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

Sent on Tuesday, 2010 Mar 30
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 - 6 of 6

1.	Nature. 2010 Feb 18;463(7283):943-7. Complete Khoisan and Bantu genomes from southern Africa. Schuster SC, Miller W, Ratan A, Tomsho LP, Giardine B, Kasson LR, Harris RS, Petersen DC, Zhao F, Qi J, Alkan C, Kidd JM, Sun Y, Drautz DI, Bouffard P, Muzny DM, Reid JG, Nazareth LV, Wang Q, Burhans R, Riemer C, Wittekindt NE, Moorjani P, Tindall EA, Danko CG, Teo WS, Buboltz AM, Zhang Z, Ma Q, Oosthuysen A, Steenkamp AW, Oostuisen H, Venter P, Gajewski J, Zhang Y, Pugh BF, Makova KD, Nekrutenko A, Mardis ER, Patterson N, Pringle TH, Chiaromonte F, Mullikin JC, Eichler EE, Hardison RC, Gibbs RA, Harkins TT, Hayes VM. Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Lab, University Park, Pennsylvania 16802, USA. scs@bx.psu.edu Comment in: Nature. 2010 Feb 18;463(7283):857. Nature. 2010 Mar 25;464(7288):487; author reply 487. The genetic structure of the indigenous hunter-gatherer peoples of southern Africa, the oldest known lineage of modern human, is important for understanding human diversity. Studies based on mitochondrial and small sets of nuclear markers have shown that these hunter-gatherers, known as Khoisan, San, or Bushmen, are genetically divergent from other humans. However, until now, fully sequenced human genomes have been limited to recently diverged populations. Here we present the complete genome sequences of an indigenous hunter-gatherer from the Kalahari Desert and a Bantu from southern Africa, as well as protein-coding regions from an additional three hunter-gatherers from disparate regions of the Kalahari. We characterize the extent of whole-genome and exome diversity among the five men, reporting 1.3 million novel DNA differences genome-wide, including 13,146 novel amino acid variants. In terms of nucleotide substitutions, the Bushmen seem to be, on average, more different from each other than, for example, a European and an Asian. Observed genomic differences between the hunter-gatherers and others may help to pinpoint genetic adaptations to an agricultural lifestyle. Adding the described variants to current databases will facilitate inclusion of southern Africans in medical research efforts, particularly when family and medical histories can be correlated with genome-wide data.
	PMID: 20164927 [PubMed - indexed for MEDLINE]
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	Publication Types: Comparative Study Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. MeSH Terms: African Continental Ancestry Group/genetics* Asian Continental Ancestry Group/genetics Ethnic Groups/genetics* European Continental Ancestry Group/genetics Exons/genetics Genetics, Medical Genome, Human/genetics* Humans Phylogeny Polymorphism, Single Nucleotide/genetics South Africa/ethnology Secondary Source ID: GEO/GSE19048 Grant Support: R01GM087472/GM/NIGMS NIH HHS/United States

2.	Nature. 2010 Feb 18;463(7283):899-905. The landscape of somatic copy-number alteration across human cancers. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M. Cancer Program and Medical and Population Genetics Group, The Broad Institute of M.I.T. and Harvard, 7 Cambridge Center. A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we present high-resolution analyses of somatic copy-number alterations (SCNAs) from 3,131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-kappaBeta pathway. We show that cancer cells containing amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend on the expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types. PMCID: PMC2826709 [Available on 2010/8/18]
	PMID: 20164920 [PubMed - indexed for MEDLINE]
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	Publication Types: Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't MeSH Terms: Apoptosis/genetics Cell Line, Tumor Cell Survival/genetics DNA Copy Number Variations/genetics* Gene Amplification/genetics Gene Dosage/genetics* Genomics Humans Multigene Family/genetics Neoplasms/classification Neoplasms/genetics* Neoplasms/pathology Proto-Oncogene Proteins c-bcl-2/genetics Signal Transduction bcl-X Protein/genetics Substances: BCL2L1 protein, human Proto-Oncogene Proteins c-bcl-2 bcl-X Protein myeloid cell leukemia sequence 1 protein Secondary Source ID: GEO/GSE19399 Grant Support: K08CA122833/CA/NCI NIH HHS/United States P01CA 098101/CA/NCI NIH HHS/United States P01CA085859/CA/NCI NIH HHS/United States P50CA90578/CA/NCI NIH HHS/United States R01CA109038/CA/NCI NIH HHS/United States R01CA109467/CA/NCI NIH HHS/United States Howard Hughes Medical Institute/United States

3.	Nature. 2010 Feb 18;463(7283):877. Outcry stopped approved pig study of avalanche survival. Brugger H, Paal P, Falk M.
	PMID: 20164903 [PubMed - indexed for MEDLINE]
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	Publication Types: Letter MeSH Terms: Altitude Anesthesia Animal Experimentation/standards Animal Rights* Animals Avalanches* Disasters* Europe Models, Animal* Public Opinion* Snow Survival/physiology* Swine/physiology*

4.	Nature. 2010 Feb 18;463(7283):859. Genomics firms turn to other markets. Hayden EC.
	PMID: 20164890 [PubMed - indexed for MEDLINE]
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	Publication Types: News MeSH Terms: Costs and Cost Analysis Genome, Human Genomics/economics* Genomics/instrumentation Genomics/trends* Humans Rhodopseudomonas/genetics Rhodopseudomonas/metabolism Sequence Analysis, DNA/economics* Sequence Analysis, DNA/instrumentation Sequence Analysis, DNA/trends*

5.	Nature. 2010 Feb 18;463(7283):858. How accurate are cancer cell lines? Borrell B.
	PMID: 20164888 [PubMed - indexed for MEDLINE]
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	Publication Types: News MeSH Terms: Cell Line, Tumor/metabolism* Genetics, Medical/methods* Genetics, Medical/trends* Genomics/methods* Genomics/trends* Humans Neoplasms/genetics* Neoplasms/pathology* Reproducibility of Results Sequence Analysis, DNA/trends

6.	Nature. 2010 Feb 18;463(7283):857. Africa yields two full human genomes. Ledford H. Comment on: Nature. 2010 Feb 18;463(7283):943-7.
	PMID: 20164887 [PubMed - indexed for MEDLINE]
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	Publication Types: Comment News MeSH Terms: African Continental Ancestry Group/genetics* Ethnic Groups/genetics* Genetic Variation/genetics Genome, Human/genetics* Genomics*/trends Humans Malaria, Vivax/genetics Male Minority Groups Phylogeny South Africa/ethnology