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https://www.readbyqxmd.com/read/30429576/author-correction-germline-havcr2-mutations-altering-tim-3-characterize-subcutaneous-panniculitis-like-t-cell-lymphomas-with-hemophagocytic-lymphohistiocytic-syndrome
#1
Tenzin Gayden, Fernando E Sepulveda, Dong-Anh Khuong-Quang, Jonathan Pratt, Elvis T Valera, Alexandrine Garrigue, Susan Kelso, Frank Sicheri, Leonie G Mikael, Nancy Hamel, Andrea Bajic, Rola Dali, Shriya Deshmukh, Dzana Dervovic, Daniel Schramek, Frédéric Guerin, Mikko Taipale, Hamid Nikbakht, Jacek Majewski, Despina Moshous, Janie Charlebois, Sharon Abish, Christine Bole-Feysot, Patrick Nitschke, Brigitte Bader-Meunier, David Mitchell, Catherine Thieblemont, Maxime Battistella, Simon Gravel, Van-Hung Nguyen, Rachel Conyers, Jean-Sebastien Diana, Chris McCormack, H Miles Prince, Marianne Besnard, Stephane Blanche, Paul G Ekert, Sylvie Fraitag, William D Foulkes, Alain Fischer, Bénédicte Neven, David Michonneau, Geneviève de Saint Basile, Nada Jabado
In the version of this article originally published, the main-text sentence "In three patients of European ancestry, we identified the germline variant encoding p.Ile97Met in TIM-3, which was homozygous in two (P12 and P13) and heterozygous in one (P15) in the germline but with no TIM-3 plasma membrane expression in the tumor" misstated the identifiers of the two homozygous individuals, which should have been P13 and P14. The error has been corrected in the HTML, PDF and print versions of the paper...
November 14, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30429575/publisher-correction-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
In the version of this article originally published, the name of author Martin H. de Borst was coded incorrectly in the XML. The error has now been corrected in the HTML version of the paper.
November 14, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30425353/publisher-correction-allele-defined-genome-of-the-autopolyploid-sugarcane-saccharum-spontaneum-l
#3
Jisen Zhang, Xingtan Zhang, Haibao Tang, Qing Zhang, Xiuting Hua, Xiaokai Ma, Fan Zhu, Tyler Jones, Xinguang Zhu, John Bowers, Ching Man Wai, Chunfang Zheng, Yan Shi, Shuai Chen, Xiuming Xu, Jingjing Yue, David R Nelson, Lixian Huang, Zhen Li, Huimin Xu, Dong Zhou, Yongjun Wang, Weichang Hu, Jishan Lin, Youjin Deng, Neha Pandey, Melina Mancini, Dessireé Zerpa, Julie K Nguyen, Liming Wang, Liang Yu, Yinghui Xin, Liangfa Ge, Jie Arro, Jennifer O Han, Setu Chakrabarty, Marija Pushko, Wenping Zhang, Yanhong Ma, Panpan Ma, Mingju Lv, Faming Chen, Guangyong Zheng, Jingsheng Xu, Zhenhui Yang, Fang Deng, Xuequn Chen, Zhenyang Liao, Xunxiao Zhang, Zhicong Lin, Hai Lin, Hansong Yan, Zheng Kuang, Weimin Zhong, Pingping Liang, Guofeng Wang, Yuan Yuan, Jiaxian Shi, Jinxiang Hou, Jingxian Lin, Jingjing Jin, Peijian Cao, Qiaochu Shen, Qing Jiang, Ping Zhou, Yaying Ma, Xiaodan Zhang, Rongrong Xu, Juan Liu, Yongmei Zhou, Haifeng Jia, Qing Ma, Rui Qi, Zhiliang Zhang, Jingping Fang, Hongkun Fang, Jinjin Song, Mengjuan Wang, Guangrui Dong, Gang Wang, Zheng Chen, Teng Ma, Hong Liu, Singha R Dhungana, Sarah E Huss, Xiping Yang, Anupma Sharma, Jhon H Trujillo, Maria C Martinez, Matthew Hudson, John J Riascos, Mary Schuler, Li-Qing Chen, David M Braun, Lei Li, Qingyi Yu, Jianping Wang, Kai Wang, Michael C Schatz, David Heckerman, Marie-Anne Van Sluys, Glaucia Mendes Souza, Paul H Moore, David Sankoff, Robert VanBuren, Andrew H Paterson, Chifumi Nagai, Ray Ming
In the version of this article originally published, the accession codes listed in the data availability section were incorrect and the section was incomplete. The text for this section should have read "The genome assembly and gene annotation have been deposited in the NCBI database under accession number QVOL00000000, BioProject number PRJNA483885 and BioSample number SAMN09753102. The data can also be downloaded from the following link: http://www.life.illinois.edu/ming/downloads/Spontaneum_genome/ ...
