Conservatoire national des arts et métiers

About: Conservatoire national des arts et métiers is a education organization based out in Paris, France. It is known for research contribution in the topics: Population & Context (language use). The organization has 3573 authors who have published 7127 publications receiving 141430 citations. The organization is also known as: CNAM & Conservatoire des arts et métiers.

Improved whole-chromosome phasing for disease and population genetic studies.

Abstract: SHAPEIT2 uses multithreading so that multiple cores can be used to phase whole chromosomes, allowing users to make the best use of their computational resources. We tested SHAPEIT2 on several large-sample, whole-chromosome data sets from a range of SNP genotyping chips (Supplementary Note 1). SHAPEIT2 outperforms other methods (Fig. 1a–c) in terms of switch error rate (SER) and the mean distance between switch errors (Supplementary Figs. 1 and 2). As compared to SHAPEIT1, SHAPEIT2 reduced SER by as much as 45% on these data sets. For example, on 1,229 Vietnamese samples assayed on the Illumina 660K chip on chromosome 22, the SERs of SHAPEIT2 (K = 100, W = 2 Mb), SHAPEIT1 (K = 100) (ref. 2), HAPI-UR (v1.01) (ref. 4), Beagle (v3.3) (ref. 5), Impute2 v2.1.2 (K = 100) (ref. 3), MaCH v1.0.18 (K = 100) (ref. 6) and fastPHASE (v1.4) (ref. 7) were 2.87%, 4.64%, 4.75%, 5.14%, 5.57%, 6.05% and 6.34%, respectively. In general, SHAPEIT2 with low values of K outperformed SHAPEIT1 with high values of K (Fig. 1a–c). As the number of samples increased (up to ~9,000 samples in our tests), we found that SHAPEIT2 outperformed other methods and had the property that SER decreases as sample size increases (Fig. 1d). We assessed accuracy on sequence data by phasing 381 European samples from the 1000 Genomes Project (TGP) together with genotypes from two trio parents sequenced at high coverage. We found that SHAPEIT2 (K = 100, W = 0.3 Mb) reduced SER by 38% compared to Beagle (Supplementary Table 1 and Supplementary Note 2), illustrating that the SHAPEIT2 model can adapt to data sets with very high SNP density. The computational performance of SHAPEIT2 is competitive compared to other methods. Figure 1e shows the computational Improved whole-chromosome phasing for disease and population genetic studies

Estimating the burden of SARS-CoV-2 in France.

Abstract: France has been heavily affected by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic and went into lockdown on 17 March 2020. Using models applied to hospital and death data, we estimate the impact of the lockdown and current population immunity. We find that 2.9% of infected individuals are hospitalized and 0.5% of those infected die (95% credible interval: 0.3 to 0.9%), ranging from 0.001% in those under 20 years of age to 8.3% in those 80 years of age or older. Across all ages, men are more likely to be hospitalized, enter intensive care, and die than women. The lockdown reduced the reproductive number from 2.90 to 0.67 (77% reduction). By 11 May 2020, when interventions are scheduled to be eased, we project that 3.5 million people (range: 2.1 million to 6.0 million), or 5.3% of the population (range: 3.3 to 9.3%), will have been infected. Population immunity appears to be insufficient to avoid a second wave if all control measures are released at the end of the lockdown.