Hot off the presses! Nov 01 Nat Rev Genet

The Nov 01 issue of the Nat Rev Genet is now up on Pubget (About Nat Rev Genet): if you're at a subscribing institution, just click the link in the latest link at the home page. (Note you'll only be able to get all the PDFs in the issue if your institution subscribes to Pubget.)

Latest Articles Include:

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  - Nat Rev Genet 12(11):737 (2011)
  
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  - Nat Rev Genet 12(11):738 (2011)
  
• Epigenomics: Epigenetic variation across the generations | PDF (314 KB)
  - Nat Rev Genet 12(11):740 (2011)
  Advances in DNA-sequencing technologies have driven the cataloguing of genetic variation in humans and an increasing number of model organisms. The same technologies are now being extended to epigenetic modifications.
• Cancer genomics: Translocation patterns revealed | PDF (223 KB)
  - Nat Rev Genet 12(11):741 (2011)
  Somatic genomic rearrangements are crucial for the immune functions of lymphocytes and involve re-ligating DNA ends from different double-stranded breaks (DSBs). This occurs during V(D)J recombination and activation-induced cytidine deaminase (AID)-induced immunoglobulin class-switch recombination.
• Complex traits: Genome-wide association mapping in rice | PDF (97 KB)
  - Nat Rev Genet 12(11):741 (2011)
  This study advances research aiming to understand the genetic basis of agriculturally important traits in Asian rice, Oryza sativa. The authors present a genome-wide association study (GWAS) including 413 rice varieties from 82 countries and provide a public resource of all of the genotypes and phenotypes and of the seed stocks.
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  - Nat Rev Genet 12(11):741 (2011)
  
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  - Nat Rev Genet 12(11):741 (2011)
  
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  - Nat Rev Genet 12(11):741 (2011)
  
• RNA: Genome-wide views of long non-coding RNAs | PDF (194 KB)
  - Nat Rev Genet 12(11):742 (2011)
  Two recent papers present approaches that promise to increase the understanding of the functions of long non-coding RNAs (lncRNAs).
• Model organisms: The dangers lurking in the genetic background | PDF (216 KB)
  - Nat Rev Genet 12(11):742 (2011)
  Two new reports reveal that the effects of sirtuins on longevity — which have aroused great interest in lifespan research — were confounded by background mutations in previous studies. These new studies have important general lessons for genetic studies in model systems.
• Genome engineering: Synthetic genome technology for yeast | PDF (83 KB)
  - Nat Rev Genet 12(11):742 (2011)
  The authors have constructed a synthetic chromosome arm of the yeast Saccharomyces cerevisiae, laying the groundwork for creating a synthetic eukaryotic genome. A ~90 kb stretch of the right arm of chromosome IX was designed in silico to remove unstable elements such as transposons and to facilitate genome manipulations.
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  - Nat Rev Genet 12(11):742 (2011)
  
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  - Nat Rev Genet 12(11):742 (2011)
  
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  - Nat Rev Genet 12(11):742 (2011)
  
