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

Sent on Wednesday, 2014 May 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 - 2 of 2

1.	Nat Genet. 2014 Apr;46(4):409-15. doi: 10.1038/ng.2924. Epub 2014 Mar 16. Ancestry estimation and control of population stratification for sequence-based association studies. Wang C1, Zhan X2, Bragg-Gresham J3, Kang HM3, Stambolian D4, Chew EY5, Branham KE6, Heckenlively J6; FUSION Study, Fulton R7, Wilson RK7, Mardis ER7, Lin X8, Swaroop A9, Zöllner S10, Abecasis GR3. Author information: 1 1] Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA. [2] Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA. [3]. 21] Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA. [2]. 3Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA. 4Department of Ophthalmology, University of Pennsylvania Medical School, Philadelphia, Pennsylvania, USA. 5Division of Epidemiology and Clinical Research, National Eye Institute, Bethesda, Maryland, USA. 6Department of Ophthalmology, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, USA. 7Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA. 8Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA. 9Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, Bethesda, Maryland, USA. 101] Department of Biostatistics, Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, Michigan, USA. [2] Department of Psychiatry, University of Michigan Medical School, Ann Arbor, Michigan, USA. Abstract Estimating individual ancestry is important in genetic association studies where population structure leads to false positive signals, although assigning ancestry remains challenging with targeted sequence data. We propose a new method for the accurate estimation of individual genetic ancestry, based on direct analysis of off-target sequence reads, and implement our method in the publicly available LASER software. We validate the method using simulated and empirical data and show that the method can accurately infer worldwide continental ancestry when used with sequencing data sets with whole-genome shotgun coverage as low as 0.001×. For estimates of fine-scale ancestry within Europe, the method performs well with coverage of 0.1×. On an even finer scale, the method improves discrimination between exome-sequenced study participants originating from different provinces within Finland. Finally, we show that our method can be used to improve case-control matching in genetic association studies and to reduce the risk of spurious findings due to population structure.
	PMID: 24633160 [PubMed - indexed for MEDLINE]
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2.	Nat Genet. 2014 Apr;46(4):329-35. doi: 10.1038/ng.2900. Epub 2014 Feb 16. Recurrent somatic mutations of PTPN1 in primary mediastinal B cell lymphoma and Hodgkin lymphoma. Gunawardana J1, Chan FC2, Telenius A3, Woolcock B3, Kridel R1, Tan KL3, Ben-Neriah S3, Mottok A3, Lim RS3, Boyle M3, Rogic S4, Rimsza LM5, Guiter C6, Leroy K7, Gaulard P7, Haioun C8, Marra MA9, Savage KJ3, Connors JM3, Shah SP10, Gascoyne RD1, Steidl C1. Author information: 11] Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada. [2] Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. 21] Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada. [2] Bioinformatics Training Program, University of British Columbia, Vancouver, British Columbia, Canada. 3Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada. 4Centre for High-Throughput Biology, University of British Columbia, Vancouver, British Columbia, Canada. 5Department of Pathology, University of Arizona, Tucson, Arizona, USA. 6INSERM U955, Créteil, France. 71] INSERM U955, Créteil, France. [2] Université Paris Est, Créteil, France. [3] Département de Pathologie-Service d'Hématologie-Plateforme de Ressources Biologiques, Groupe Hospitalier Henri-MONDOR, Assistance Publique-Hôpitaux de Paris, Créteil, France. 81] Université Paris Est, Créteil, France. [2] Département de Pathologie-Service d'Hématologie-Plateforme de Ressources Biologiques, Groupe Hospitalier Henri-MONDOR, Assistance Publique-Hôpitaux de Paris, Créteil, France. 91] Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada. [2] Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada. 10Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada. Abstract Classical Hodgkin lymphoma and primary mediastinal B cell lymphoma (PMBCL) are related lymphomas sharing pathological, molecular and clinical characteristics. Here we discovered by whole-genome and whole-transcriptome sequencing recurrent somatic coding-sequence mutations in the PTPN1 gene. Mutations were found in 6 of 30 (20%) Hodgkin lymphoma cases, in 6 of 9 (67%) Hodgkin lymphoma-derived cell lines, in 17 of 77 (22%) PMBCL cases and in 1 of 3 (33%) PMBCL-derived cell lines, consisting of nonsense, missense and frameshift mutations. We demonstrate that PTPN1 mutations lead to reduced phosphatase activity and increased phosphorylation of JAK-STAT pathway members. Moreover, silencing of PTPN1 by RNA interference in Hodgkin lymphoma cell line KM-H2 resulted in hyperphosphorylation and overexpression of downstream oncogenic targets. Our data establish PTPN1 mutations as new drivers in lymphomagenesis.
	PMID: 24531327 [PubMed - indexed for MEDLINE]
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