What's new for 'JKB_daily1' in PubMed

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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Saturday, 2012 April 21
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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PubMed Results

Items 1 - 4 of 4

1.	Nat Genet. 2012 Feb 27;44(3):233. doi: 10.1038/ng.2216. On not reinventing the wheel. [No authors listed] Abstract An alphabet soup of organizations and initiatives across the world are concerned with identifying, collecting and evaluating disease-causing human gene variants and using them to diagnose and treat rare diseases. Despite increasing standardization of nomenclature and technology, our efforts still need coordination to produce a pipeline leading from discovery to delivery.
	PMID: 22366856 [PubMed - indexed for MEDLINE]
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2.	Nat Genet. 2012 Feb 5;44(3):243-6. doi: 10.1038/ng.1074. Differential confounding of rare and common variants in spatially structured populations. Mathieson I, McVean G. Source Wellcome Trust Centre for Human Genetics, University of Oxford, UK. mathii@well.ox.ac.uk Abstract Well-powered genome-wide association studies, now made possible through advances in technology and large-scale collaborative projects, promise to characterize the contribution of rare variants to complex traits and disease. However, while population structure is a known confounder of association studies, it remains unknown whether methods developed to control stratification are equally effective for rare variants. Here, we demonstrate that rare variants can show a stratification that is systematically different from, and typically stronger than, common variants, and this is not necessarily corrected by existing methods. We show that the same process leads to inflation for load-based tests and can obscure signals at truly associated variants. Furthermore, we show that populations can display spatial structure in rare variants, even when Wright's fixation index F(ST) is low, but that allele frequency-dependent metrics of allele sharing can reveal localized stratification. These results underscore the importance of collecting and integrating spatial information in the genetic analysis of complex traits. PMCID: PMC3303124 [Available on 2012/8/5]
	PMID: 22306651 [PubMed - indexed for MEDLINE]
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3.	Nat Genet. 2012 Jan 29;44(3):352-5. doi: 10.1038/ng.1072. Pneumococcal genome sequencing tracks a vaccine escape variant formed through a multi-fragment recombination event. Golubchik T, Brueggemann AB, Street T, Gertz RE Jr, Spencer CC, Ho T, Giannoulatou E, Link-Gelles R, Harding RM, Beall B, Peto TE, Moore MR, Donnelly P, Crook DW, Bowden R. Source Department of Statistics, University of Oxford, UK. Abstract Streptococcus pneumoniae ('pneumococcus') causes an estimated 14.5 million cases of serious disease and 826,000 deaths annually in children under 5 years of age(1). The highly effective introduction of the PCV7 pneumococcal vaccine in 2000 in the United States(2,3) provided an unprecedented opportunity to investigate the response of an important pathogen to widespread, vaccine-induced selective pressure. Here, we use array-based sequencing of 62 isolates from a US national monitoring program to study five independent instances of vaccine escape recombination(4), showing the simultaneous transfer of multiple and often large (up to at least 44 kb) DNA fragments. We show that one such new strain quickly became established, spreading from east to west across the United States. These observations clarify the roles of recombination and selection in the population genomics of pneumococcus and provide proof of principle of the considerable value of combining genomic and epidemiological information in the surveillance and enhanced understanding of infectious diseases. PMCID: PMC3303117 [Available on 2012/7/29]
	PMID: 22286217 [PubMed - indexed for MEDLINE]
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4.	Nat Genet. 2012 Jan 29;44(3):285-90. doi: 10.1038/ng.1050. Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity. Andersen EC, Gerke JP, Shapiro JA, Crissman JR, Ghosh R, Bloom JS, Félix MA, Kruglyak L. Source Lewis-Sigler Institute for Integrative Genomics, Princeton University, New Jersey, USA. Comment in Nat Genet. 2012 Mar;44(3):237-8. Abstract The nematode Caenorhabditis elegans is central to research in molecular, cell and developmental biology, but nearly all of this research has been conducted on a single strain of C. elegans. Little is known about the population genomic and evolutionary history of this species. We characterized C. elegans genetic variation using high-throughput selective sequencing of a worldwide collection of 200 wild strains and identified 41,188 SNPs. Notably, C. elegans genome variation is dominated by a set of commonly shared haplotypes on four of its six chromosomes, each spanning many megabases. Population genetic modeling showed that this pattern was generated by chromosome-scale selective sweeps that have reduced variation worldwide; at least one of these sweeps probably occurred in the last few hundred years. These sweeps, which we hypothesize to be a result of human activity, have drastically reshaped the global C. elegans population in the recent past.
	PMID: 22286215 [PubMed - indexed for MEDLINE]
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