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Nature Genetics

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https://www.readbyqxmd.com/read/30237445/author-correction-the-rate-of-meiotic-gene-conversion-varies-by-sex-and-age
#1
Bjarni V Halldorsson, Marteinn T Hardarson, Birte Kehr, Unnur Styrkarsdottir, Arnaldur Gylfason, Gudmar Thorleifsson, Florian Zink, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Patrick Sulem, Gisli Masson, Unnur Thorsteinsdottir, Agnar Helgason, Augustine Kong, Daniel F Gudbjartsson, Kari Stefansson
In the version of this article published, statements about the impact of insertions and deletions on gene conversions were incorrect. We reported a bias toward deletions, whereas in fact the bias was toward insertions. We are deeply indebted to Laurent Duret and Brice Letcher for noticing this mistake in our manuscript. The following statements are incorrect in the published manuscript.
September 20, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224653/genetic-analysis-of-over-1-million-people-identifies-535-new-loci-associated-with-blood-pressure-traits
#2
Evangelos Evangelou, Helen R Warren, David Mosen-Ansorena, Borbala Mifsud, Raha Pazoki, He Gao, Georgios Ntritsos, Niki Dimou, Claudia P Cabrera, Ibrahim Karaman, Fu Liang Ng, Marina Evangelou, Katarzyna Witkowska, Evan Tzanis, Jacklyn N Hellwege, Ayush Giri, Digna R Velez Edwards, Yan V Sun, Kelly Cho, J Michael Gaziano, Peter W F Wilson, Philip S Tsao, Csaba P Kovesdy, Tonu Esko, Reedik Mägi, Lili Milani, Peter Almgren, Thibaud Boutin, Stéphanie Debette, Jun Ding, Franco Giulianini, Elizabeth G Holliday, Anne U Jackson, Ruifang Li-Gao, Wei-Yu Lin, Jian'an Luan, Massimo Mangino, Christopher Oldmeadow, Bram Peter Prins, Yong Qian, Muralidharan Sargurupremraj, Nabi Shah, Praveen Surendran, Sébastien Thériault, Niek Verweij, Sara M Willems, Jing-Hua Zhao, Philippe Amouyel, John Connell, Renée de Mutsert, Alex S F Doney, Martin Farrall, Cristina Menni, Andrew D Morris, Raymond Noordam, Guillaume Paré, Neil R Poulter, Denis C Shields, Alice Stanton, Simon Thom, Gonçalo Abecasis, Najaf Amin, Dan E Arking, Kristin L Ayers, Caterina M Barbieri, Chiara Batini, Joshua C Bis, Tineka Blake, Murielle Bochud, Michael Boehnke, Eric Boerwinkle, Dorret I Boomsma, Erwin P Bottinger, Peter S Braund, Marco Brumat, Archie Campbell, Harry Campbell, Aravinda Chakravarti, John C Chambers, Ganesh Chauhan, Marina Ciullo, Massimiliano Cocca, Francis Collins, Heather J Cordell, Gail Davies, Martin H de Borst, Eco J de Geus, Ian J Deary, Joris Deelen, Fabiola Del Greco M, Cumhur Yusuf Demirkale, Marcus Dörr, Georg B Ehret, Roberto Elosua, Stefan Enroth, A Mesut Erzurumluoglu, Teresa Ferreira, Mattias Frånberg, Oscar H Franco, Ilaria Gandin, Paolo Gasparini, Vilmantas Giedraitis, Christian Gieger, Giorgia Girotto, Anuj Goel, Alan J Gow, Vilmundur Gudnason, Xiuqing Guo, Ulf Gyllensten, Anders Hamsten, Tamara B Harris, Sarah E Harris, Catharina A Hartman, Aki S Havulinna, Andrew A Hicks, Edith Hofer, Albert Hofman, Jouke-Jan Hottenga, Jennifer E Huffman, Shih-Jen Hwang, Erik Ingelsson, Alan James, Rick Jansen, Marjo-Riitta Jarvelin, Roby Joehanes, Åsa Johansson, Andrew D Johnson, Peter K Joshi, Pekka Jousilahti, J Wouter Jukema, Antti Jula, Mika Kähönen, Sekar Kathiresan, Bernard D Keavney, Kay-Tee Khaw, Paul Knekt, Joanne Knight, Ivana Kolcic, Jaspal S Kooner, Seppo Koskinen, Kati Kristiansson, Zoltan Kutalik, Maris Laan, Marty Larson, Lenore J Launer, Benjamin Lehne, Terho Lehtimäki, David C M Liewald, Li Lin, Lars Lind, Cecilia M Lindgren, YongMei Liu, Ruth J F Loos, Lorna M Lopez, Yingchang