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

Sent on Tuesday, 2015 January 13
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 Aug;46(8):818-25. doi: 10.1038/ng.3021. Epub 2014 Jun 29. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Genome of the Netherlands Consortium. Collaborators: Francioli LC, Menelaou A, Pulit SL, van Dijk F, Palamara PF, Elbers CC, Neerincx PB, Ye K, Guryev V, Kloosterman WP, Deelen P, Abdellaoui A, van Leeuwen EM, van Oven M, Vermaat M, Li M, Laros JF, Karssen LC, Kanterakis A, Amin N, Hottenga JJ, Lameijer EW, Kattenberg M, Dijkstra M, Byelas H, van Setten J, van Schaik BD, Bot J, Nijman IJ, Renkens I, Marschall T, Schönhuth A, Hehir-Kwa JY, Handsaker RE, Polak P, Sohail M, Vuzman D, Hormozdiari F, van Enckevort D, Mei H, Koval V, Moed MH, van der Velde KJ, Rivadeneira F, Estrada K, Medina-Gomez C, Isaacs A, McCarroll SA, Beekman M, de Craen AJ, Suchiman HE, Hofman A, Oostra B, Uitterlinden AG, Willemsen G, Study LC, Platteel M, Veldink JH, van den Berg LH, Pitts SJ, Potluri S, Sundar P, Cox DR, Sunyaev SR, den Dunnen JT, Stoneking M, de Knijff P, Kayser M, Li Q, Li Y, Du Y, Chen R, Cao H, Li N, Cao S, Wang J, Bovenberg JA, Pe'er I, Slagboom PE, van Duijn CM, Boomsma DI, van Ommen GJ, de Bakker PI, Swertz MA, Wijmenga C. Abstract Whole-genome sequencing enables complete characterization of genetic variation, but geographic clustering of rare alleles demands many diverse populations be studied. Here we describe the Genome of the Netherlands (GoNL) Project, in which we sequenced the whole genomes of 250 Dutch parent-offspring families and constructed a haplotype map of 20.4 million single-nucleotide variants and 1.2 million insertions and deletions. The intermediate coverage (∼13×) and trio design enabled extensive characterization of structural variation, including midsize events (30-500 bp) previously poorly catalogued and de novo mutations. We demonstrate that the quality of the haplotypes boosts imputation accuracy in independent samples, especially for lower frequency alleles. Population genetic analyses demonstrate fine-scale structure across the country and support multiple ancient migrations, consistent with historical changes in sea level and flooding. The GoNL Project illustrates how single-population whole-genome sequencing can provide detailed characterization of genetic variation and may guide the design of future population studies.
	PMID: 24974849 [PubMed - indexed for MEDLINE]
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2.	Nat Genet. 2014 Aug;46(8):919-25. doi: 10.1038/ng.3015. Epub 2014 Jun 22. Inferring human population size and separation history from multiple genome sequences. Schiffels S1, Durbin R1. Comment in Human evolution: multigenome coalescence for modern demographic insights. [Nat Rev Genet. 2014] Human evolution: multigenome coalescence for modern demographic insights.Burgess DJ. Nat Rev Genet. 2014 Aug; 15(8):514. Epub 2014 Jul 8. Abstract The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model ancestral relationships under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20,000-30,000 years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings. The multiple sequentially Markovian coalescent (MSMC) analyzes the observed pattern of mutations in multiple individuals, focusing on the first coalescence between any two individuals. Results from applying MSMC to genome sequences from nine populations across the world suggest that the genetic separation of non-African ancestors from African Yoruban ancestors started long before 50,000 years ago and give information about human population history as recent as 2,000 years ago, including the bottleneck in the peopling of the Americas and separations within Africa, East Asia and Europe. PMCID: PMC4116295 [Available on 2015/2/1]
	PMID: 24952747 [PubMed - indexed for MEDLINE]
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3.	Nat Genet. 2014 Aug;46(8):866-71. doi: 10.1038/ng.3006. Epub 2014 Jun 22. The genomic landscape of nasopharyngeal carcinoma. Lin DC1, Meng X2, Hazawa M3, Nagata Y4, Varela AM3, Xu L3, Sato Y4, Liu LZ3, Ding LW3, Sharma A3, Goh BC5, Lee SC5, Petersson BF6, Yu FG7, Macary P8, Oo MZ8, Ha CS9, Yang H10, Ogawa S11, Loh KS12, Koeffler HP13. Comment in Fingerprints of Epstein-Barr virus in nasopharyngeal carcinoma. [Nat Genet. 2014] Fingerprints of Epstein-Barr virus in nasopharyngeal carcinoma.West RB. Nat Genet. 2014 Aug; 46(8):809-10. Abstract Nasopharyngeal carcinoma (NPC) has extremely skewed ethnic and geographic distributions, is poorly understood at the genetic level and is in need of effective therapeutic approaches. Here we determined the mutational landscape of 128 cases with NPC using whole-exome and targeted deep sequencing, as well as SNP array analysis. These approaches revealed a distinct mutational signature and nine significantly mutated genes, many of which have not been implicated previously in NPC. Notably, integrated analysis showed enrichment of genetic lesions affecting several important cellular processes and pathways, including chromatin modification, ERBB-PI3K signaling and autophagy machinery. Further functional studies suggested the biological relevance of these lesions to the NPC malignant phenotype. In addition, we uncovered a number of new druggable candidates because of their genomic alterations. Together our study provides a molecular basis for a comprehensive understanding of, and exploring new therapies for, NPC.
	PMID: 24952746 [PubMed - indexed for MEDLINE]
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