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Björn Usadel and colleagues report the genome sequence of the wild tomato species Solanum pennellii. The authors identify genes important for stress tolerance, metabolism and fruit maturation and suggest that transposable elements have had an important role in the evolution of the S. penellii stress response.
Rachael Stolzenberg-Solomon, Laufey Amundadottir and colleagues report a genome-wide association study of pancreatic cancer. They identify four new susceptibility loci.
Dongxin Lin, Philip Taylor, Li-Dong Wang and colleagues have now pooled three genome-wide association analyses of esophageal squamous cell carcinoma, finding two new risk loci at genome-wide significance and an HLA class II locus of significance in high-risk populations. They reanalyze the strength of evidence for previously published risk loci.
Josef Penninger and colleagues generate mice with conditional knockout of Jagn1 in hematopoietic cells. They show that the mice have a defective neutrophil-mediated immune response to Candida albicans, and GM-CSF treatment restored the defective fungicidal activity.
Andrew Singleton and colleagues report a large-scale meta-analysis of genome-wide association data in Parkinson's disease using over 13,000 cases and 95,000 controls plus additional samples for replication. They identify 6 new risk loci and replicate 28 independent risk variants for Parkinson's disease across 24 loci.
Shiro Ikegawa and colleagues report the results of a genome-wide association study for ossification of the posterior longitudinal ligament of the spine in a Japanese cohort. They identify six new loci, three of which showed decreased expression in a mouse model of endochondral ossification.
Jamie Craig, Puya Gharahkhani and colleagues report results of a genome-wide association study of primary open-angle glaucoma. They identify common variants near ABCA1, AFAP1 and GMDS that are associated with risk of this disease.
Tin Aung, Christopher Hammond and colleagues report the results of a large genome-wide association study of intraocular pressure. They identify four new loci associated with this trait and show that three of these loci are associated with risk of primary open-angle glaucoma.
Frank Uhlmann and colleagues show that the yeast Scc2–Scc4 cohesin loader complex is recruited to nucleosome-free regions in the promoters of highly expressed genes by the RSC chromatin remodeling complex and acts to maintain the nucleosome-free status of its binding sites. These findings suggest that human disorders caused by disruption of cohesin or RSC complex function, such as Cornelia de Lange and Coffin-Siris syndromes, could arise from related changes in the nucleosome landscape.
Zhenglin Yang, Xinghuai Sun and colleagues report the results of a genome-wide association study of primary open-angle glaucoma in East Asians. They show that common variants near ABCA1 and in PPM2 are associated with increased risk of this disease.
Jie He and colleagues report exome sequencing of 113 tumor-normal pairs of esophageal squamous cell carcinoma. They highlight mutations in genes involved in cell cycle and apoptosis regulation, histone modifier genes and genes encoding members of the Hippo and Notch pathways.
Bin Tean Teh and colleagues report exome sequencing of 8 breast fibroadenomas and follow-up targeted sequencing in 90 additional samples. They find that 59% of samples contain somatic mutations in exon 2 of MED12, a mutational pattern shared with another female-specific benign tumor, uterine leiomyoma.
Qiuyin Cai and colleagues report a genome-wide association analysis for breast cancer in 22,780 cases and 24,181 controls from 14 studies as part of the Asia Breast Cancer Consortium. They identify three loci newly associated with breast cancer susceptibility.
Joseph Buxbaum and colleagues use an epidemiological sample from Sweden to investigate the genetic architecture of autism spectrum disorders. They conclude that most inherited risk for autism is determined by common variation and that rare variation explains a smaller fraction of total heritability.
Marc Rothenberg, John Harley and colleagues present the results of a genome-wide association study of eosinophilic esophagitis. They discover an association with variants near CAPN14 and show that CAPN14 is expressed specifically in the esophagus and is upregulated in esophageal biopsies of individuals with active disease.
Johannes Schumacher and colleagues report the results of a genetic association study of idiopathic achalasia, a rare motility disorder of the esophagus. They show that common variation in the HLA-DQ region is strongly associated with achalasia risk, implicating immune-mediated processes in this disorder.
Yingbin Liu, Yun Liu, Hui Wang and colleagues perform whole-exome and targeted gene sequencing of gallbladder carcinoma. They identify recurrent somatic alterations in components of the ErbB signaling pathway and show that these alterations are associated with poor clinical outcomes.
Maxence Nachury, Christel Thauvin-Robinet and colleagues identify mutations in C2CD3 in two families with oral-facial-digital syndrome. They further show that C2CD3 localizes to the distal end of centrioles and acts as a positive regulator of centriole elongation.
Ana Vega and colleagues report the results of a three-stage genome-wide association study of radiotherapy toxicity following treatment for prostate cancer. They find that susceptibility to late radiation-induced toxicity is associated with variants in the TANC1 gene at 2q24.1.
De-Chen Lin and colleagues report whole-exome sequencing, targeted sequencing and SNP array analysis of 128 cases of nasopharyngeal carcinoma (NPC), a tumor type connected to Epstein-Barr virus infection. Their results identify a distinct mutational signature with nine significantly mutated genes and mutations enriched in cellular processes, including chromatin modification and autophagy.