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Douglas Easton and colleagues report a genome-wide association analyses for breast cancer in ~70,000 cases and ~68,000 controls. They identify three new breast cancer susceptibility loci, two of which show association only with estrogen receptor–positive disease.
Julius Gudmundsson and colleagues report a genome-wide association study for circulating levels of thyroid-stimulating hormone in 27,758 individuals not known to have thyroid cancer. They follow with thyroid cancer association analyses and identify common variants at three loci newly associated with susceptibility to thyroid cancer.
Albrecht Melchinger and colleagues report a complementary approach to phenotype-based screening for hybrid maize. The new approach accurately predicts the combining abilities of agronomical traits based on genomic and metabolomic information comprising 56,110 SNPs and 130 metabolite measurements.
Catherine André, Judith Fischer and colleagues report that mutations in PNPLA1 cause congenital ichthyosis in humans and golden retriever dogs. Their findings suggest a role for PNPLA1 in the formation of the epidermal lipid barrier.
Joseph Gleeson and colleagues identify CEP41 mutations as a cause of Joubert syndrome. Their functional studies suggest that CEP41 regulates ciliary entry of TTLL6, an enzyme required for tubulin glutamylation at the cilium.
Robin Gasser and his colleagues report the whole-genome sequence of Schistosoma haematobium. They include comparisons to the genome sequences of S. mansoni and S. japonicum, the two other species that cause schistosomiasis in humans.
Joy Bergelson and colleagues characterize genome-wide patterns of genetic variation in a collection of 1,307 worldwide Arabidopsis thaliana accessions from the Regional Mapping (RegMap) panel, a publicly available genomic resource that includes large regional panels. They characterize signatures of selection and patterns of recombination and identify an enrichment of hotspots in intergenic regions and in repetitive DNA.
Eileen Furlong and colleagues report the development and application of BiTS-ChIP (batch isolate tissue specific chromatin immunoprecipitation), in which a tagged nuclear protein is expressed in developing cells of interest. They apply this method to investigate six chromatin markers and RNA Pol II occupancy in mesodermal cells in developing Drosophila embryos and find that histone modifications and Pol II occupancy can predict enhancer activity.
Huda Zoghbi and colleagues report that MECP2 transgenic mice display heightened anxiety and social approach deficits and that genetic and pharmacological inhibition of Crh or its receptor, Crhr1, suppresses the anxiety phenotypes. The authors also report that genetic reduction of Oprm1 improves social approach behaviors in MECP2 transgenic mice.
Andy Fire and colleagues report the finding of histone H3 lysine 9 trimethylation footprints extending several kilobases from siRNA targets at specific loci across the C. elegans genome. Such exogenous RNA–induced chromatin modification was mediated by secondary amplification of siRNA and was maintained across two or more generations.
Gil McVean and colleagues report algorithms for de novo assembly and genotyping of variants using colored de Bruijn graphs and provide these in a software implementation called Cortex. Their methods can detect and genotype both simple and complex genetic variants in either an individual or a population.