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Nature genetics 17건

  1. [해외논문]   Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error   SCI SCIE

    Tedja, Milly S. , Wojciechowski, Robert , Hysi, Pirro G. , Eriksson, Nicholas , Furlotte, Nicholas A. , Verhoeven, Virginie J. M. , Iglesias, Adriana I. , Meester-Smoor, Magda A. , Tompson, Stuart W. , Fan, Qiao , Khawaja, Anthony P. , Cheng, Ching-Yu , Hö , hn, René , , Yamashiro, Kenji , Wenocur, Adam , Grazal, Clare , Haller, Toomas , Metspalu, Andres , Wedenoja, Juho , Jonas, Jost B. , Wang, Ya Xing , Xie, Jing , Mitchell, Paul , Foster, Paul J. , Klein, Barbara E. K. , Klein, Ronald , Paterson, Andrew D. , Hosseini, S. Mohsen , Shah, Rupal L. , Williams, Cathy , Teo, Yik Ying , Tham, Yih Chung , Gupta, Preeti , Zhao, Wanting , Shi, Yuan , Saw, Woei-Yuh , Tai, E-Shyong , Sim, Xue Ling , Huffman, Jennifer E. , Polaš , ek, Ozren , Hayward, Caroline , Bencic, Goran , Rudan, Igor , Wilson, James F. , Joshi, Peter K. , Tsujikawa, Akitaka , Matsuda, Fumihiko , Whisenhunt, Kristina N. , Zeller, Tanja , van der Spek, Peter J. , Haak, Roxanna , Meijers-Heijboer, Hanne , van Leeuwe
    Nature genetics v.50 no.6 ,pp. 834 - 848 , 2018 , 1061-4036 ,

    초록

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  2. [해외논문]   Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for EsxW Beijing variant in Vietnam   SCI SCIE

    Holt, Kathryn E (Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia ) , McAdam, Paul (Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia ) , Thai, Phan Vuong Khac (Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, District 5, Viet Nam ) , Thuong, Nguyen Thuy Thuong (Oxford University Clinical Research Unit, Ho Chi Minh City, District 5, Viet Nam ) , Ha, Dang Thi Minh (Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, District 5, Viet Nam ) , Lan, Nguyen Ngoc (Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, District 5, Viet Nam ) , Lan, Nguyen Huu (Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, District 5, Viet Nam ) , Nhu, Nguyen Thi Quynh (Oxford University Clinical Research Unit, Ho Chi Minh City, District 5, Viet Nam ) , Hai, Hoang Thanh (Oxford University Clinical Research Unit, Ho Chi Minh City, District 5, Viet Nam ) , Ha, Vu Thi Ngoc (Oxford Univer) , Thwaites, Guy , Edwards, David J , Nath, Artika P , Pham, Kym , Ascher, David B , Farrar, Jeremy , Khor, Chiea Chuen , Teo, Yik Ying , Inouye, Michael , Caws, Maxine , Dunstan, Sarah J
    Nature genetics v.50 no.6 ,pp. 849 - 856 , 2018 , 1061-4036 ,

    초록

    To examine transmission dynamics of Mtb isolated from TB patients in Ho Chi Minh City, Vietnam we sequenced whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data reveal an underlying burden of disease caused by endemic Mtb Lineage 1 associated with activation of long-term latent infection, and a three-fold higher burden associated with more recently introduced Beijing lineage and Lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than endemic Lineage 1 Mtb . Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify a mutation in the ESX-5 type VII secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  3. [해외논문]   A genome-wide cross trait analysis from UK Biobank highlights the shared genetic architecture of asthma and allergic diseases   SCI SCIE

    Zhu, Zhaozhong (Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA ) , Lee, Phil H. (Center for Genomic Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA ) , Chaffin, Mark D. (Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA ) , Chung, Wonil (Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA ) , Loh, Po-Ru (Program in Genetic Epidemiology and Statistical Genetics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA ) , Lu, Quan (Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA ) , Christiani, David C. (Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachuset) , Liang, Liming
    Nature genetics v.50 no.6 ,pp. 857 - 864 , 2018 , 1061-4036 ,

