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Daniel Gudbjartsson, Kari Stefansson and colleagues propose a new weighted Bonferroni approach for determining significance thresholds for human genome-wide association studies (GWAS). They demonstrate that the weighted approach, which is based on sequence annotation enrichments, improves power over standard GWAS methods.
José Luis Gómez-Skarmeta, Hector Escrivá, Ignacio Maeso, Damien Devos and colleagues perform 4C-seq profiling of the Hox cluster in amphioxus embryos and find that, unlike in vertebrate embryos, the cluster is organized into a single chromatin interaction domain. They suggest that the vertebrate Hox bipartite regulatory system is an evolutionary novelty.
Ingileif Jonsdottir, Kari Stefansson and colleagues show that variants in the HLA class II region contribute to tuberculosis risk in populations of European ancestry. They propose that the associated variants influence disease risk by altering expression of HLA class II molecules presenting protective M. tuberculosis antigens to T cells.
Swapan Nath, Sang-Cheol Bae and colleagues report the results of a large-scale association study of systemic lupus erythematosus in individuals of Asian ancestry. They identify several new susceptibility loci and find enrichment for signals near genes implicated in B cell and T cell function.
Owen Rackham, Jose Polo, Julian Gough and colleagues present a method, Mogrify, for predicting sets of transcription factors that can induce transdifferentiation between cell types. They show that Mogrify is able to predict known factors for published cell conversions and experimentally validate factors for two new conversions.
Janey Wiggs, Jonathan Haines and colleagues identify three new susceptibility loci for primary open-angle glaucoma. The association signals map near genes implicated in ocular development (FOXC1), neurodegeneration (ATXN2) and mitochondrial function (TXNRD2).
Beat Keller, Thomas Wicker and colleagues compare the genomes of 46 isolates of powdery mildew, Blumeria graminis. They find that B. graminis f. sp. triticale, a pathogen growing on triticale (a wheat × rye hybrid plant), is a hybrid of B. graminis f. sp. tritici and B. graminis f. sp. secalis, which grow on wheat and rye, respectively.
Elodie Ghedin, Benjamin Cowling and colleagues quantify the frequency at which variants of influenza virus were transmitted between individual hosts during the 2009 H1N1 pandemic in Hong Kong. They find transmission of multiple variants between donor-recipient pairs and provide estimates of the number of viral particles that can infect and replicate within a host.