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Yurii Aulchenko and colleagues report a variance components–based method, GRAMMAR-Gamma, for genome-wide association studies including a large number of individuals and genetic markers. They demonstrate, using simulations as well as human and Arabidopsis thaliana data sets, that their method provides unbiased estimates of SNP effect and increases computational efficiency, which may facilitate analysis of human whole-genome resequencing studies.
Xue-Jun Zhang, Jun Wang and colleagues identify mutations in MVK in disseminated superficial actinic porokeratosis, a disorder characterized by defects in epidermal keratinization. MVK encodes mevalonate kinase, an enzyme involved in the biosynthesis of cholesterol and isoprenoids.
Albena Jordanova and colleagues report mutations in HINT1 in autosomal recessive axonal neuropathy with neuromyotonia. Using linkage analysis and whole-genome sequencing, they identify 8 mutations in 33 affected families.
Peter Donnelly and colleagues report a genome-wide association study for Barrett's esophagus, a common premalignant condition associated with stomach acid reflux and predisposing to esophageal adenocarcinoma. They identify two loci associated with susceptibility to Barrett's esophagus.
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.
Carl Anderson and colleagues report dense genotyping, using the Immunochip array, of 2,861 primary biliary cirrhosis (PBC) cases and 8,514 controls. They identify three loci newly associated with PBC, and their fine-mapping of previous susceptibility loci identifies five regions with multiple independent common, low-frequency and rare variant associations.
Elizabeth Holliday and colleagues report a genome-wide association study for ischemic stroke. They identify common variants at 6p21.1 associated with large artery atherosclerosis (LAA), a major subtype of ischemic stroke.
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.
Roman Thomas and colleagues report exome sequencing of 29 small-cell lung cancers (SCLCs), 2 SCLC genomes and transcriptomes of 15 SCLCs. They identify recurrent mutations in the CREBBP, EP300 and MLL genes encoding histone modifiers. They identify mutations in SLIT2 and EPHA7, which have a role in axon guidance and cell migration, and focal amplifications of FGFR1.
Sekar Seshagiri and colleagues report exome, transcriptome and copy-number alteration data in small-cell lung cancer. The authors find SOX2 amplification in 27% of samples and also identify a recurrent RFL-MYCL1 fusion.
John Maris and colleagues identify common variants at 6q16 associated with neuroblastoma susceptibility. The risk variants are located near the HACE1 and LIN28B genes, both of which show altered expression in advanced neuroblastomas.
Robert Jenkins and colleagues report fine mapping of the glioma risk region at 8q24.21. They identify a new low-frequency variant in the region that is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation.
Brian Fowler, David Rosenblatt and colleagues show that mutations in the ABC transporter gene ABCD4 cause a new inborn error of vitamin B12 metabolism. ABCD4 colocalizes with the lysosomal proteins LAMP1 and LMBD1 and may be involved in intracellular processing of vitamin B12.
Ningli Wang, Tin Aung and colleagues report genome-wide association analyses for primary angle closure glaucoma, a major cause of blindness worldwide. They identify three loci newly associated with this disease.
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.
Ze-Guang Han and colleagues report exome sequencing of ten hepatitis B virus–positive hepatocellular carcinomas. They identify recurrent somatic mutations in ARID1A and mutation signatures that may reflect mutagenic exposures.
David Reich and colleagues report direct characterization of the human mutation rate based on analysis of 85,289 Icelandic individuals genotyped at 2,477 autosomal microsatellite loci. They use this mutation rate to build a model of microsatellite evolution and estimate key evolutionary parameters.
Alex Meissner and colleagues report base pair–resolution methylation maps from donor fibroblasts and nuclear transfer–reconstructed mouse embryos. They compare methylation profiles to that present during normal fertilization and find that specific promoters and repeat elements exhibit differential dynamics.
Joel Hirschhorn and colleagues examine height-associated SNPs in northern- and southern-European populations. They report evidence of widespread weak selection on standing variation for height in humans.
Magnus Nordborg and colleagues report a parameterized multi-trait mixed model (MTMM) method applied to genome-wide association studies of correlated phenotypes. They test this approach, using both human and Arabidopsis thaliana data sets, and demonstrate how it can be used to identify pleiotropic loci and gene by environment interactions.