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"structural variation"

Jacob Lulewicz
Network approaches in archaeology offer a promising avenue for facilitating bottom-up, comparative approaches to sociopolitical organization. While recent applications have focused primarily on migration and demographic trends, identity and identity politics, and the dynamics of geopolitical and regional interaction, little in the way of comparative sociopolitical organization has been attempted. In this study, I present an alternative approach to the use of sociotypological models across southern Appalachia...
February 19, 2019: Proceedings of the National Academy of Sciences of the United States of America
Ben D Fulcher, John D Murray, Valerio Zerbi, Xiao-Jing Wang
The primate cerebral cortex displays a hierarchy that extends from primary sensorimotor to association areas, supporting increasingly integrated function underpinned by a gradient of heterogeneity in the brain's microcircuits. The extent to which these hierarchical gradients are unique to primate or may reflect a conserved mammalian principle of brain organization remains unknown. Here we report the topographic similarity of large-scale gradients in cytoarchitecture, gene expression, interneuron cell densities, and long-range axonal connectivity, which vary from primary sensory to prefrontal areas of mouse cortex, highlighting an underappreciated spatial dimension of mouse cortical specialization...
February 19, 2019: Proceedings of the National Academy of Sciences of the United States of America
Rong Zhou, Chaoji Shi, Wenjie Tao, Jiang Li, Jing Wu, Yong Han, Guizhu Yang, Ziyue Gu, Shengming Xu, Yujue Wang, Lizhen Wang, Yanan Wang, Guoyu Zhou, Chenping Zhang, Zhiyuan Zhang, Shuyang Sun
PURPOSE: Unlike advances in the genomics-driven precision treatment of cutaneous melanomas, the poor current understanding of the molecular basis of mucosal melanomas (MMs) has hindered such progress for MM patients. Thus, we sought to characterize the genomic landscape of MM to identify genomic alterations with prognostic and/or therapeutic implications. EXPERIMENTAL DESIGN: Whole-genome sequencing (WGS) was performed on 65 MM samples, including 63 paired tumor blood samples and 2 matched lymph node metastases, with a further ddPCR-based validation study of an independent MM cohort (n = 80)...
February 19, 2019: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Xiaoqiang Wang, Emilie Lebarbier, Julie Aubert, Stéphane Robin
Hidden Markov models provide a natural statistical framework for the detection of the copy number variations (CNV) in genomics. In this context, we define a hidden Markov process that underlies all individuals jointly in order to detect and to classify genomics regions in different states (typically, deletion, normal or amplification). Structural variations from different individuals may be dependent. It is the case in agronomy where varietal selection program exists and species share a common phylogenetic past...
February 19, 2019: International Journal of Biostatistics
Yaoyao Li, Xiguo Yuan, Junying Zhang, Liying Yang, Jun Bai, Shan Jiang
BACKGROUND: Copy number variation (CNV) is an important form of genomic structural variation and is linked to dozens of human diseases. Using next-generation sequencing (NGS) data and developing computational methods to characterize such structural variants is significant for understanding the mechanisms of diseases. OBJECTIVE: The objective of this study is to develop a new statistical method of detection recurrent CNVs across multiple samples from genomic sequences...
February 18, 2019: Genes & Genomics
Tanmoy Roychowdhury, Alexej Abyzov
Structural variations (SVs) in the human genome originate from different mechanisms related to DNA repair, replication errors, and retrotransposition. Our analyses of 26 927 SVs from the 1000 Genomes Project revealed differential distributions and consequences of SVs of different origin, e.g. deletions from non-allelic homologous recombination (NAHR) are more prone to disrupt chromatin organization while processed pseudogenes can create accessible chromatin. Spontaneous double stranded breaks (DSBs) are the best predictor of enrichment of NAHR deletions in open chromatin...
February 18, 2019: Nucleic Acids Research
Rui-Qian Zhang, Jun-Jie Wang, Teng Zhang, Hong-Li Zhai, Wei Shen
Copy number variation (CNV), as an important component of genomic structural variation (SV), plays essential roles in phenotypic variability, disease susceptibility and species evolution. To investigate whether critical CNVs exist in dairy goats with differing fecundity, we performed genome-wide sequencing of two populations of Laoshan dairy goats with large differences in litter size. After reference genome aligning, CNV calling, and annotation, we screened identified CNVs in the high-fecundity (HF) and low-fecundity (LF) groups to identify discrepant CNVs and their distribution within the genome...