November 13, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30420650/author-correction-reference-component-analysis-of-single-cell-transcriptomes-elucidates-cellular-heterogeneity-in-human-colorectal-tumors
#4
Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan, Kok Hao Chen, Jolene Jie Lin Goh, Say Li Kong, Clarinda Chua, Lim Kiat Hon, Wah Siew Tan, Mark Wong, Igor Cima, Min-Han Tan, Lawrence J K Wee, Axel M Hillmer, Iain Beehuat Tan, Paul Robson, Shyam Prabhakar
In the version of the article published, the author list is not accurate. Igor Cima and Min-Han Tan should have been authors, appearing after Mark Wong in the author list, while Paul Jongjoon Choi should not have been listed as an author. Igor Cima and Min-Han Tan both have the affiliation Institute of Bioengineering and Nanotechnology, Singapore, Singapore, and their contributions should have been noted in the Author Contributions section as "I.C. preprocessed Primary Cell Atlas data with inputs from M...
November 12, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30420649/subtype-specific-regulatory-network-rewiring-in-acute-myeloid-leukemia
#5
Salam A Assi, Maria Rosaria Imperato, Daniel J L Coleman, Anna Pickin, Sandeep Potluri, Anetta Ptasinska, Paulynn Suyin Chin, Helen Blair, Pierre Cauchy, Sally R James, Joaquin Zacarias-Cabeza, L Niall Gilding, Andrew Beggs, Sam Clokie, Justin C Loke, Phil Jenkin, Ash Uddin, Ruud Delwel, Stephen J Richards, Manoj Raghavan, Michael J Griffiths, Olaf Heidenreich, Peter N Cockerill, Constanze Bonifer
Acute myeloid leukemia (AML) is a heterogeneous disease caused by a variety of alterations in transcription factors, epigenetic regulators and signaling molecules. To determine how different mutant regulators establish AML subtype-specific transcriptional networks, we performed a comprehensive global analysis of cis-regulatory element activity and interaction, transcription factor occupancy and gene expression patterns in purified leukemic blast cells. Here, we focused on specific subgroups of subjects carrying mutations in genes encoding transcription factors (RUNX1, CEBPα), signaling molecules (FTL3-ITD, RAS) and the nuclear protein NPM1)...
November 12, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30420648/cilia-driven-cerebrospinal-fluid-flow-directs-expression-of-urotensin-neuropeptides-to-straighten-the-vertebrate-body-axis
#6
Xiaoli Zhang, Shuo Jia, Zhe Chen, Yan Ling Chong, Haibo Xie, Dong Feng, Xiaotong Wu, Don Zhu Song, Sudipto Roy, Chengtian Zhao
Straightening of the body axis is a major morphogenetic event that produces the typical head-to-tail shape of the vertebrate embryo. Defects in axial straightening can lead to debilitating disorders such as idiopathic scoliosis, characterized by three-dimensional curvatures of the spine1 . Although abnormal cerebrospinal fluid (CSF) flow has been implicated in the development of idiopathic scoliosis2 , the molecular mechanisms operating downstream of CSF flow remain obscure. Here we show that, in zebrafish embryos, cilia-driven CSF flow transports adrenergic signals that induce urotensin neuropeptides in CSF-contacting neurons along the spinal cord...
November 12, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30420647/genebank-genomics-highlights-the-diversity-of-a-global-barley-collection
#7
Sara G Milner, Matthias Jost, Shin Taketa, Elena Rey Mazón, Axel Himmelbach, Markus Oppermann, Stephan Weise, Helmut Knüpffer, Martín Basterrechea, Patrick König, Danuta Schüler, Rajiv Sharma, Raj K Pasam, Twan Rutten, Ganggang Guo, Dongdong Xu, Jing Zhang, Gerhard Herren, Thomas Müller, Simon G Krattinger, Beat Keller, Yong Jiang, Maria Y González, Yusheng Zhao, Antje Habekuß, Sandra Färber, Frank Ordon, Matthias Lange, Andreas Börner, Andreas Graner, Jochen C Reif, Uwe Scholz, Martin Mascher, Nils Stein
Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world's major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans...
November 12, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30405215/human-disease-mutations-highlight-the-inhibitory-function-of-tim-3
#8
Karen O Dixon, Madhumita Das, Vijay K Kuchroo
No abstract text is available yet for this article.
November 7, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30401984/author-correction-distinguishing-genetic-correlation-from-causation-across-52-diseases-and-complex-traits
#9
Luke J O'Connor, Alkes L Price
In the version of this article originally published, there were errors in equations. In the HTML and PDF, the initial term of equation 10 was estimated GCP but should have been estimated standard error, while a 'hat' was missing from the first alpha in the second term of the expression at the end of the paragraph following equation (6) in the Methods. In addition, in the abstract in the PDF, a subscript 1 was used instead of a subscript 2 for the final term of the first fourth-moment expression. These errors have been corrected in the HTML, PDF and print versions of the paper...