Lu, Leo-Pekka Lyytikäinen, Anubha Mahajan, Chrysovalanto Mamasoula, Jaume Marrugat, Jonathan Marten, Yuri Milaneschi, Anna Morgan, Andrew P Morris, Alanna C Morrison, Peter J Munson, Mike A Nalls, Priyanka Nandakumar, Christopher P Nelson, Teemu Niiranen, Ilja M Nolte, Teresa Nutile, Albertine J Oldehinkel, Ben A Oostra, Paul F O'Reilly, Elin Org, Sandosh Padmanabhan, Walter Palmas, Aarno Palotie, Alison Pattie, Brenda W J H Penninx, Markus Perola, Annette Peters, Ozren Polasek, Peter P Pramstaller, Quang Tri Nguyen, Olli T Raitakari, Meixia Ren, Rainer Rettig, Kenneth Rice, Paul M Ridker, Janina S Ried, Harriëtte Riese, Samuli Ripatti, Antonietta Robino, Lynda M Rose, Jerome I Rotter, Igor Rudan, Daniela Ruggiero, Yasaman Saba, Cinzia F Sala, Veikko Salomaa, Nilesh J Samani, Antti-Pekka Sarin, Reinhold Schmidt, Helena Schmidt, Nick Shrine, David Siscovick, Albert V Smith, Harold Snieder, Siim Sõber, Rossella Sorice, John M Starr, David J Stott, David P Strachan, Rona J Strawbridge, Johan Sundström, Morris A Swertz, Kent D Taylor, Alexander Teumer, Martin D Tobin, Maciej Tomaszewski, Daniela Toniolo, Michela Traglia, Stella Trompet, Jaakko Tuomilehto, Christophe Tzourio, André G Uitterlinden, Ahmad Vaez, Peter J van der Most, Cornelia M van Duijn, Anne-Claire Vergnaud, Germaine C Verwoert, Veronique Vitart, Uwe Völker, Peter Vollenweider, Dragana Vuckovic, Hugh Watkins, Sarah H Wild, Gonneke Willemsen, James F Wilson, Alan F Wright, Jie Yao, Tatijana Zemunik, Weihua Zhang, John R Attia, Adam S Butterworth, Daniel I Chasman, David Conen, Francesco Cucca, John Danesh, Caroline Hayward, Joanna M M Howson, Markku Laakso, Edward G Lakatta, Claudia Langenberg, Olle Melander, Dennis O Mook-Kanamori, Colin N A Palmer, Lorenz Risch, Robert A Scott, Rodney J Scott, Peter Sever, Tim D Spector, Pim van der Harst, Nicholas J Wareham, Eleftheria Zeggini, Daniel Levy, Patricia B Munroe, Christopher Newton-Cheh, Morris J Brown, Andres Metspalu, Adriana M Hung, Christopher J O'Donnell, Todd L Edwards, Bruce M Psaty, Ioanna Tzoulaki, Michael R Barnes, Louise V Wain, Paul Elliott, Mark J Caulfield
High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also highlight shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224652/publisher-correction-the-sea-lamprey-germline-genome-provides-insights-into-programmed-genome-rearrangement-and-vertebrate-evolution
#3
Jeramiah J Smith, Nataliya Timoshevskaya, Chengxi Ye, Carson Holt, Melissa C Keinath, Hugo J Parker, Malcolm E Cook, Jon E Hess, Shawn R Narum, Francesco Lamanna, Henrik Kaessmann, Vladimir A Timoshevskiy, Courtney K M Waterbury, Cody Saraceno, Leanne M Wiedemann, Sofia M C Robb, Carl Baker, Evan E Eichler, Dorit Hockman, Tatjana Sauka-Spengler, Mark Yandell, Robb Krumlauf, Greg Elgar, Chris T Amemiya
When published, this article did not initially appear open access. This error has been corrected, and the open access status of the paper is noted in all versions of the paper. Additionally, affiliation 16 denoting equal contribution was missing from author Robb Krumlauf in the PDF originally published. This error has also been corrected.
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224651/mutations-in-recql-are-not-associated-with-breast-cancer-risk-in-an-australian-population
#4
LETTER
Na Li, Simone M Rowley, David L Goode, Kaushalya C Amarasinghe, Simone McInerny, Lisa Devereux, Michelle W Wong-Brown, Richard Lupat, Jue Er Amanda Lee, Siobhan Hughes, Ella R Thompson, Magnus Zethoven, Jason Li, Alison H Trainer, Kylie L Gorringe, Rodney J Scott, Paul A James, Ian G Campbell
No abstract text is available yet for this article.
