14 research outputs found
Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale
Benchmarking the HLA typing performance of Polysolver and Optitype in 50 Danish parental trios
Analysis of 62 hybrid assembled human Y chromosomes exposes rapid structural changes and high rates of gene conversion
Sequencing and de novo assembly of 150 genomes from Denmark as a population reference
Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark
Discovery of Novel PPAR Ligands by a Virtual Screening Approach Based on Pharmacophore Modeling, 3D Shape, and Electrostatic Similarity Screening
Nitrate reduction in geologically heterogeneous catchments:a framework for assessing the scale of predictive capability of hydrological models
International audienceIn order to fulfil the requirements of the EU Water Framework Directive nitrate load from agricultural areas to surface water in Denmark needs to be reduced by about 40%. The regulations imposed until now have been uniform, i.e. the same restrictions for all areas independent of the subsurface conditions. Studies have shown that on a national basis about 2/3 of the nitrate leaching from the root zone is reduced naturally, through denitrification, in the subsurface before reaching the streams. Therefore, it is more cost-effective to identify robust areas, where nitrate leaching through the root zone is reduced in the saturated zone before reaching the streams, and vulnerable areas, where no subsurface reduction takes place, and then only impose regulations/restrictions on the vulnerable areas. Distributed hydrological models can make predictions at grid scale, i.e. at much smaller scale than the entire catchment. However, as distributed models often do not include local scale hydrogeological heterogeneities, they are typically not able to make accurate predictions at scales smaller than they are calibrated. We present a framework for assessing nitrate reduction in the subsurface and for assessing at which spatial scales modelling tools have predictive capabilities. A new instrument has been developed for airborne geophysical measurements, Mini-SkyTEM, dedicated to identifying geological structures and heterogeneities with horizontal and lateral resolutions of 30-50 m and 2 in, respectively, in the upper 30 m. The geological heterogeneity and uncertainty are further analysed by use of the geostatistical software TProGS by generating stochastic geological realisations that are soft conditioned against the geophysical data. Finally, the flow paths within the catchment are simulated by use of the MIKE SHE hydrological modelling system for each of the geological models generated by TProGS and the prediction uncertainty is characterised by the variance between the predictions of the different models. (C) 2013 Elsevier B.V. All rights reserved
Discovery of a Novel Selective PPARÎł Ligand with Partial Agonist Binding Properties by Integrated <i>in Silico</i>/<i>in Vitro</i> Work Flow
Full agonists to the peroxisome proliferator-activated
receptor
(PPAR)ÂÎł, such as Rosiglitazone, have been associated with a
series of undesired side effects, such as weight gain, fluid retention,
cardiac hypertrophy, and hepatotoxicity. Nevertheless, PPARÎł
is involved in the expression of genes that control glucose and lipid
metabolism and is an important target for drugs against type 2 diabetes,
dyslipidemia, atherosclerosis, and cardiovascular disease. In an effort
to identify novel PPARÎł ligands with an improved pharmacological
profile, emphasis has shifted to selective ligands with partial agonist
binding properties. Toward this end we applied an integrated <i>in silico</i>/<i>in vitro</i> workflow, based on pharmacophore-
and structure-based virtual screening of the ZINC library, coupled
with competitive binding and transactivation assays, and adipocyte
differentiation and gene expression studies. Hit compound <b>9</b> was identified as the most potent ligand (IC<sub>50</sub> = 0.3
ÎźM) and a relatively poor inducer of adipocyte differentiation.
The binding mode of compound <b>9</b> was confirmed by molecular
dynamics simulation, and the calculated free energy of binding was
â8.4 kcal/mol. A novel functional group, the carbonitrile group,
was identified to be a key substituent in the ligandâprotein
interactions. Further studies on the transcriptional regulation properties
of compound <b>9</b> revealed a gene regulatory profile that
was to a large extent unique, however functionally closer to that
of a partial agonist