Genome sequencing of large numbers of individuals promises to advance the understanding, treatment, and prevention of human diseases, among other applications. We describe a genome sequencing ...platform that achieves efficient imaging and low reagent consumption with combinatorial probe anchor ligation chemistry to independently assay each base from patterned nanoarrays of self-assembling DNA nanoballs. We sequenced three human genomes with this platform, generating an average of 45-to 87-fold coverage per genome and identifying 3.2 to 4.5 million sequence variants per genome. Validation of one genome data set demonstrates a sequence accuracy of about 1 false variant per 100 kilobases. The high accuracy, affordable cost of $4400 for sequencing consumables, and scalability of this platform enable complete human genome sequencing for the detection of rare variants in large-scale genetic studies.
Lung cancer is the leading cause of cancer-related mortality worldwide, with non-small-cell lung carcinomas in smokers being the predominant form of the disease. Although previous studies have ...identified important common somatic mutations in lung cancers, they have primarily focused on a limited set of genes and have thus provided a constrained view of the mutational spectrum. Recent cancer sequencing efforts have used next-generation sequencing technologies to provide a genome-wide view of mutations in leukaemia, breast cancer and cancer cell lines. Here we present the complete sequences of a primary lung tumour (60x coverage) and adjacent normal tissue (46x). Comparing the two genomes, we identify a wide variety of somatic variations, including >50,000 high-confidence single nucleotide variants. We validated 530 somatic single nucleotide variants in this tumour, including one in the KRAS proto-oncogene and 391 others in coding regions, as well as 43 large-scale structural variations. These constitute a large set of new somatic mutations and yield an estimated 17.7 per megabase genome-wide somatic mutation rate. Notably, we observe a distinct pattern of selection against mutations within expressed genes compared to non-expressed genes and in promoter regions up to 5 kilobases upstream of all protein-coding genes. Furthermore, we observe a higher rate of amino acid-changing mutations in kinase genes. We present a comprehensive view of somatic alterations in a single lung tumour, and provide the first evidence, to our knowledge, of distinct selective pressures present within the tumour environment.
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Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The paper presents the results of theoretical study for the influence of an additional magnetostatic field applied to the radio-frequency discharge region on the operating parameters of ...radio-frequency ion injector, taking into account the shape of its discharge chamber. The integral characteristics are calculated for three injector configurations: with a cylindrical, conical, and hemispherical discharge chamber. For calculations, we used a mathematical model, in which the charged particle behavior in plasma is described by relations close to magnetohydrodynamic, while the neutral particle distribution is determined using an approximate analytical solution obtained when considering a one-dimensional problem of gas flow in a tube. Simulation was carried out in the COMSOL Multiphysics software package. According to the calculation results, an additional magnetostatic field can improve the ion injector performance with any discharge chamber configuration. The greatest operation efficiency increase was observed with a cylindrical discharge chamber. However, according to calculations, the best performance can be obtained if a hemispherical chamber is used.
•An additional magnetostatic field can increase the efficiency of RF ion injector.•Positive effect can be expected with any shape of the ion injector discharge chamber.•Optimal induction of an additional magnetostatic field for RF ion injector.
The work is devoted to the theoretical assessment of the efficiency increase possibility for the radio-frequency ion injector, which is designed for the contactless removal of space debris from ...near-earth orbit by using an antenna located inside the discharge chamber. Four internal antenna configurations and two external ones—end and side—are considered. Expected characteristics were estimated using an engineering mathematical model built in COMSOL Multiphysics using an approximate magnetohydrodynamic description of the charged particle behavior. According to the simulation results, the best characteristics can be obtained with an internal antenna with a conical arrangement of turns. Calculations showed that in some operating modes, such an antenna configuration makes it possible to halve the radio-frequency power consumption compared to the classical antenna located on the discharge chamber side surface. The performed theoretical study showed that the internal antenna can significantly increase the ion injector efficiency. In the future, verification of the obtained results by test is planned.
