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More data than we can handle is no excuse to give up our efforts to promote data access, but it may make us think about new ways to make it sustainable.
Identifying causal variants for complex traits and understanding their function remain arduous tasks. A new study combines the advantages of gene mapping in livestock with elegant genetic and functional analyses to address these challenges and identifies candidate regulatory variants affecting stature in cattle.
A study characterizes the in vitro replicative capacity of over 70,000 clinical isolates of HIV-1 in the absence of drugs, or in the presence of one of 15 individual drugs. The largest survey of the effects of mutations on fitness undertaken in any organism, this study finds extensive pairwise interactions among over 1,800 variable sites identified through sequencing the protease and reverse transcriptase genes.
Current models of Mycobacterium tuberculosis latency presume very low mycobacterial replication and mutation rates. In contrast to these models, a study reporting whole-genome sequencing of mycobacteria isolated from infected macaques shows that the mutational capacity of M. tuberculosis during latency is not reduced, a finding with important implications for tuberculosis research and control.
Michel Georges and colleagues report fine mapping and functional characterization of a quantitative trait locus with a large effect on bovine stature. They show that the likely causal variants at this locus modulate expression of a chromosomal domain encompassing PLAG1 and several other genes.
Julia Zeitlinger, Alexander Stark and colleagues report genome-wide binding profiles for the transcription factor Twist across six Drosophila species. They find that the binding pattern is highly conserved across species, suggesting strong functional constraints at the enhancers that Twist regulates.
Julie Williams, Michael Owen and colleagues report staged follow-up and meta-analyses of genome-wide association studies for Alzheimer's disease from the GERAD+ consortium. They identify common variants at ABCA7 and MS4A6A/MS4A4E associated with Alzheimer's disease and support for several additional susceptibility loci.
Gerard Schellenberg and colleagues report a genome-wide association study of late-onset Alzheimer's disease (LOAD), as part of the Alzheimer Disease Genetics Consortium. They identify common variants in MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 associated with LOAD.
Yardena Samuels and colleagues report the sequencing of 14 melanoma exomes. They identify a recurrent mutation in TRRAP in 4% of cases as well as mutations in GRIN2A in 33% of tumors.
Yusuke Nakamura and colleagues report a genome-wide association study for uterine fibroids. They identify three loci associated with susceptibility to this benign tumor.
Amanda Spurdle and colleagues report results of a genome-wide association study of endometrial cancer. They identify a risk variant near HNF1B that has previously been associated with increased risk of prostate cancer and with reduced risk of type 2 diabetes.
Koichi Matsuda and colleagues report a genome-wide association study for hepatitis C virus–induced hepatocellular carcinoma. They identify a susceptibility locus at MICA in individuals of Japanese ancestry.
Eisei Noiri and colleagues show that intronic variants in GPC5 are associated with acquired nephrotic syndrome. They further show that knockdown of Gpc5 in mice confers resistance to podocyte injury in two different models of experimentally induced nephrosis.
Tatsuhiro Shibata and colleagues report the sequencing of a hepatocellular carcinoma. The authors identified 63 somatic non-synonymous substitutions and 22 somatic chromosomal rearrangements in this liver tumor.
George Vassiliou, Allan Bradley and colleagues perform a Sleeping Beauty transposon mutagenesis screen to identify insertions that cooperate with mutant Npm1 to produce acute myeloid leukemia (AML) in mice. They observed mutually exclusive integrations in Csf2, Flt3 or Rasgrp1 in a high percentage of cases, providing insights into the molecular pathogenesis of this AML subtype.
Detlef Weigel and colleagues report the genome sequence of Arabidopsis lyrata. In comparison with the much smaller genome of A. thaliana, from which A. lyrata diverged about 10 million years ago, they find that the reduction in genome size is attributed to a large number of deletions across the genome.
Sarah Fortune and colleagues report the whole-genome sequencing of Mycobacterium tuberculosis strains isolated from cynomolgus macaques with either active, latent or early reactivation disease. They estimate a similar mutation rate for these disease states in vivo, as well as for the bacterium in vitro. This suggests that M. tuberculosis has a greater mutational rate during latent and early reactivation disease than previously predicted and may be able to acquire drug resistance during these states.
Sebastian Bonhoeffer, Christos Petropoulos and colleagues report a systems analysis of the fitness landscape of HIV-1 protease and reverse transcriptase. They use a dataset of over 70,000 virus samples, isolated from HIV-1 subtype B infected individuals, assayed for in vitro replicative capacity alone or under drug selection.
Mark DePristo and colleagues report an analytical framework to discover and genotype variation using whole exome and genome resequencing data from next-generation sequencing technologies. They apply these methods to low-pass population sequencing data from the 1000 Genomes Project.