February 14, 2019: Gene
Andrew Catanach, Ross Crowhurst, Cecilia Deng, Charles David, Louis Bernatchez, Maren Wellenreuther
Recent studies have highlighted an important role of structural variation (SV) in ecological and evolutionary processes, but few have studied non-model species in the wild. As part of our long-term research programme on the non-model teleost fish Australasian snapper (Chrysophrys auratus) we aim to build one of the first catalogues of genomic variants (SNPs and indels, and deletions, duplications and inversions) in fishes, and evaluate overlap of genomic variants with regions under putative selection (Tajima's D and π), and coding sequences (genes)...
February 15, 2019: Molecular Ecology
Matthew Hayes
The author originally had the wrong programming command and the chapter was inadvertently published with error. The same has been updated later as below.
2019: Methods in Molecular Biology
Amrit Kaphle, Elena Echeverria, David N Mcllroy, Kenneth Roberts, Parameswar Hari
Thermo-optical and structural properties of cobalt-doped zinc oxide (ZnO) nanorods grown by chemical bath deposition were investigated. The average nanorods diameter was found to increase with cobalt doping. X-ray diffraction (XRD), Raman, and Fourier Transform Infrared (FTIR) analysis confirm the substitution of cobalt into ZnO lattice without forming any impurities at higher doping and preserving the hexagonal wurtzite structure. Variations in the absorption spectrum, band gap, photoluminescence, electronic structure by X-ray photoelectron spectroscopy (XPS), and index of refraction were analyzed at different cobalt doping levels and annealing temperatures...
July 1, 2019: Journal of Nanoscience and Nanotechnology
Maha Daghestani, Rituraj Purohit, Mazin Daghestani, Mamoon Daghistani, Arjumand Warsy
The Gln233Arg (A>G; rs1137101) polymorphism of the leptin receptor gene (LEPR) has been investigated extensively and is reported to be associated with different metabolic states. In this investigation, we aimed to study the frequency of Gln233Arg genotypes and alleles in a group of Saudi women stratified by their body mass index (BMI), to correlate the LEPR genotypes with variations in anthropometric, lipid and hormonal parameters and to investigate conformational and structural variations in the mutant LEPR using molecular dynamic (MD) investigations...
2019: PloS One
Takeshi Mizuguchi, Takeshi Suzuki, Chihiro Abe, Ayako Umemura, Katsushi Tokunaga, Yosuke Kawai, Minoru Nakamura, Masao Nagasaki, Kengo Kinoshita, Yasunobu Okamura, Satoko Miyatake, Noriko Miyake, Naomichi Matsumoto
We report a family with progressive myoclonic epilepsy who underwent whole-exome sequencing but was negative for pathogenic variants. Similar clinical courses of a devastating neurodegenerative phenotype of two affected siblings were highly suggestive of a genetic etiology, which indicates that the survey of genetic variation by whole-exome sequencing was not comprehensive. To investigate the presence of a variant that remained unrecognized by standard genetic testing, PacBio long-read sequencing was performed...
February 13, 2019: Journal of Human Genetics
Alexander R Gawronski, Yen-Yi Lin, Brian McConeghy, Stephane LeBihan, Hossein Asghari, Can Koçkan, Baraa Orabi, Nabil Adra, Roberto Pili, Colin C Collins, S Cenk Sahinalp, Faraz Hach
Motivation: Cancer is a complex disease that involves rapidly evolving cells, often forming multiple distinct clones. In order to effectively understand progression of a patient-specific tumor, one needs to comprehensively sample tumor DNA at multiple time points, ideally obtained through inexpensive and minimally invasive techniques. Current sequencing technologies make the 'liquid biopsy' possible, which involves sampling a patient's blood or urine and sequencing the circulating cell free DNA (cfDNA)...
February 13, 2019: Nucleic Acids Research
Tao Jiang, Bo Liu, Junyi Li, Yadong Wang
Summary: Mobile element insertion (MEI) is a major category of structure variations (SVs). The rapid development of long read sequencing technologies provides the opportunity to detect MEIs sensitively. However, the signals of MEI implied by noisy long reads are highly complex due to the repetitiveness of mobile elements as well as the high sequencing error rates. Herein, we propose the Realignment-based Mobile Element insertion detection Tool for Long read (rMETL). Benchmarking results of simulated and real datasets demonstrate that rMETL enables to handle the complex signals to discover MEIs sensitively...
