switch is critical for transmitting and amplifying intracellular signaling cascades initiated by an activated G protein Coupled Receptor (GPCR). Despite their biochemical and therapeutic importance, the study of G protein evolution has been limited to the scope of a few model organisms. Furthermore, of the five primary Gα subfamilies, the underlying gene structure of only two families has been thoroughly investigated outside of Mammalia evolution...
April 11, 2018: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29642840/iseg-an-efficient-algorithm-for-segmentation-of-genomic-and-epigenomic-data
#13
Senthil B Girimurugan, Yuhang Liu, Pei-Yau Lung, Daniel L Vera, Jonathan H Dennis, Hank W Bass, Jinfeng Zhang
BACKGROUND: Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments where adjacent segments have different properties, such as different mean values. Despite dozens of algorithms developed to address this problem in genomics research, methods with improved accuracy and speed are still needed to effectively tackle both existing and emerging genomic and epigenomic segmentation problems. RESULTS: We designed an efficient algorithm, called iSeg, for segmentation of genomic and epigenomic profiles...
April 11, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29628935/neurodevelopmental-genetic-diseases-associated-with-microdeletions-and-microduplications-of-chromosome-17p13-3
#14
REVIEW
Sara M Blazejewski, Sarah A Bennison, Trevor H Smith, Kazuhito Toyo-Oka
Chromosome 17p13.3 is a region of genomic instability that is linked to different rare neurodevelopmental genetic diseases, depending on whether a deletion or duplication of the region has occurred. Chromosome microdeletions within 17p13.3 can result in either isolated lissencephaly sequence (ILS) or Miller-Dieker syndrome (MDS). Both conditions are associated with a smooth cerebral cortex, or lissencephaly, which leads to developmental delay, intellectual disability, and seizures. However, patients with MDS have larger deletions than patients with ILS, resulting in additional symptoms such as poor muscle tone, congenital anomalies, abnormal spasticity, and craniofacial dysmorphisms...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29628933/fancm-limits-meiotic-crossovers-in-brassica-crops
#15
Aurélien Blary, Adrián Gonzalo, Frédérique Eber, Aurélie Bérard, Hélène Bergès, Nadia Bessoltane, Delphine Charif, Catherine Charpentier, Laurence Cromer, Joelle Fourment, Camille Genevriez, Marie-Christine Le Paslier, Maryse Lodé, Marie-Odile Lucas, Nathalie Nesi, Andrew Lloyd, Anne-Marie Chèvre, Eric Jenczewski
Meiotic crossovers (COs) are essential for proper chromosome segregation and the reshuffling of alleles during meiosis. In WT plants, the number of COs is usually small, which limits the genetic variation that can be captured by plant breeding programs. Part of this limitation is imposed by proteins like FANCM, the inactivation of which results in a 3-fold increase in COs in Arabidopsis thaliana . Whether the same holds true in crops needed to be established. In this study, we identified EMS induced mutations in FANCM in two species of economic relevance within the genus Brassica ...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29626644/mitochondrial-haplotypes-are-not-associated-with-mice-selectively-bred-for-high-voluntary-wheel-running
#16
Bernard W M Wone, Won C Yim, Heidi Schutz, Thomas H Meek, Theodore Garland
Mitochondrial haplotypes have been associated with human and rodent phenotypes, including nonshivering thermogenesis capacity, learning capability, and disease risk. Although the mammalian mitochondrial D-loop is highly polymorphic, D-loops in laboratory mice are identical, and variation occurs elsewhere mainly between nucleotides 9820 and 9830. Part of this region codes for the tRNAArg gene and is associated with mitochondrial densities and number of mtDNA copies. We hypothesized that the capacity for high levels of voluntary wheel-running behavior would be associated with mitochondrial haplotype...
April 4, 2018: Mitochondrion
https://www.readbyqxmd.com/read/29626128/braf-gene-copy-number-and-mutant-allele-frequency-correlate-with-time-to-progression-in-metastatic-melanoma-patients-treated-with-mapk-inhibitors
#17
Camilla Stagni, Carolina Zamuner, Lisa Elefanti, Tiziana Zanin, Paola Del Bianco, Antonio Sommariva, Alessio Fabozzi, Jacopo Pigozzo, Simone Mocellin, Maria Cristina Montesco, Vanna Chiarion-Sileni, Arcangela De Nicolo, Chiara Menin
Metastatic melanoma is characterized by complex genomic alterations including a high rate of mutations in driver genes and widespread deletions and amplifications encompassing various chromosome regions. Among them, chromosome 7 is frequently gained in BRAF mutant melanoma, inducing a mutant allele-specific imbalance. Although BRAF amplification is a known mechanism of acquired resistance to therapy with MAPK inhibitors, it is still unclear if BRAF copy number variation and BRAF mutant allele imbalance at baseline can be associated with response to treatment...
April 6, 2018: Molecular Cancer Therapeutics
https://www.readbyqxmd.com/read/29623515/dna-methylation-based-subclassification-of-psoriasis-in-the-chinese-han-population
#18
Fusheng Zhou, Changbing Shen, Yi-Hsiang Hsu, Jing Gao, Jinfa Dou, Randy Ko, Xiaodong Zheng, Liangdan Sun, Yong Cui, Xuejun Zhang
Psoriasis (Ps) is an inflammatory skin disease caused by genetic and environmental factors. Previous studies on DNA methylation (DNAm) found genetic markers that are closely associated with Ps, and evidence has shown that DNAm mediates genetic risk in Ps. In this study, Consensus Clustering was used to analyze DNAm data, and 114 Ps patients were divided into three subclassifications. Investigation of the clinical characteristics and copy number variations (CNVs) of DEFB4, IL22, and LCE3C in the three subclassifications revealed no significant differences in gender ratio and in Ps area and severity index (PASI) score...
April 5, 2018: Frontiers of Medicine
https://www.readbyqxmd.com/read/29623014/genetic-alterations-and-pik3ca-gene-mutations-and-amplifications-analysis-in-cervical-cancer-by-racial-groups-in-the-united-states
#19
Odekunle Florence Femi
Introduction: A number of studies indicated racial differences in cervical cancer outcomes and several factors are associated with it such as stage, comorbidities, treatment pattern, and socioeconomic status. However, the associations of tumor genomic patterns such as phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) gene mutations and amplifications with cervical cancer racial disparities are largely unexplored. Objectives: Therefore, the present investigation aimed to identify genetic alterations (mutations and copy number variations) in cervical cancer and determine whether the PIK3CA gene mutations and amplifications in cervical cancer differ across racial/ethnic groups in the United States...
January 2018: International Journal of Health Sciences
https://www.readbyqxmd.com/read/29622783/genetics-of-male-infertility
#20
REVIEW
Csilla Krausz, Antoni Riera-Escamilla
Male infertility is a multifactorial pathological condition affecting approximately 7% of the male population. The genetic landscape of male infertility is highly complex as semen and testis histological phenotypes are extremely heterogeneous, and at least 2,000 genes are involved in spermatogenesis. The highest frequency of known genetic factors contributing to male infertility (25%) is in azoospermia, but the number of identified genetic anomalies in other semen and aetiological categories is constantly growing...
April 5, 2018: Nature Reviews. Urology
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