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Ian Tomlinson and colleagues report the identification of germline variants in POLE and POLD1 that are susceptibility alleles for colorectal cancer. POLE and POLD1 encode DNA polymerases that function in DNA replication.
Anna Köttgen and colleagues report genome-wide association studies for serum urate in over 140,000 individuals from the Global Urate Genetics Consortium (GUGC). They identify 18 loci newly associated with serum urate concentrations and confirm 10 known loci, characterize their associations with gout and include a network analysis suggesting a role for inhibins-activins pathways in regulating urate homeostasis.
Maize oil is an important food and energy source. Now, Jianbing Yan and colleagues report a genome-wide association study in maize for maize kernel oil composition. They analyzed 368 maize lines with 1.06 million SNPs genome-wide and found 74 loci associated with maize kernel oil concentration and fatty acid composition.
Carlo Gambacorti-Passerini and colleagues identify recurrent SETBP1 mutations in atypical chronic myeloid leukemia. The mutations, which cluster in a small region of SETBP1, are associated with high white blood cell counts and poor prognosis.
Panos Deloukas, Nilesh Samani and colleagues report a large-scale association analysis using the Metabochip array in 63,746 coronary artery disease cases and 130,681 controls. They identify 15 susceptibility loci, refine previous associations and use network analysis to highlight biological pathways.
Duanqing Pei and colleagues show that BMP signaling to histone H3 lysine 9 methylation is a barrier to reprogramming somatic cells into induced pluripotent cells (iPSCs) and that its removal promotes the formation of fully reprogrammed iPSCs from pre-iPSCs. pre-iPSCs exhibit pluripotent properties but do not activate the core pluripotent network.
Victor Velculescu, Michael Hogarty and colleagues report whole-genome and exome sequences of neuroblastoma, the most common solid tumor in children. They identify recurrent somatic mutations in the chromatin-remodeling genes ARID1A and ARID1B.
Zhangjun Fei and colleagues report the draft genome of a Chinese elite watermelon inbred line 97103 and resequencing of 20 diverse accessions that represent the three subspecies of Citrullus lunatus. Comparative genome-wide analyses identify the extent of genetic diversity and population structure of watermelon germplasm.
Yijun Ruan and colleagues report the draft genome of the sweet orange, Citrus sinensis. Their data suggests sweet orange originated from a cross between pummelo and mandarin.
Peter Donnelly and colleagues report fine mapping of 14 susceptibility loci in 8,000 cases and controls for type 2 diabetes, coronary artery disease and Graves' disease. They apply a new Bayesian method for analysis of fine-mapping data sets, using this to define sets of SNPs likely to contain causal disease-associated variants.
Aaron Gitler, Robert Farese Jr. and colleagues identify the RNA lariat debranching enzyme Dbr1 as a potent suppressor of TDP-43 toxicity in yeast. They further show that Dbr1 knockdown reduces TDP-43 toxicity in mammalian cells, identifying this enzyme as a possible therapeutic target in amyotrophic lateral sclerosis and other diseases marked by TDP-43 accumulation.
Amos Tanay and colleagues characterize DNA methylation polymorphism within cell populations and track immortalized fibroblasts in culture for over 300 generations to show that formation of differentially methylated regions occurs through a stochastic process and nearly deterministic epigenetic remodeling.
Jan Molenaar and colleagues show that LIN28B is overexpressed and amplified in human neuroblastomas and that LIN28B regulates let-7 family miRNAs and MYCN. They create a transgenic mouse model of LIN28B overexpression and show that these mice develop neuroblastoma tumors.
Gordon Dougan and colleagues report whole-genome sequencing of a global collection of 179 Salmonella Typhimurium isolates, including 129 diverse sub-Saharan African isolates associated with invasive disease. They determine the phylogenetic structure of invasive Salmonella Typhimurium in sub-Saharan Africa and find that the majority are from two closely related highly conserved lineages, which emerged in the last 60 years in close temporal association with the current HIV epidemic.
Mathieu Lupien, Jason Moore and colleagues show that breast cancer risk–associated SNPs commonly disrupt the binding of FOXA1 to chromatin, thereby directly affecting gene expression.
Dongxin Lin and colleagues report a genome-wide association study for esophageal squamous cell carcinoma (ESCC) in Chinese populations, identifying nine new susceptibility loci. They also perform a genome-wide gene-environment interaction analysis with alcohol consumption, a known risk factor for ESCC.
The MuTHER Consortium reports an analysis of the genetics of gene expression in three tissues from approximately 850 mono- and dizygotic twins. They systematically dissect cis and trans genetic effects and estimate non-genetic effects on gene expression.
Yuxian Zhu and colleagues report the draft genome of a diploid cotton Gossypium raimondii. This species is a wild South American cotton, whose progenitor is thought to have been the contributor of the D subgenome of the allotetraploid commercial species Gossypium hirsutum and Gossypium barbadense, which account for ~95% of the worldwide cotton crop.
Mark McCarthy, Michael Boehnke, Andrew Morris and colleagues perform large-scale association analyses using the Metabochip to gain insights into the genetic architecture of type 2 diabetes. They report several new susceptibility loci, including two that show sex-differentiated effects on disease risk.
Jose Florez, Claudia Langenberg, Erik Ingelsson, Inga Prokopenko, Inês Barroso and colleagues perform large-scale association analyses using the Metabochip to gain further insights into the genetic architecture of glucose regulation. They identify 38 new loci influencing 1 or more glycemic traits and show that many of these loci also modify risk of type 2 diabetes.