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Montserrat Garcia-Closas and colleagues report a meta-analysis of three genome-wide association studies for estrogen receptor (ER)-negative breast cancer, including 4,193 ER-negative breast cancer cases and 35,194 controls, with replication using the iCOGS custom genotyping array in 40 studies, including 6,514 cases and 41,455 controls. They identify four loci associated with ER-negative but not ER-positive breast cancer.
Douglas Easton, Per Hall and colleagues report meta-analyses of genome-wide association studies for breast cancer, including 10,052 cases and 12,575 controls, followed by genotyping using the iCOGS array in an additional 52,675 cases and 49,436 controls from studies within the Breast Cancer Association Consortium (BCAC). They identify 41 loci newly associated with susceptibility to breast cancer.
Nilesh Samani and colleagues report a meta-analysis of genome-wide association studies for mean leukocyte telomere length in 37,684 individuals, with replication of selected variants in an additional 10,739 individuals. They identify seven loci associated with mean telomere length, including two that have been associated with several cancers, and also find that alleles associated with shorter telomere length were associated with a higher risk of coronary artery disease.
Rosalind Eeles and colleagues report meta-analysis of genome-wide association studies for prostate cancer and genotyping on the custom iCOGS array in 25,074 cases and 24,272 controls from 32 studies available in the PRACTICAL Consortium. They identify 23 new prostate cancer susceptibility loci, 20 of which are associated with both aggressive and non-aggressive disease.
Paul Pharoah, Joellen Schildkraut, Thomas Sellers and colleagues report a meta-analysis of genome-wide association studies for epithelial ovarian cancer and genotyping using the iCOGS array in 18,174 cases and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. They identify three new ovarian cancer susceptibility loci, including one specific to the serous subtype, and their integrated molecular analysis of genes and regulatory regions at these loci suggests disease mechanisms.
Stig Bojesen, Georgia Chenevix-Trench, Alison Dunning and colleagues report common variants at the TERT-CLPTM1L locus associated with mean telomere length measured in whole blood. They also identify associations at this locus to breast or ovarian cancer susceptibility and report functional studies in breast and ovarian cancer tissue and cell lines.
The International Peach Genome Initiative reports the high quality draft genome sequence of peach (Prunus persica). They also resequenced ten additional P. persica accessions, as well as those of Prunus ferganensis, Prunus kansuensis, Prunus davidiana and Prunus mira.
Michael Bruford and colleagues report whole-genome sequencing of the peregrine (Falco peregrinus) and saker falcon (Falco cherrug). Their comparative analysis with five avian species provides insight into falcon evolution and adaptation to a predatory lifestyle.
Thomas Nutman and colleagues report the draft genome of the filarial pathogen Loa loa, the African eyeworm. They also report coverage of two other filarial pathogens, Wuchereria bancrofti and Onchocerca volvulus. Unlike most filariae, L. loa lacks an obligate intracellular Wolbachia endosymbiont, and comparative genomic analyses suggest that the L. loa genome does not contain new metabolic synthesis or transport pathways compared to other filariae.
Adam Bass, Gad Getz and colleagues report whole-exome sequencing of 149 esophageal adenocarcinomas (EACs) and whole-genome sequencing of 15 EACs. They identify a mutational signature defined by a high prevalence of A>C transversions, as well as 26 genes mutated at high frequency in EACs.
Richard Houlston, Kari Hemminki and colleagues report a meta-analysis of genome-wide association studies of multiple myeloma and identify a variant in the CCDN1 gene that influences risk for developing a specific tumor karyotype with the t(11;14)(q13;q32) translocation.
Carlos López-Otín and colleagues report recurrent mutations in POT1 in chronic lymphocytic leukemia. This is the first member of the telomeric shelterin complex reported to be mutated in human cancer.
Florent Soubrier and colleagues report a genome-wide association study of pulmonary arterial hypertension. They identify a susceptibility locus near CBLN2 associated with a twofold elevated risk of developing this life-threatening disease.
Yao-Guang Liu and colleagues identify the molecular basis of male sterility in the Wild Abortive CMS (CMS-WA) system that has been widely used for hybrid rice breeding. They report that a new mitochondrial gene, WA532, confers male sterility because its protein product interacts with the mitochondrial protein COX11 and leads to cytoplasmic-nuclear incompatibility.
Gonçalo Abecasis and colleagues report a large-scale meta-analysis of genome-wide association studies for age-related macular degeneration (AMD), including over 17,100 advanced cases and 60,000 controls. They identify seven loci newly associated with AMD and report pathway analysis that shows enrichment in the complement system and atherosclerosis signaling.
The GenoMEL consortium reports a genome-wide association study of melanoma based on imputation and identifies a variant in the FTO gene associated with susceptibility to melanoma.
Nilanjan Chatterjee and colleagues report a theoretical framework to assess the predictive performance of polygenic models for risk prediction, based on analysis of genome-wide association study data sets. Across a range of common diseases and quantitative traits, they examine how predictive performance depends on the sample size, the total heritability and the underlying effect-size distributions.
Takashige Ishii and colleagues report that the closed panicle phenotype in the cultivated rice, Oryza sativa, is controlled by the OsLG1 gene. Closed panicles lead to higher seed retention, and the authors show evidence for selection at this locus during rice domestication.
Steven McCarroll, Giulio Genovese and colleagues report a new approach to help complete maps of the human genome reference sequence. They use a population-based admixture mapping approach and report the successful mapping of ~4 Mb of unplaced human euchromatic sequences.
Bin Han and colleagues report the draft genome of moso bamboo, an important non-timber forest product. RNA sequencing analysis of bamboo flowering tissues suggests a connection between drought-responsive genes and potential flowering genes.
