Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

On the mechanisms governing gas penetration into a tokamak plasma during a massive gas injection

A new 1D radial fluid code, IMAGINE, is used to simulate the penetration of gas into a tokamak plasma during a massive gas injection (MGI). The main result is that the gas is in general strongly braked as it reaches the plasma, due to mechanisms related to charge exchange and (to a smaller extent) recombination. As a result, only a fraction of the gas penetrates into the plasma. Also, a shock wave is created in the gas which propagates away from the plasma, braking and compressing the incoming gas. Simulation results are quantitatively consistent, at least in terms of orders of magnitude, with experimental data for a D 2 MGI into a JET Ohmic plasma. Simulations of MGI into the background plasma surrounding a runaway electron beam show that if the background electron density is too high, the gas may not penetrate, suggesting a possible explanation for the recent results of Reux et al in JET (2015 Nucl. Fusion 55 093013)

Apprendre du passé pour prédire le futur : réponses des poissons migrateurs amphihalins européens au changement climatique

International audienceClimate change can have an effect on species distributions. The 1900 distribution and potential future distribution of diadromous fish in Europe, North Africa, and the Middle East were explored using generalized additive models (GAMs) and selected habitat characteristics of 196 basins. Robust presenceabsence models were built for 20 of the 28 diadromous species in the study area using longitude, annual temperature, drainage surface area, annual precipitation, and source elevation as explanatory variables. Inspection of the relationship between each variable and species presenceabsence revealed that the GAMs were generally interpretable and plausible. Given the predicted rise in annual temperature in climate models ranging between 18C and 78C by 2100, the fish species were classified according to those losing suitable basins, those gaining suitable basins, and those showing little or no change. It was found that the climate envelopes based on temperature and precipitation for diadromous species would, in general, be shifted farther northeastwards by 2100, and these shifting ranges were comparable with those assessed in other studies. The uncertain future of some species was highlighted, and it was concluded that conservation policy and management plans will need to be revised in the face of climate change