    초록

    Clinical and epidemiological data suggest that asthma and allergic diseases are associated and may share a common genetic etiology. We analyzed genome-wide single-nucleotide polymorphism (SNP) data for asthma and allergic diseases in 33,593 cases and 76,768 controls of European ancestry from the UK Biobank. Two publicly available independent genome wide association studies (GWAS) were used for replication. We have found a strong genome-wide genetic correlation between asthma and allergic diseases ( r g = 0.75, P = 6.84×10 −62 ). Cross trait analysis identified 38 genome-wide significant loci, including 7 novel shared loci. Computational analysis showed that shared genetic loci are enriched in immune/inflammatory systems and tissues with epithelium cells. Our work identifies common genetic architectures shared between asthma and allergy and will help to advance our understanding of the molecular mechanisms underlying co-morbid asthma and allergic diseases.

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  4. [해외논문]   Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family   SCI SCIE

    Zhou, Ming (Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA. ) , Palanca, Ana Marie S. (Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA. ) , Law, Julie A. (Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.)
    Nature genetics v.50 no.6 ,pp. 865 - 873 , 2018 , 1061-4036 ,

    초록

    DNA methylation is essential for gene regulation, transposon silencing, and imprinting. Although the generation of specific DNA methylation patterns is critical for these processes, how methylation is regulated at individual loci remains unclear. Here we show that a family of four putative chromatin remodeling factors, CLASSY (CLSY) 1–4, are required for both locus-specific and global regulation of DNA methylation in Arabidopsis. Mechanistically, these factors act in connection with RNA polymerase-IV (Pol-IV) to control the production of 24-nucleotide small interfering RNAs (24nt-siRNAs), which guide DNA methylation. Individually, the CLSYs regulate Pol-IV-chromatin association and 24nt-siRNA production at thousands of distinct loci, and together, they regulate essentially all 24nt-siRNAs. Depending on the CLSYs involved, this regulation relies on different repressive chromatin modifications to facilitate locus-specific control of DNA methylation. Given the conservation between methylation systems in plants and mammals, analogous pathways likely operate in a broad range of organisms.

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  5. [해외논문]   Multiplex Assessment of Protein Variant Abundance by Massively Parallel Sequencing   SCI SCIE

    Matreyek, Kenneth A. (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Starita, Lea M. (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Stephany, Jason J. (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Martin, Beth (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Chiasson, Melissa A. (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Gray, Vanessa E. (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Kircher, Martin (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Khechaduri, Arineh (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Dines, Jennifer N. (Department of Medical Genetics, University of Washington, Seattle, Washington, USA ) , Hause, Ronald J. (Department of Genome Sciences, University of Washington, Seattle, Washington, USA ) , Bhatia, Smita (School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA ) , Evans, William E. (Department of Pharmaceutical Sciences, St. Jude Children's Research Hospi) , Relling, Mary V. , Yang, Wenjian , Shendure, Jay , Fowler, Douglas M.
    Nature genetics v.50 no.6 ,pp. 874 - 882 , 2018 , 1061-4036 ,

    초록

    Determining the pathogenicity of genetic variants is a critical challenge, and functional assessment is often the only option. Experimentally characterizing millions of possible missense variants in thousands of clinically important genes requires generalizable, scalable assays. We describe Variant Abundance by Massively Parallel Sequencing (VAMP-seq), which measures the effects of thousands of missense variants of a protein on intracellular abundance simultaneously. We apply VAMP-seq to quantify the abundance of 7,801 single amino acid variants of PTEN and TPMT, proteins in which functional variants are clinically actionable. We identify 1,138 PTEN and 777 TPMT variants that result in low protein abundance, and may be pathogenic or alter drug metabolism, respectively. We observe selection for low-abundance PTEN variants in cancer, and reveal that p.Pro38Ser, which accounts for ~10% of PTEN missense variants in melanoma, functions via a dominant negative mechanism. Finally, we demonstrate that VAMP-seq is applicable to other genes, highlighting its generalizability.