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224650/promoter-bivalency-favors-an-open-chromatin-architecture-in-embryonic-stem-cells
#5
Glòria Mas, Enrique Blanco, Cecilia Ballaré, Miriam Sansó, Yannick G Spill, Deqing Hu, Yuki Aoi, François Le Dily, Ali Shilatifard, Marc A Marti-Renom, Luciano Di Croce
In embryonic stem cells (ESCs), developmental gene promoters are characterized by their bivalent chromatin state, with simultaneous modification by MLL2 and Polycomb complexes. Although essential for embryogenesis, bivalency is functionally not well understood. Here, we show that MLL2 plays a central role in ESC genome organization. We generate a catalog of bona fide bivalent genes in ESCs and demonstrate that loss of MLL2 leads to increased Polycomb occupancy. Consequently, promoters lose accessibility, long-range interactions are redistributed, and ESCs fail to differentiate...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224649/fine-mapping-and-functional-studies-highlight-potential-causal-variants-for-rheumatoid-arthritis-and-type-1-diabetes
#6
Harm-Jan Westra, Marta Martínez-Bonet, Suna Onengut-Gumuscu, Annette Lee, Yang Luo, Nikola Teslovich, Jane Worthington, Javier Martin, Tom Huizinga, Lars Klareskog, Solbritt Rantapaa-Dahlqvist, Wei-Min Chen, Aaron Quinlan, John A Todd, Steve Eyre, Peter A Nigrovic, Peter K Gregersen, Stephen S Rich, Soumya Raychaudhuri
To define potentially causal variants for autoimmune disease, we fine-mapped1,2 76 rheumatoid arthritis (11,475 cases, 15,870 controls)3 and type 1 diabetes loci (9,334 cases, 11,111 controls)4 . After sequencing 799 1-kilobase regulatory (H3K4me3) regions within these loci in 568 individuals, we observed accurate imputation for 89% of common variants. We defined credible sets of ≤5 causal variants at 5 rheumatoid arthritis and 10 type 1 diabetes loci. We identified potentially causal missense variants at DNASE1L3, PTPN22, SH2B3, and TYK2, and noncoding variants at MEG3, CD28-CTLA4, and IL2RA...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224648/reply-to-mutations-in-recql-are-not-associated-with-breast-cancer-risk-in-an-australian-population
#7
LETTER
Humayun Ahmed, Jordan Lerner-Ellis, Cezary Cybulski, Kelly Metcalfe, Jan Lubiński, Steven A Narod, Mohammad R Akbari
No abstract text is available yet for this article.
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224647/de-novo-mutations-in-msl3-cause-an-x-linked-syndrome-marked-by-impaired-histone-h4-lysine-16-acetylation
#8
M Felicia Basilicata, Ange-Line Bruel, Giuseppe Semplicio, Claudia Isabelle Keller Valsecchi, Tuğçe Aktaş, Yannis Duffourd, Tobias Rumpf, Jenny Morton, Iben Bache, Witold G Szymanski, Christian Gilissen, Olivier Vanakker, Katrin Õunap, Gerhard Mittler, Ineke van der Burgt, Salima El Chehadeh, Megan T Cho, Rolph Pfundt, Tiong Yang Tan, Maria Kirchhoff, Björn Menten, Sarah Vergult, Kristin Lindstrom, André Reis, Diana S Johnson, Alan Fryer, Victoria McKay, Richard B Fisher, Christel Thauvin-Robinet, David Francis, Tony Roscioli, Sander Pajusalu, Kelly Radtke, Jaya Ganesh, Han G Brunner, Meredith Wilson, Laurence Faivre, Vera M Kalscheuer, Julien Thevenon, Asifa Akhtar
The etiological spectrum of ultra-rare developmental disorders remains to be fully defined. Chromatin regulatory mechanisms maintain cellular identity and function, where misregulation may lead to developmental defects. Here, we report pathogenic variations in MSL3, which encodes a member of the chromatin-associated male-specific lethal (MSL) complex responsible for bulk histone H4 lysine 16 acetylation (H4K16ac) in flies and mammals. These variants cause an X-linked syndrome affecting both sexes. Clinical features of the syndrome include global developmental delay, progressive gait disturbance, and recognizable facial dysmorphism...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224646/functional-classification-of-long-non-coding-rnas-by-k-mer-content
#9
Jessime M Kirk, Susan O Kim, Kaoru Inoue, Matthew J Smola, David M Lee, Megan D Schertzer, Joshua S Wooten, Allison R Baker, Daniel Sprague, David W Collins, Christopher R Horning, Shuo Wang, Qidi Chen, Kevin M Weeks, Peter J Mucha, J Mauro Calabrese
