A cross-sample statistical model for SNP detection in short-read sequencing data

Highly multiplex DNA sequencers have greatly expanded our ability to survey human genomes for previously unknown single nucleotide polymorphisms (SNPs). However, sequencing and mapping errors, though rare, contribute substantially to the number of false discoveries in current SNP callers. We demonstrate that we can significantly reduce the number of false positive SNP calls by pooling information across samples. Although many studies prepare and sequence multiple samples with the same protocol, most existing SNP callers ignore cross-sample information. In contrast, we propose an empirical Bayes method that uses cross-sample information to learn the error properties of the data. This error information lets us call SNPs with a lower false discovery rate than existing methods

Safety, efficacy, and immunogenicity of an inactivated influenza vaccine in healthy adults: a randomized, placebo-controlled trial over two influenza seasons

<p>Abstract</p> <p>Background</p> <p>Seasonal influenza imposes a substantial personal morbidity and societal cost burden. Vaccination is the major strategy for influenza prevention; however, because antigenically drifted influenza A and B viruses circulate annually, influenza vaccines must be updated to provide protection against the predicted prevalent strains for the next influenza season. The aim of this study was to assess the efficacy, safety, reactogenicity, and immunogenicity of a trivalent inactivated split virion influenza vaccine (TIV) in healthy adults over two influenza seasons in the US.</p> <p>Methods</p> <p>The primary endpoint of this double-blind, randomized study was the average efficacy of TIV versus placebo for the prevention of vaccine-matched, culture-confirmed influenza (VMCCI) across the 2005-2006 and 2006-2007 influenza seasons. Secondary endpoints included the prevention of laboratory-confirmed (defined by culture and/or serology) influenza, as well as safety, reactogenicity, immunogenicity, and consistency between three consecutive vaccine lots. Participants were assessed actively during both influenza seasons, and nasopharyngeal swabs were collected for viral culture from individuals with influenza-like illness. Blood specimens were obtained for serology one month after vaccination and at the end of each influenza season's surveillance period.</p> <p>Results</p> <p>Although the point estimate for efficacy in the prevention of all laboratory-confirmed influenza was 63.2% (97.5% confidence interval [CI] lower bound of 48.2%), the point estimate for the primary endpoint, efficacy of TIV against VMCCI across both influenza seasons, was 46.3% with a 97.5% CI lower bound of 9.8%. This did not satisfy the pre-specified success criterion of a one-sided 97.5% CI lower bound of >35% for vaccine efficacy. The VMCCI attack rates were very low overall at 0.6% and 1.2% in the TIV and placebo groups, respectively. Apart from a mismatch for influenza B virus lineage in 2005-2006, there was a good match between TIV and the circulating strains. TIV was highly immunogenic, and immune responses were consistent between three different TIV lots. The most common reactogenicity events and spontaneous adverse events were associated with the injection site, and were mild in severity.</p> <p>Conclusions</p> <p>Despite a good immune response, and an average efficacy over two influenza seasons against laboratory-confirmed influenza of 63.2%, the pre-specified target (lower one-sided 97.5% confidence bound for efficacy > 35%) for the primary efficacy endpoint, the prevention of VMCCI, was not met. However, the results should be interpreted with caution in view of the very low attack rates we observed at the study sites in the 2005-2006 and 2006-2007, which corresponded to relatively mild influenza seasons in the US. Overall, the results showed that TIV has an acceptable safety profile and offered clinical benefit that exceeded risk.</p> <p>Trial registration</p> <p>NCT00216242</p

Sport, genetics and the `natural athlete': The resurgence of racial science

This article explores the ethical implications of recent discussions that naturalize the relationship between race, the body and sport within the frame of genetic science. Many suggestions of a racially distributed genetic basis for athletic ability and performance are strategically posited as a resounding critique of the `politically correct' meta-narratives of established sociological and anthropological forms of explanation that emphasize the social and cultural construction of race. I argue that this use of genetic science in order to describe and explain common-sense impressions of racial physiology and sporting ability is founded on erroneous premises of objectivity and disinterest, and inflates the analytical efficacy of scientific truth claims. I suggest that assertions of a value-free science of racial athletic ability reify race as inherited permanent biological characteristics that produce social hierarchies and are more characteristic of a longer history of `racial science'

​New Roles for Black Athletes? ​Post-Ferguson and Post-Kaepernick in the Age of Trump

Sports are America's public square, drawing millions to playing fields and courts around the country. John Hoberman disagrees. For black America, Hoberman argues that the effect of sports is damaging - it helps sustain racial myths and stereotypes and it lures the young to over-invest in the hope that it is the "ticket" out of depressed economic circumstances.Center for the Study of Politics and Governance, Humphrey School of Public Affairs, UM

Testosterone dreams: rejuvenation, aphrodisia, doping

John Hoberman.381 p. ; 23 cm

World Sport and its Public. On Historical Relations of Modern Sport and the Media

Werron T. World Sport and its Public. On Historical Relations of Modern Sport and the Media. In: Wagner U, Storm R, Hoberman J, eds. Observing Sport. Modern system theoretical approaches. Reihe Sportsoziologie. Schorndorf: Hofmann; 2010: 33-60