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Hongbing Shen and colleagues report a genome-wide association study for chronic hepatitis B virus (HBV) infection in Han Chinese populations. They identify two loci newly associated with HBV infection near HLA-C and UBLE2L3 and replicate previous associations at HLA-DP and HLA-DQ.
Philippe Amouyel, Julie Williams, Gerard Schellenberg, Sudha Seshadri and colleagues report a meta-analysis of genome-wide association studies for late-onset Alzheimer's disease in 17,008 cases and 37,154 controls with replication in an additional 8,572 cases and 11,312 controls. They identify 11 loci newly associated with Alzheimer's disease.
Sanwen Huang and colleagues report a genomic variation map of cucumber. They report the resequencing of 115 cucumber accessions and de novo assembly of the wild cucumber genome.
Jun Yang and colleagues show that common variants in GATA3 are associated with risk of Ph-like acute lymphoblastic leukemia (ALL). They further show that these variants are associated with variation in GATA3 expression levels and with risk of ALL relapse.
Thomas Vaughan and colleagues report a genome-wide association study of esophageal adenocarcinoma together with its precancerous lesion, Barrett's esophagus. They identified three loci associated with susceptibility to this cancer.
Zhiming Cai and colleagues report whole-genome and whole-exome sequencing of 99 paired tumor-normal samples of transitional cell carcinoma of the bladder. They find that 32% of tumors harbor alterations in genes involved in sister chromatid cohesion, including STAG2, ESPL1, NIPBL, SMC1A and SMC3.
Francisco Real and colleagues report exome sequencing in urothelial bladder tumors. They show that STAG2, a subunit of the cohesin complex, is recurrently mutated and provide evidence that STAG2 loss does not lead to increases in aneuploidy.
David Altshuler and colleagues sequenced seven genes for maturity-onset diabetes of the young (MODY), a dominant Mendelian disorder, in 4,003 individuals drawn from three population-based cohorts. They find ~2% of individuals unselected for phenotype carry low frequency variants in one of these MODY genes, predicted as likely to be pathogenic; however most of these individuals remain asymptomatic through middle age.
Jing Wang, Fengchun Zhang and colleagues report the results of a genome-wide association study of primary Sjögren's syndrome, a common autoimmune disease. They confirm associations in the STAT4, TNFAIP3 and HLA regions and identify a new susceptibility locus in the GTF2I region at 7q11.23.
Sekar Kathiresan and colleagues examine 185 common variants using a modified mendelian randomization approach and provide evidence supporting a causal role of triglyceride-rich lipoproteins in the development of coronary artery disease.
Christian Schaaf, Manuel Gonzalez-Garay and colleagues report the identification of four individuals with truncating mutations on the paternal allele of MAGEL2, a gene within the imprinted domain linked to Prader-Willi syndrome (PWS). The four individuals have PWS or PWS-related phenotypes, and all have autism.
Arul Chinnaiyan and colleagues report that the long noncoding RNA SChLAP1 is overexpressed in a subset of prostate cancers and predicts poor outcome. Mechanistically, they show that SChLAP1 promotes invasiveness and metastasis and antagonizes the functions of the SWI/SNF chromatin-remodeling complex.
Frank Stegmeier, Levi Garraway and colleagues apply a targeted mass spectrometry approach that measures level of histone modifications and identify a recurrent p.E1099K variant in NSD2 in acute lymphoblastic leukemia. When ectopically expressed in a cancer cell line, this variant promotes transformation.
The International Multiple Sclerosis Genetics Consortium reports the discovery of 48 new susceptibility variants for multiple sclerosis through targeted follow-up of immune-related loci. They also report fine mapping of association signals at established susceptibility loci and provide insights into the immune system processes underlying this disease.
Ingo Kurth and colleagues show that a specific de novo missense mutation in SCN11A results in an inability to experience pain. They further show that mutant channels display higher activity at resting voltages, causing sustained depolarization of pain receptors, impaired generation of action potentials and aberrant synaptic transmission.
Patrick Sulem, Kari Stefansson and colleagues report the identification of a rare nonsynonymous variant in the C3 gene, encoding complement factor 3, that is associated with age-related macular degeneration.
Goncalo Abecasis and colleagues report identification of a rare coding variant in the complement 3 gene that is associated with age-related macular degeneration.
Johanna Seddon, Soumya Raychaudhuri and colleagues report the identification of rare variants in C3, CFI and C9 associated with risk of advanced age-related macular degeneration.
Marshall Horwitz, Charles Mullighan, Kenneth Offit and colleagues report the identification of a recurrent germline PAX5 mutation in families with pre–B cell acute lymphoblastic leukemia. They also identify sporadic cases of this leukemia with the same mutation that arose somatically.
Lude Franke and colleagues report the results of a large expression QTL study performed on peripheral blood samples from 5,311 individuals. They identify trans-eQTL effects for 103 independent loci that were previously associated with complex traits at genome-wide significance, suggesting that this approach can provide insights into the downstream effects of many trait-associated variants.