The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called k-mers. We found that lncRNAs of related function often had similar k-mer profiles despite lacking linear homology, and that k-mer profiles correlated with protein binding to lncRNAs and with their subcellular localization...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224645/genomic-history-of-the-sardinian-population
#10
Charleston W K Chiang, Joseph H Marcus, Carlo Sidore, Arjun Biddanda, Hussein Al-Asadi, Magdalena Zoledziewska, Maristella Pitzalis, Fabio Busonero, Andrea Maschio, Giorgio Pistis, Maristella Steri, Andrea Angius, Kirk E Lohmueller, Goncalo R Abecasis, David Schlessinger, Francesco Cucca, John Novembre
The population of the Mediterranean island of Sardinia has made important contributions to genome-wide association studies of complex disease traits and, based on ancient DNA studies of mainland Europe, Sardinia is hypothesized to be a unique refuge for early Neolithic ancestry. To provide new insights on the genetic history of this flagship population, we analyzed 3,514 whole-genome sequenced individuals from Sardinia. Sardinian samples show elevated levels of shared ancestry with Basque individuals, especially samples from the more historically isolated regions of Sardinia...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224644/mutational-processes-shape-the-landscape-of-tp53-mutations-in-human-cancer
#11
Andrew O Giacomelli, Xiaoping Yang, Robert E Lintner, James M McFarland, Marc Duby, Jaegil Kim, Thomas P Howard, David Y Takeda, Seav Huong Ly, Eejung Kim, Hugh S Gannon, Brian Hurhula, Ted Sharpe, Amy Goodale, Briana Fritchman, Scott Steelman, Francisca Vazquez, Aviad Tsherniak, Andrew J Aguirre, John G Doench, Federica Piccioni, Charles W M Roberts, Matthew Meyerson, Gad Getz, Cory M Johannessen, David E Root, William C Hahn
Unlike most tumor suppressor genes, the most common genetic alterations in tumor protein p53 (TP53) are missense mutations1,2 . Mutant p53 protein is often abundantly expressed in cancers and specific allelic variants exhibit dominant-negative or gain-of-function activities in experimental models3-8 . To gain a systematic view of p53 function, we interrogated loss-of-function screens conducted in hundreds of human cancer cell lines and performed TP53 saturation mutagenesis screens in an isogenic pair of TP53 wild-type and null cell lines...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30224643/promoter-capture-hi-c-based-identification-of-recurrent-noncoding-mutations-in-colorectal-cancer
#12
Giulia Orlando, Philip J Law, Alex J Cornish, Sara E Dobbins, Daniel Chubb, Peter Broderick, Kevin Litchfield, Fadi Hariri, Tomi Pastinen, Cameron S Osborne, Jussi Taipale, Richard S Houlston
Efforts are being directed to systematically analyze the non-coding regions of the genome for cancer-driving mutations1-6 . cis-regulatory elements (CREs) represent a highly enriched subset of the non-coding regions of the genome in which to search for such mutations. Here we use high-throughput chromosome conformation capture techniques (Hi-C) for 19,023 promoter fragments to catalog the regulatory landscape of colorectal cancer in cell lines, mapping CREs and integrating these with whole-genome sequence and expression data from The Cancer Genome Atlas7,8 ...
September 17, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30202056/integrative-detection-and-analysis-of-structural-variation-in-cancer-genomes
#13
Jesse R Dixon, Jie Xu, Vishnu Dileep, Ye Zhan, Fan Song, Victoria T Le, Galip Gürkan Yardımcı, Abhijit Chakraborty, Darrin V Bann, Yanli Wang, Royden Clark, Lijun Zhang, Hongbo Yang, Tingting Liu, Sriranga Iyyanki, Lin An, Christopher Pool, Takayo Sasaki, Juan Carlos Rivera-Mulia, Hakan Ozadam, Bryan R Lajoie, Rajinder Kaul, Michael Buckley, Kristen Lee, Morgan Diegel, Dubravka Pezic, Christina Ernst, Suzana Hadjur, Duncan T Odom, John A Stamatoyannopoulos, James R Broach, Ross C Hardison, Ferhat Ay, William Stafford Noble, Job Dekker, David M Gilbert, Feng Yue
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms. Despite their importance, the identification of SVs in cancer genomes remains challenging. Here, we present a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole-genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines. We identify the unique strengths of each method and demonstrate that only integrative approaches can comprehensively identify SVs in the genome...