Unchained base reads on self-assembling DNA nanoarrays have recently emerged as a promising approach to low-cost, high-quality resequencing of human genomes. Because of unique characteristics of ...these mated pair reads, existing computational methods for resequencing assembly, such as those based on map-consensus calling, are not adequate for accurate variant calling. We describe novel computational methods developed for accurate calling of SNPs and short substitutions and indels (<100 bp); the same methods apply to evaluation of hypothesized larger, structural variations. We use an optimization process that iteratively adjusts the genome sequence to maximize its a posteriori probability given the observed reads. For each candidate sequence, this probability is computed using Bayesian statistics with a simple read generation model and simplifying assumptions that make the problem computationally tractable. The optimization process iteratively applies one-base substitutions, insertions, and deletions until convergence is achieved to an optimum diploid sequence. A local de novo assembly procedure that generalizes approaches based on De Bruijn graphs is used to seed the optimization process in order to reduce the chance of converging to local optima. Finally, a correlation-based filter is applied to reduce the false positive rate caused by the presence of repetitive regions in the reference genome.
Abstract
Complete Genomics has sequenced the genomes of over 100 tumor-normal sample pairs from a variety of cancers (e.g. Lee, et al., Nature 465: 473-477, 2010) using a unique high throughput ...sequencing platform (Drmanac, et al., Science 327:78-81, 2010). We have assembled a tool set to investigate somatic mutations in these samples, including small variations (SNVs, deletions, insertions and substitutions), as well as larger structural variations, copy number variations and regions of LOH (Loss of Heterozygosity). Included in this sample set are 12 cancer cell lines and matched normal cell lines obtained from the American Type Tissue Culture collection (ATCC), comprising 10 breast cancers and 2 lung cancers. We have developed and characterized somatic variation scoring methods for each variant class that can be tuned for particular applications and sample types. Comparative analyses with previously published data show high specificity and sensitivity of somatic variation detection. We will discuss the application of these methods for somatic variation analysis in larger cancer genome studies.
Citation Format: {Authors}. {Abstract title} abstract. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4821. doi:10.1158/1538-7445.AM2011-4821
Epigenetic mechanisms of gene regulation in context of cardiovascular diseases are of considerable interest. So far, our current knowledge of the DNA methylation profiles for atherosclerosis affected ...and healthy human vascular tissues is still limited. Using the Illumina Infinium Human Methylation27 BeadChip, we performed a genome-wide analysis of DNA methylation in right coronary artery in the area of advanced atherosclerotic plaques, atherosclerotic-resistant internal mammary arteries, and great saphenous veins obtained from same patients with coronary heart disease. The resulting DNA methylation patterns were markedly different between all the vascular tissues. The genes hypomethylated in athero-prone arteries to compare with atherosclerotic-resistant arteries were predominately involved in regulation of inflammation and immune processes, as well as development. The great saphenous veins exhibited an increase of the DNA methylation age in comparison to the internal mammary arteries. Gene ontology analysis for genes harboring hypermethylated CpG-sites in veins revealed the enrichment for biological processes associated with the development. Four CpG-sites located within the MIR10B gene sequence and about 1 kb upstream of the HOXD4 gene were also confirmed as hypomethylated in the independent dataset of the right coronary arteries in the area of advanced atherosclerotic plaques in comparison with the other vascular tissues. The DNA methylation differences observed in vascular tissues of patients with coronary heart disease can provide new insights into the mechanisms underlying the development of pathology and explanation for the difference in graft patency after coronary artery bypass grafting surgery.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The synthesis of barium and strontium stannates in the process of decomposition of hydrothermally obtained precursors has been investigated. It was found that endothermic weight loss during the ...synthesis of barium stannate occurs in two stages, whereas during the synthesis of strontium stannate it occurs in one stage. From the summary of the results of thermogravimetric analysis, X-ray diffraction, and Mössbauer spectroscopy, the composition and local structure of X-ray amorphous phases are proposed. It is shown that the improvement of the crystal structure of the perovskite phases of MSnO3 (M = Ba, Sr) and the symmetry of the local environment of 119Sn continues up to high temperatures (1250–1500 °C) and is associated with the elimination of defects in the anion sublattice. The photocatalytic activity of hydrothermal phases MSn(OH)6 and their thermolysis products has been studied and was found not to be directly related to the specific surface area of the photocatalysts. The degradation of rhodamine B (RhB) occurs during the “dark” stages of catalysis due to the interaction of the dye with reactive oxygen species (mainly singlet oxygen). At the first stage, the decomposition of the RhB photochromic system is observed, whereas at the final stage of bleaching the dye is deethylated.
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