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Robert Plenge and colleagues report the results of a meta-analysis of published genome-wide association studies that led to the identification of two previously unknown variants associated with rheumatoid arthritis.
Evan Eichler and colleagues present an analysis of how well current commercial SNP platforms accurately capture copy number variants (CNVs). Although they were able accurately predict from Illumina Human 1M genotype data many sites identified in their recent study assessing CNVs in nine human individuals with a fosmid paired-end sequence approach, they find that commonly used platforms offer limited coverage for a large fraction of CNVs.
Hakon Hakonarson and colleagues report the identification of two new susceptibility loci for inflammatory bowel disease (IBD). One variant is near a gene encoding tumor necrosis factor receptor subfamily member 6B and is associated with increased levels of this protein in serum from individuals with IBD.
Ras family genes are common targets for somatic mutations in human cancer: KRAS is frequently mutated in lung carcinomas, whereas HRAS mutations are common in skin tumors. Allan Balmain and colleagues use genetic engineering of ras genes in mice to show that specificity for ras mutations is determined by local regulatory elements, and that Kras 4A is the major oncogenic isoform of Kras.
Richard Houlston and colleagues identify variants at six loci associated with risk of chronic lymphocytic leukemia. These findings confirm that common, low-penetrance susceptibility alleles contribute to this hematological malignancy and provide new insights into disease etiology.
Gil McVean and colleagues examine recombination hot spots in the human genome, using new search methods and drawing on HapMap II to identify an extended family of hot spot–associated motifs. They report a common sequence motif estimated to be found in ∼40% of recombination hot spots.
Mark Daly, Ramnik Xavier and colleagues report that a 20-kb deletion polymorphism upstream of IRGM is associated with altered IRGM expression and Crohn's disease. They also show that manipulation of IRGM levels in cells modulated the efficiency of autophagic responses to internalized bacteria, suggesting a mechanism by which the deletion variant might influence disease risk.
Masato Kasuga and colleagues and Shiro Maeda and colleagues each report the independent identification of SNPs in KCNQ1 associated with type 2 diabetes in the Japanese population. Each group replicated the associations in other populations of East Asian and European descent.
Frank Baas and colleagues report mutations in three of the four subunits of the tRNA-splicing endonuclease complex in families with two subtypes of pontocerebellar hypoplasia. The findings implicate tRNA processing in neurological disorders.
Masato Kasuga and colleagues and Shiro Maeda and colleagues each report the independent identification of SNPs in KCNQ1 associated with type 2 diabetes in the Japanese population. Each group replicated the associations in other populations of East Asian and European descent.
Miltos Tsiantis and colleagues examine leaf formation in Arabidopsis thaliana, which has simple, undivided leaves, and Cardamine hirsuta, which has a subdivided leaf blade with individual leaflets. Using genetics, marker gene expression and cell lineage tracing, the authors show that lateral leaflet formation in C. hirsuta requires establishment of growth foci that form after leaf initiation.
Stefan Schreiber and colleagues report the results of a genome-wide association study for sarcoidosis, a complex chronic inflammatory disorder. Variants near ANXA11 and PLAC9 are associated with elevated risk of the disease, with ANXA11 as the stronger candidate.
Valerie Cormier-Daire and colleagues report mutations in ADAMTSL2 in geleophysic dysplasia, a connective tissue disorder. The authors present evidence that ADAMTSL2 is an extracellular matrix protein regulating the bioavailability of TGF-β.
Gray horses are born colored but gradually lose hair pigmentation and become white, a trait that is transmitted in an autosomal dominant manner. Leif Andersson and colleagues report that the the mutation causing the Gray phenotype is a 4.6-kb duplication in intron 6 of STX17, which promotes overexpression of both STX17 and the neighboring gene NR4A3 in melanomas from Gray horses.
Shiro Ikegawa and colleagues identify a variant in a newly identified gene, DVWA, that is associated with susceptibility to knee osteoarthritis. DVWA contains von Willebrand factor domains and is expressed specifically in cartilage.
Mitinori Saitou and colleagues report that Prdm14, which encodes a transcription factor expressed exclusively in the germ cell lineage, is essential for re-acquisition of pluripotency and epigenetic reprogramming of primordial germ cells.
Takeshi Izawa and colleagues report the cloning of a gene underlying a rice quantitative trait locus influencing grain width. A deletion in qSW5 increases yield of rice grains, and the authors show that this mutation has likely been selected for during the domestication of rice.
Helen McNeill and colleagues show that loss of Fat4, a homolog of the Drosophila planar cell polarity protein Fat, disrupts oriented cell division, leading to a failure of tubule elongation and cystic kidney disease in mice. The findings suggest that loss of planar cell polarity may underlie some forms of cystic kidney disease in humans.
Daniel Cohn and colleagues identify mutations in the gene encoding the calcium-permeable cation channel TRPV4 in families with autosomal dominant brachyolmia. Functional studies show that the mutations result in gain-of-function of channel activation.