February 13, 2019: Bioinformatics
Song Wu, Tong Ou, Nianzeng Xing, Jiang Lu, Shengqing Wan, Changxi Wang, Xi Zhang, Feiya Yang, Yi Huang, Zhiming Cai
Bladder cancer is one of the most common and highly vascularized cancers. To better understand its genomic structure and underlying etiology, we conduct whole-genome and targeted sequencing in urothelial bladder carcinomas (UBCs, the most common type of bladder cancer). Recurrent mutations in noncoding regions affecting gene regulatory elements and structural variations (SVs) leading to gene disruptions are prevalent. Notably, we find recurrent ADGRG6 enhancer mutations and FRS2 duplications which are associated with higher protein expression in the tumor and poor prognosis...
February 12, 2019: Nature Communications
V Sureshkumar, Bipratip Dutta, Vishesh Kumar, G Prakash, Dwijesh C Mishra, K K Chaturvedi, Anil Rai, Amitha Mithra Sevanthi, Amolkumar U Solanke
Nearly two decades of revolution in the area of genomics serves as the basis of present-day molecular breeding in major food crops such as rice. Here we report an open source database on two major biotic stresses of rice, named RiceMetaSysB, which provides detailed information about rice blast and bacterial blight (BB) responsive genes (RGs). Meta-analysis of microarray data from different blast- and BB-related experiments across 241 and 186 samples identified 15135 unique genes for blast and 7475 for BB. A total of 9365 and 5375 simple sequence repeats (SSRs) in blast and BB RGs were identified for marker development...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Damien G Hicks, Terence P Speed, Mohammed Yassin, Sarah M Russell
New approaches to lineage tracking have allowed the study of differentiation in multicellular organisms over many generations of cells. Understanding the phenotypic variability observed in these lineage trees requires new statistical methods. Whereas an invariant cell lineage, such as that for the nematode Caenorhabditis elegans, can be described by a lineage map, defined as the pattern of phenotypes overlaid onto the binary tree, a traditional lineage map is static and does not describe the variability inherent in the cell lineages of higher organisms...
February 12, 2019: PLoS Computational Biology
Pravin A Mane, Sandip Dey, Arup Kumar Pathak, Mukesh Kumar, Nattamai Bhuvanesh
The self-assembly of Xantphos-capped M(OTf)2 (M = cis-[M'(Xantphos)]2+ ; M' = Pd, Pt) with bridging ligands 1,4-benezenedithiol or 4,4'-biphenyldithiol has been investigated. The reactions have yielded complexes [M{S(C6 H4 ) n SH}]2 (OTf)2 (I) and [M2 {S(C6 H4 ) n S}]2 (OTf)4 (II) ( n = 1 or 2). The equilibrium between I and II has been established in platinum complexes for n = 2, whereas the analogous Pd complex exclusively exist as II. These results are different from our previously reported dppe or triethyl phosphine-capped complexes which showed only type II...
February 11, 2019: Inorganic Chemistry
Juan J Gutierrez-Gonzalez, Martin Mascher, Jesse Poland, Gary J Muehlbauer
Wheat (Triticum aestivum) genetic maps are a key enabling tool for genetic studies. We used genotyping-by-sequencing-(GBS) derived markers to map recombinant inbred line (RIL) and doubled haploid (DH) populations from crosses of W7984 by Opata, and used the maps to explore features of recombination control. The RIL and DH populations, SynOpRIL and SynOpDH, were composed of 906 and 92 individuals, respectively. Two high-density genetic linkage framework maps were constructed of 2,842 and 2,961 cM, harboring 3,634 and 6,580 markers, respectively...
February 11, 2019: Scientific Reports
Xi Tan, Kai Xiang, Liang Liu, Jing Wang, Shan Tan
The total variation (TV) regularization has been widely used in statistically iterative cone-beam computed tomography (CBCT) reconstruction, showing ability to preserve object edges. However, the TV regularization can also produce staircase effect and tend to over-smooth the reconstructed images due to its piecewise constant assumption. In this study, we proposed to use the structure tensor total variation (STV) that penalizes the eigenvalues of the structure tensor for CBCT reconstruction. The STV penalty extends the TV penalty, with many important properties maintained such as convexity and rotation and translation invariance...
February 7, 2019: Journal of X-ray Science and Technology
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