September 10, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30177863/genome-wide-association-analyses-identify-39-new-susceptibility-loci-for-diverticular-disease
#14
Lillias H Maguire, Samuel K Handelman, Xiaomeng Du, Yanhua Chen, Tune H Pers, Elizabeth K Speliotes
Diverticular disease is common and has a high morbidity. Treatments are limited owing to the poor understanding of its pathophysiology. Here, to elucidate its etiology, we performed a genome-wide association study of diverticular disease (27,444 cases; 382,284 controls) from the UK Biobank and tested for replication in the Michigan Genomics Initiative (2,572 cases; 28,649 controls). We identified 42 loci associated with diverticular disease; 39 of these loci are novel. Using data-driven expression-prioritized integration for complex traits (DEPICT), we show that genes in these associated regions are significantly enriched for expression in mesenchymal stem cells and multiple connective tissue cell types and are co-expressed with genes that have a role in vascular and mesenchymal biology...
September 3, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30177862/detecting-genome-wide-directional-effects-of-transcription-factor-binding-on-polygenic-disease-risk
#15
Yakir A Reshef, Hilary K Finucane, David R Kelley, Alexander Gusev, Dylan Kotliar, Jacob C Ulirsch, Farhad Hormozdiari, Joseph Nasser, Luke O'Connor, Bryce van de Geijn, Po-Ru Loh, Sharon R Grossman, Gaurav Bhatia, Steven Gazal, Pier Francesco Palamara, Luca Pinello, Nick Patterson, Ryan P Adams, Alkes L Price
Biological interpretation of genome-wide association study data frequently involves assessing whether SNPs linked to a biological process, for example, binding of a transcription factor, show unsigned enrichment for disease signal. However, signed annotations quantifying whether each SNP allele promotes or hinders the biological process can enable stronger statements about disease mechanism. We introduce a method, signed linkage disequilibrium profile regression, for detecting genome-wide directional effects of signed functional annotations on disease risk...
September 3, 2018: Nature Genetics
https://www.readbyqxmd.com/read/29973711/author-correction-reduced-mutation-rate-in-exons-due-to-differential-mismatch-repair
#16
Joan Frigola, Radhakrishnan Sabarinathan, Loris Mularoni, Ferran Muiños, Abel Gonzalez-Perez, Núria López-Bigas
In the version of this article initially published, the x axis on the fourth plot in Fig. 2e was incorrectly labeled "H3K36me3 exon-to-intron ratio (lower to higher)." The x axis on this plot should read "Genic H3K36me3 coverage bins (higher to lower)".
July 4, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30158687/gps-for-navigating-healthcare
#17
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
September 2018: Nature Genetics
https://www.readbyqxmd.com/read/30158686/visualizing-long-range-enhancer-promoter-interaction
#18
Albert Tsai, Justin Crocker
No abstract text is available yet for this article.
September 2018: Nature Genetics
https://www.readbyqxmd.com/read/30158685/analysis-and-visualization-of-linked-molecular-and-clinical-cancer-data-by-using-oncoscape
#19
LETTER
Lisa G McFerrin, Michael Zager, Jianan Zhang, Gretchen Krenn, Robert McDermott, Desert Horse-Grant, Emily Silgard, Kara Colevas, Paul Shannon, Hamid Bolouri, Eric C Holland
No abstract text is available yet for this article.
September 2018: Nature Genetics
https://www.readbyqxmd.com/read/30158684/cancer-genetics-precision-prevention-and-a-call-to-action
#20
REVIEW
Clare Turnbull, Amit Sud, Richard S Houlston
More than 15 years have passed since the identification, through linkage, of 'first-wave' susceptibility genes for common cancers (BRCA1, BRCA2, MLH1 and MSH2). These genes have strong frequency-penetrance profiles, such that the associated clinical utility probably remains relevant regardless of the context of ascertainment. 'Second-wave' genes, not tractable by linkage, were subsequently identified by mutation screening of candidate genes (PALB2, ATM, CHEK2, BRIP1, RAD51C and RAD51D). Their innately weaker frequency-penetrance profiles have rendered delineation of cancer associations, risks and variant pathogenicity challenging, thereby compromising their clinical application...
September 2018: Nature Genetics
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