• Human disease: Huge boost for genetics of cognitive disorders | PDF (156 KB)
  - Nat Rev Genet 12(11):743 (2011)
  A large-scale study has identified 50 new candidate genes that may be involved in autosomal-recessive forms of intellectual disability in humans — almost doubling the number of genes implicated in non-syndromic intellectual disability and highlighting the power of next-generation sequencing to elucidate the molecular genetic basis of a complex disorder.
• Chromatin: A haul of new histone modifications | PDF (292 KB)
  - Nat Rev Genet 12(11):744 (2011)
  In recent years there has been great progress in uncovering the roles of histone post-translational modifications (PTMs) in regulating chromatin-based processes, such as transcription. But, as a new paper reveals, there is still a lot to learn even about the basic repertoire of PTMs.
• Genomics: Getting personal and regional | PDF (216 KB)
  - Nat Rev Genet 12(11):744 (2011)
  A major challenge of personal genomics is identifying the most medically relevant information from the wealth of data in the genome sequences of individuals. A recent study combined various bioinformatic approaches to make predictions about disease risk and pharmacological complications in a sequenced family.
• Exome sequencing as a tool for Mendelian disease gene discovery
  - Nat Rev Genet 12(11):745 (2011)
  Exome sequencing — the targeted sequencing of the subset of the human genome that is protein coding — is a powerful and cost-effective new tool for dissecting the genetic basis of diseases and traits that have proved to be intractable to conventional gene-discovery strategies. Over the past 2 years, experimental and analytical approaches relating to exome sequencing have established a rich framework for discovering the genes underlying unsolved Mendelian disorders. Additionally, exome sequencing is being adapted to explore the extent to which rare alleles explain the heritability of complex diseases and health-related traits. These advances also set the stage for applying exome and whole-genome sequencing to facilitate clinical diagnosis and personalized disease-risk profiling.
• Variation in the mutation rate across mammalian genomes
  - Nat Rev Genet 12(11):756 (2011)
  It has been known for many years that the mutation rate varies across the genome. However, only with the advent of large genomic data sets is the full extent of this variation becoming apparent. The mutation rate varies over many different scales, from adjacent sites to whole chromosomes, with the strongest variation seen at the smallest scales. Some of these patterns have clear mechanistic bases, but much of the rate variation remains unexplained, and some of it is deeply perplexing. Variation in the mutation rate has important implications in evolutionary biology and underexplored implications for our understanding of hereditary disease and cancer.
• Molecular spandrels: tests of adaptation at the genetic level
  - Nat Rev Genet 12(11):767 (2011)
  Although much progress has been made in identifying the genes (and, in rare cases, mutations) that contribute to phenotypic variation, less is known about the effects that these genes have on fitness. Nonetheless, genes are commonly labelled as 'adaptive' if an allele has been shown to affect a phenotype with known or suspected functional importance or if patterns of nucleotide variation at the locus are consistent with positive selection. In these cases, the 'adaptive' designation may be premature and may lead to incorrect conclusions about the relationships between gene function and fitness. Experiments to test targets and agents of natural selection within a genomic context are necessary for identifying the adaptive consequences of individual alleles.
• Understanding type 1 diabetes through genetics: advances and prospects
  - Nat Rev Genet 12(11):781 (2011)
  Starting with early crucial discoveries of the role of the major histocompatibility complex, genetic studies have long had a role in understanding the biology of type 1 diabetes (T1D), which is one of the most heritable common diseases. Recent genome-wide association studies (GWASs) have given us a clearer picture of the allelic architecture of genetic susceptibility to T1D. Fine mapping and functional studies are gradually revealing the complex mechanisms whereby immune self-tolerance is lost, involving multiple aspects of adaptive immunity. The triggering of these events by dysregulation of the innate immune system has also been implicated by genetic evidence. Finally, genetic prediction of T1D risk is showing promise of use for preventive strategies.
• The early bird catches the worm: new technologies for the Caenorhabditis elegans toolkit
  - Nat Rev Genet 12(11):793 (2011)
  The inherent simplicity of Caenorhabditis elegans and its extensive genetic toolkit make it ideal for studying complex biological processes. Recent developments further increase the usefulness of the worm, including new methods for: altering gene expression, altering physiology using optogenetics, manipulating large numbers of worms, automating laborious processes and processing high-resolution images. These developments both enhance the worm as a model for studying processes such as development and ageing and make it an attractive model in areas such as neurobiology and behaviour.
• Assessing and managing risk when sharing aggregate genetic variant data
  - Nat Rev Genet 12(11):801 (2011)
  In the above article, the incorrect link was provided for GWAS Central. The correct link should have been http://www.gwascentral.org. In the Further Information Box, the link to http://gwas.nih.gov was incorrectly described as 'GWAS Central (includes policy)'. This link should have been described as 'NIH GWAS policy'. The corrected article is available at: http://www.nature.com/nrg/journal/v12/n10/abs/nrg3067.html. The editors apologize for this error.