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Sergey Nikolaev, Stylianos Antonarakis and colleagues report exome sequencing of seven melanoma cell lines and matched germline cells. They identify recurring somatic mutations in MAP2K1 and MAP2K2 occurring at an overall frequency of 8%.
Bin Han and colleagues report low-coverage sequencing for 950 diverse rice accessions. They develop a framework for haplotype-based de novo assembly, phenotyped the 950 lines for 11 agronomic traits and used this information to conduct genome-wide association studies. They identify 32 new loci associated with these traits.
Margaret Goodell, Wei Li and colleagues report conditional ablation of the Dnmt3a DNA methyltransferase in hematopoietic stem cells (HSCs) in mice. They show that Dnmt3a is critical for epigenetic silencing of HSC regulatory genes and for HSC differentiation.
David van Heel, Cisca Wijmenga and colleagues used a custom, high-density genotyping chip to examine 183 immune-related loci for their role in celiac disease. They report 13 new regions associated with celiac disease risk, identify multiple independent signals at several loci and refine the localization of many previously reported risk signals.
Douglas Winton and colleagues report the results of a large insertional mutagenesis screen to identify drivers of intestinal tumorigenesis in mice. The study identifies a large number of potential cancer drivers, including new modifiers of canonical Wnt signaling and components of the FGF pathway.
Mark Daly, Manuel Rivas and colleagues used next-generation sequencing to study the coding exons of 56 genes from regions previously associated with Crohn's disease. Follow-up analyses in independent case-control series confirmed association of many newly discovered rare variants with disease risk.
Jim Lupski and colleagues report characterization of complex genomic rearrangements at the MECP2 and PLP1 loci. They show that all the complex rearrangement products share a common genomic organization wherein the triplicated segment is inverted and located between directly oriented duplicated genomic segments; these structures are mediated by inverted repeats that can be separated by over 300 kb.
Dirk Schübeler and colleagues report an experimental strategy to identify genetic elements that autonomously determine DNA methylation states in murine stem cells. They identified promoter sequences that supported proper de novo methylation during differentiation and determined that this activity is contained within small methylation-determining regions.
Martin Tobin and colleagues report a meta-analysis of 23 genome-wide association studies for pulmonary function. They identify 16 loci newly associated with variation in two cross-sectional measures of lung function, used to define airway obstruction and to grade the severity of obstruction.
Joshua Bis, Christopher O'Donnell and colleagues report a meta-analysis of genome-wide association studies from the CHARGE Consortium that identifies loci associated with carotid intima media thickness and plaque. These are established measures of subclinical atherosclerosis that predict future cardiovascular disease events.
João Barata and colleagues identify somatic gain-of-function IL7R mutations in childhood T-cell acute lymphoblastic leukemia. The mutations result in constitutive receptor activation, implicating the IL-7R pathway as a potential therapeutic target in a subset of T-ALL cases.
Detlef Weigel and colleagues report results from the first phase of the Arabidopsis 1001 Genomes Project, based on short-read sequencing of 80 geographically diverse strains. This collection of strains has been made available to the scientific community, and the authors show that the identified polymorphisms in these strains can be useful for imputation and genome-wide association studies.
Duncan Odom and colleagues map Pol III occupancy genome-wide in liver tissue from six mammals. The analysis showed variable binding of Pol III at individual tRNA genes that nevertheless led to conserved expression of amino acid isotypes.
Alexander van Oudenaarden and colleagues examine microRNA-mediated regulation of gene expression using single-cell measurements of a target gene's expression. They find that microRNAs can repress gene expression either as a switch or through fine-tuning and that the strength of repression can vary widely between cells.
Evan Eichler and colleagues analyze copy number variation in 15,767 children with intellectual disability, developmental delay, congenital birth defects and/or other related phenotypes. They identify 59 likely pathogenic CNV regions, including 14 new candidate regions, and estimate that ~14% of disorders in this sample collection are caused by large CNVs.
Laura Pasqualucci and Riccardo Dalla-Favera and colleagues report exome sequencing and copy-number analyses of diffuse large B-cell lymphomas. Their analyses identified mutations in genes not previously implicated in DLBCL pathogenesis, such as genes encoding chromatin modifiers such as MLL2.
John Novembre and colleagues present a new approach for constructing recombination maps based on ancestry switch points among individuals. They construct a high-resolution genome-wide recombination map based on admixed African-American and African-Caribbean individuals and compare this to previous recombination maps.
Matthew Brown, Peter Donnelly and colleagues report results of a genome-wide association meta-analysis and follow-up study of ankylosing spondylitis. They identify three new risk variants and report a genetic interaction between ERAP1 and HLA-B27, implicating aberrant peptide handling in the pathophysiology of this disease.
Jeremy Reiter and colleagues show that Tctn1 is a component of a transition zone complex that regulates ciliogenesis and ciliary membrane composition. They also identify a likely causal mutation in TCTN1 in two siblings with Joubert syndrome.
Jeong Sun-Seo and colleagues report whole-genome sequencing of ten Korean individuals and exome sequencing on an additional eight Korean individuals. They also performed transcriptome sequencing on 17 of these individuals. The authors identified approximately 1.83 million previously unidentified SNPs.