Identification of regulatory variants associated with genetic susceptibility to meningococcal disease.

Non-coding genetic variants play an important role in driving susceptibility to complex diseases but their characterization remains challenging. Here, we employed a novel approach to interrogate the genetic risk of such polymorphisms in a more systematic way by targeting specific regulatory regions relevant for the phenotype studied. We applied this method to meningococcal disease susceptibility, using the DNA binding pattern of RELA - a NF-kB subunit, master regulator of the response to infection - under bacterial stimuli in nasopharyngeal epithelial cells. We designed a custom panel to cover these RELA binding sites and used it for targeted sequencing in cases and controls. Variant calling and association analysis were performed followed by validation of candidate polymorphisms by genotyping in three independent cohorts. We identified two new polymorphisms, rs4823231 and rs11913168, showing signs of association with meningococcal disease susceptibility. In addition, using our genomic data as well as publicly available resources, we found evidences for these SNPs to have potential regulatory effects on ATXN10 and LIF genes respectively. The variants and related candidate genes are relevant for infectious diseases and may have important contribution for meningococcal disease pathology. Finally, we described a novel genetic association approach that could be applied to other phenotypes

Probing near-solid density plasmas using soft x-ray scattering

X-ray scattering using highly brilliant x-ray free-electron laser (FEL) radiation provides new access to probe free-electron density, temperature and ionization in near-solid density plasmas. First experiments at the soft x-ray FEL FLASH at DESY, Hamburg, show the capabilities of this technique. The ultrashort FEL pulses in particular can probe equilibration phenomena occurring after excitation of the plasma using ultrashort optical laser pumping. We have investigated liquid hydrogen and find that the interaction of very intense soft x-ray FEL radiation alone heats the sample volume. As the plasma establishes, photons from the same pulse undergo scattering, thus probing the transient, warm dense matter state. We find a free-electron density of (2.6 ± 0.2) × 1020 cm-3 and an electron temperature of 14 ± 3.5 eV. In pump-probe experiments, using intense optical laser pulses to generate more extreme states of matter, this interaction of the probe pulse has to be considered in the interpretation of scattering data. In this paper, we present details of the experimental setup at FLASH and the diagnostic methods used to quantitatively analyse the data. © 2010 IOP Publishing Ltd