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    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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  6. [해외논문]   UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs   SCI SCIE

    Gozdecka, Malgorzata (Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK ) , Meduri, Eshwar (Wellcome Trust–MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK ) , Mazan, Milena (Wellcome Trust–MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK ) , Tzelepis, Konstantinos (Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK ) , Dudek, Monika (Wellcome Trust–MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK ) , Knights, Andrew J. (Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK ) , Pardo, Mercedes (Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK ) , Yu, Lu (Genomics of Gene Regulation, Wellcome Trust Sanger Institute, Hinxton, UK ) , Choudhary, Jyoti S. (Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK ) , Metzakopian, Emmanouil (Proteomic Mass Spectrometry, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK ) , Iyer, Vivek (Proteomic Mass Spectrometry, Wellcome Trust S) , Yun, Haiyang , Park, Naomi , Varela, Ignacio , Bautista, Ruben , Collord, Grace , Dovey, Oliver , Garyfallos, Dimitrios A. , De Braekeleer, Etienne , Kondo, Saki , Cooper, Jonathan , Gö , ttgens, Berthold , Bullinger, Lars , Northcott, Paul A. , Adams, David , Vassiliou, George S. , Huntly, Brian J. P.
    Nature genetics v.50 no.6 ,pp. 883 - 894 , 2018 , 1061-4036 ,

    초록

    The histone H3 Lys27-specific demethylase UTX (or KDM6A) is targeted by loss-of-function mutations in multiple cancers. Here, we demonstrate that UTX suppresses myeloid leukemogenesis through noncatalytic functions, a property shared with its catalytically inactive Y-chromosome paralog, UTY (or KDM6C). In keeping with this, we demonstrate concomitant loss/mutation of KDM6A (UTX) and UTY in multiple human cancers. Mechanistically, global genomic profiling showed only minor changes in H3K27me3 but significant and bidirectional alterations in H3K27ac and chromatin accessibility; a predominant loss of H3K4me1 modifications; alterations in ETS and GATA-factor binding; and altered gene expression after Utx loss. By integrating proteomic and genomic analyses, we link these changes to UTX regulation of ATP-dependent chromatin remodeling, coordination of the COMPASS complex and enhanced pioneering activity of ETS factors during evolution to AML. Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

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  7. [해외논문]   Quantification of subclonal selection in cancer from bulk sequencing data   SCI SCIE

    Williams, Marc J. (Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK ) , Werner, Benjamin (Department of Cell and Developmental Biology, University College London, London, UK ) , Heide, Timon (Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK ) , Curtis, Christina (Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK ) , Barnes, Chris P. (Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK ) , Sottoriva, Andrea (Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA, USA ) , Graham, Trevor A. (Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA )
    Nature genetics v.50 no.6 ,pp. 895 - 903 , 2018 , 1061-4036 ,

    초록

    Subclonal architectures are prevalent across cancer types. However, the temporal evolutionary dynamics that produce tumor subclones remain unknown. Here we measure clone dynamics in human cancers by using computational modeling of subclonal selection and theoretical population genetics applied to high-throughput sequencing data. Our method determined the detectable subclonal architecture of tumor samples and simultaneously measured the selective advantage and time of appearance of each subclone. We demonstrate the accuracy of our approach and the extent to which evolutionary dynamics are recorded in the genome. Application of our method to high-depth sequencing data from breast, gastric, blood, colon and lung cancer samples, as well as metastatic deposits, showed that detectable subclones under selection, when present, consistently emerged early during tumor growth and had a large fitness advantage (>20%). Our quantitative framework provides new insight into the evolutionary trajectories of human cancers and facilitates predictive measurements in individual tumors from widely available sequencing data.

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    회원님의 원문열람 권한에 따라 열람이 불가능 할 수 있으며 권한이 없는 경우 해당 사이트의 정책에 따라 회원가입 및 유료구매가 필요할 수 있습니다.이동하는 사이트에서의 모든 정보이용은 NDSL과 무관합니다.

    NDSL에서는 해당 원문을 복사서비스하고 있습니다. 아래의 원문복사신청 또는 장바구니담기를 통하여 원문복사서비스 이용이 가능합니다.

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