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Pier Paolo Pandolfi and colleagues report that Dok family members, Dok1, Dok2 and Dok3, are lung tumor suppressors, as loss of Dok genes in mice leads to spontaneous lung adenocarcinoma. DOK2 is frequently deleted in human lung cancer and suppresses lung cancer cell growth.
Kerstin Lindblad-Toh and colleagues use genome-wide association mapping to identify risk loci for a canine systemic lupus erythematosus-related disease complex in Nova Scotia duck tolling retrievers. The study illustrates the power of using dog breeds for complex trait mapping.
Xin-zhuan Su and colleagues report genome-wide SNP genotyping of 189 culture-adapted Plasmodium falciparum parasites and examine population structure, selection and recombination hotspots. They also conduct genome-wide association studies for resistance to seven different antimalarial drugs.
Christopher Walsh and colleagues describe a new recessive genetic disease characterized by microcephaly, early-onset intractable seizures and developmental delay (MCSZ). The authors identify mutations in PNKP that result in this severe disease and show that PNKP mutations disrupt DNA repair.
Jorge Ferrer, Jason Lieb, and Karen Mohlke and colleagues identify regulatory DNA active in human pancreatic islets by formaldehyde-assisted isolation of regulatory elements (FAIRE) coupled with high-throughput sequencing. They identified 80,000 open chromatin sites and 3,300 islet-selective open chromatin sites and found that a TCF7L2 intronic variant associated with type 2 diabetes is located in islet-selective open chromatin.
Thomas Turner and colleagues have applied next-generation sequencing technology to investigate the genetic basis of adaptive variation. They sequenced pools of DNA from geographically distinct Arabidopsis lyrata populations that are locally adapted to serpentine soils and analyzed 8 million polymorphisms, identifying a putative example of convergent evolution.
Stephen Chanock and colleagues identify three new susceptibility loci for pancreatic cancer on chromosomes 13q22.1, 1q32.1 and 5p15.33. The association signal at 13q22.1 maps to a large nongenic region, whereas the signals at 1q32.1 and 5p15.33 map near the NR5A2 gene and CPTM1L-TERT region, respectively.
Jianzhi Zhang and colleagues examine epistasis within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis. They find a strong bias towards positive epistasis amongst essential genes and show that these only rarely include genes involved in biochemical reactions with related functions.
Francis McMahon and colleagues report a meta-analysis of genome-wide association data sets for major mood disorders, including bipolar disorder and major depressive disorder.
The MAGIC investigators report results of a large genome-wide association study meta-analysis to identify common variants influencing fasting glucose homeostasis. They further show that several of the newly discovered loci influencing glycemic traits are also associated with risk of type 2 diabetes.
Marco Marra and colleagues identify somatic mutations in EZH2 in diffuse large B-cell lymphomas and follicular lymphomas. EZH2 is a histone methyltransferase that participates in trimethylation of H3 Lys27 (H3K27) as part of the PRC2 complex. The mutations alter a single tyrosine residue in the SET domain of EZH2 and reduce the ability of PRC2 to trimethylate H3K27 in vitro.
Richard Watanabe and colleagues of the MAGIC consortium report meta-analyses of genome-wide association studies to glucose levels two hours after an oral glucose challenge. They identify variants in GIPR associated with glucose and insulin responses.
Joseph Gleeson and colleagues show that Ahi1 is required in mice for retinal outer segment development and displays dosage-sensitive genetic interactions with Nphp1. They further show that a missense allele of AHI1 in humans modifies risk of retinal degeneration among individuals with nephronophthisis.
John Chambers and colleagues report genome-wide association studies to several ECG measurements, identifying an association of SCN10A to PR interval. They find that Scn10a−/− mice show a shorter PR interval.
Richard Houlston and colleagues identify common variants at four loci associated with risk of chronic lymphocytic leukemia, including a coding variant in FARP2 on 2q37.3 and a noncoding variant in the region upstream of MYC on 8q24.21.
Hilma Holm and colleagues report genome-wide association studies to electrocardiographic measures of heart rate, PR interval, QRS duration and QT interval.
Matthew Brown, John Reveille and colleagues report a genome-wide association study for ankylosing spondylitis. They identify four genetic loci outside of the MHC newly associated to AS susceptibility.
Arne Pfeufer and colleagues report a genome-wide association study of the electrocardiographic measurement of PR interval in seven population-based cohorts in the CHARGE consortium. They identify nine loci associated with PR interval and highlight candidate genes with a role in ion channels and cardiac development.