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

Sent on Friday, 2014 April 25
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 - 3 of 3

1.	Nat Genet. 2014 Mar;46(3):220-4. doi: 10.1038/ng.2896. Epub 2014 Feb 9. The deleterious mutation load is insensitive to recent population history. Simons YB1, Turchin MC2, Pritchard JK3, Sella G4. Author information: 11] Department of Ecology, Evolution and Behavior, Hebrew University of Jerusalem, Jerusalem, Israel. [2]. 21] Department of Human Genetics, University of Chicago, Chicago, Illinois, USA. [2]. 31] Department of Human Genetics, University of Chicago, Chicago, Illinois, USA. [2] Howard Hughes Medical Institute, Stanford University, Stanford, California, USA. [3] Department of Biology, Stanford University, Stanford, California, USA. [4] Department of Genetics, Stanford University, Stanford, California, USA. 41] Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA. [2]. Abstract Human populations have undergone major changes in population size in the past 100,000 years, including recent rapid growth. How these demographic events have affected the burden of deleterious mutations in individuals and the frequencies of disease mutations in populations remains unclear. We use population genetic models to show that recent human demography has probably had little impact on the average burden of deleterious mutations. This prediction is supported by two exome sequence data sets showing that individuals of west African and European ancestry carry very similar burdens of damaging mutations. We further show that for many diseases, rare alleles are unlikely to contribute a large fraction of the heritable variation, and therefore the impact of recent growth is likely to be modest. However, for those diseases that have a direct impact on fitness, strongly deleterious rare mutations probably do have an important role, and recent growth will have increased their impact. PMCID: PMC3953611 [Available on 2014/9/1]
	PMID: 24509481 [PubMed - indexed for MEDLINE]
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2.	Nat Genet. 2014 Mar;46(3):225-33. doi: 10.1038/ng.2891. Epub 2014 Feb 2. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Gerlinger M1, Horswell S2, Larkin J3, Rowan AJ1, Salm MP2, Varela I4, Fisher R5, McGranahan N6, Matthews N7, Santos CR6, Martinez P6, Phillimore B7, Begum S7, Rabinowitz A7, Spencer-Dene B8, Gulati S9, Bates PA9, Stamp G8, Pickering L5, Gore M5, Nicol DL10, Hazell S11, Futreal PA12, Stewart A13, Swanton C14. Author information: 11] Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK. [2]. 21] Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK. [2]. 31] Department of Medicine, Royal Marsden Hospital, London, UK. [2]. 4Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain. 5Department of Medicine, Royal Marsden Hospital, London, UK. 6Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK. 7Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK. 8Experimental Histopathology, Cancer Research UK London Research Institute, London, UK. 9Biomolecular Modelling, Cancer Research UK London Research Institute, London, UK. 10Department of Urology, Royal Marsden Hospital, London, UK. 11Department of Pathology, Royal Marsden Hospital, London, UK. 12Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA. 13Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK. 141] Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK. [2] University College London Cancer Institute, University College London, London, UK. Comment in Kidney cancer: Intratumoral differences analysed. [Nat Rev Urol. 2014] Kidney cancer: Intratumoral differences analysed.Payton S. Nat Rev Urol. 2014 Mar; 11(3):127. Epub 2014 Feb 25. Abstract Clear cell renal carcinomas (ccRCCs) can display intratumor heterogeneity (ITH). We applied multiregion exome sequencing (M-seq) to resolve the genetic architecture and evolutionary histories of ten ccRCCs. Ultra-deep sequencing identified ITH in all cases. We found that 73-75% of identified ccRCC driver aberrations were subclonal, confounding estimates of driver mutation prevalence. ITH increased with the number of biopsies analyzed, without evidence of saturation in most tumors. Chromosome 3p loss and VHL aberrations were the only ubiquitous events. The proportion of C>T transitions at CpG sites increased during tumor progression. M-seq permits the temporal resolution of ccRCC evolution and refines mutational signatures occurring during tumor development.
	PMID: 24487277 [PubMed - indexed for MEDLINE]
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3.	PLoS One. 2013 Jun 28;8(6):e68306. doi: 10.1371/journal.pone.0068306. Print 2013. Regulated expression of PTPRJ/CD148 and an antisense long noncoding RNA in macrophages by proinflammatory stimuli. Dave RK1, Dinger ME, Andrew M, Askarian-Amiri M, Hume DA, Kellie S. Author information: 1The University of Queensland, Institute for Molecular Bioscience, Brisbane, Australia. Abstract PTPRJ/CD148 is a tyrosine phosphatase that has tumour suppressor-like activity. Quantitative PCR of various cells and tissues revealed that it is preferentially expressed in macrophage-enriched tissues. Within lymphoid tissues immunohistochemistry revealed that PTPRJ/CD148 co-localised with F4/80, indicating that macrophages most strongly express the protein. Macrophages express the highest basal level of ptprj, and this is elevated further by treatment with LPS and other Toll-like receptor ligands. In contrast, CSF-1 treatment reduced basal and stimulated Ptprj expression in human and mouse cells, and interferon also repressed Ptprj expression. We identified a 1006 nucleotide long noncoding RNA species, Ptprj-as1 that is transcribed antisense to Ptprj. Ptprj-as1 was highly expressed in macrophage-enriched tissue and was transiently induced by Toll-like receptor ligands with a similar time course to Ptprj. Finally, putative transcription factor binding sites in the promoter region of Ptprj were identified. PMCID: PMC3695918 Free PMC Article
	PMID: 23840844 [PubMed - indexed for MEDLINE]
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