November 6, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30397339/author-correction-public-resources-aid-diabetes-gene-discovery
#10
Diana L Cousminer, Struan F A Grant
In the version of this article originally published, the text was incorrect in the first paragraph of the 'Remaining challenges' section. The first two sentences appeared as "Even though this current study substantially increases the number of loci associated with T2D, only approximately 18% of the genetic component of T2D risk is explained by the total complement of genetic variants uncovered genome wide in Mahajan et al.6 . Interestingly, only a small proportion of that heritability was explained by low-frequency or rare variants (~1...
November 5, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30397338/multiple-transmissions-of-de-novo-mutations-in-families
#11
Hákon Jónsson, Patrick Sulem, Gudny A Arnadottir, Gunnar Pálsson, Hannes P Eggertsson, Snaedis Kristmundsdottir, Florian Zink, Birte Kehr, Kristjan E Hjorleifsson, Brynjar Ö Jensson, Ingileif Jonsdottir, Sigurdur Einar Marelsson, Sigurjon Axel Gudjonsson, Arnaldur Gylfason, Adalbjorg Jonasdottir, Aslaug Jonasdottir, Simon N Stacey, Olafur Th Magnusson, Unnur Thorsteinsdottir, Gisli Masson, Augustine Kong, Bjarni V Halldorsson, Agnar Helgason, Daniel F Gudbjartsson, Kari Stefansson
De novo mutations (DNMs) cause a large proportion of severe rare diseases of childhood. DNMs that occur early may result in mosaicism of both somatic and germ cells. Such early mutations can cause recurrence of disease. We scanned 1,007 sibling pairs from 251 families and identified 878 DNMs shared by siblings (ssDNMs) at 448 genomic sites. We estimated DNM recurrence probability based on parental mosaicism, sharing of DNMs among siblings, parent-of-origin, mutation type and genomic position. We detected 57...
November 5, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30397337/a-deep-learning-approach-to-automate-refinement-of-somatic-variant-calling-from-cancer-sequencing-data
#12
Benjamin J Ainscough, Erica K Barnell, Peter Ronning, Katie M Campbell, Alex H Wagner, Todd A Fehniger, Gavin P Dunn, Ravindra Uppaluri, Ramaswamy Govindan, Thomas E Rohan, Malachi Griffith, Elaine R Mardis, S Joshua Swamidass, Obi L Griffith
Cancer genomic analysis requires accurate identification of somatic variants in sequencing data. Manual review to refine somatic variant calls is required as a final step after automated processing. However, manual variant refinement is time-consuming, costly, poorly standardized, and non-reproducible. Here, we systematized and standardized somatic variant refinement using a machine learning approach. The final model incorporates 41,000 variants from 440 sequencing cases. This model accurately recapitulated manual refinement labels for three independent testing sets (13,579 variants) and accurately predicted somatic variants confirmed by orthogonal validation sequencing data (212,158 variants)...
November 5, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30397336/identification-of-phagocytosis-regulators-using-magnetic-genome-wide-crispr-screens
#13
Michael S Haney, Christopher J Bohlen, David W Morgens, James A Ousey, Amira A Barkal, C Kimberly Tsui, Braeden K Ego, Roni Levin, Roarke A Kamber, Hannah Collins, Andrew Tucker, Amy Li, Daan Vorselen, Lorenzo Labitigan, Emily Crane, Evan Boyle, Lihua Jiang, Joanne Chan, Esther Rincón, William J Greenleaf, Billy Li, Michael P Snyder, Irving L Weissman, Julie A Theriot, Sean R Collins, Ben A Barres, Michael C Bassik
Phagocytosis is required for a broad range of physiological functions, from pathogen defense to tissue homeostasis, but the mechanisms required for phagocytosis of diverse substrates remain incompletely understood. Here, we developed a rapid magnet-based phenotypic screening strategy, and performed eight genome-wide CRISPR screens in human cells to identify genes regulating phagocytosis of distinct substrates. After validating select hits in focused miniscreens, orthogonal assays and primary human macrophages, we show that (1) the previously uncharacterized gene NHLRC2 is a central player in phagocytosis, regulating RhoA-Rac1 signaling cascades that control actin polymerization and filopodia formation, (2) very-long-chain fatty acids are essential for efficient phagocytosis of certain substrates and (3) the previously uncharacterized Alzheimer's disease-associated gene TM2D3 can preferentially influence uptake of amyloid-β aggregates...
November 5, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30397335/retinoic-acid-and-bmp4-cooperate-with-p63-to-alter-chromatin-dynamics-during-surface-epithelial-commitment
#14
Jillian M Pattison, Sandra P Melo, Samantha N Piekos, Jessica L Torkelson, Elizaveta Bashkirova, Maxwell R Mumbach, Charlotte Rajasingh, Hanson Hui Zhen, Lingjie Li, Eric Liaw, Daniel Alber, Adam J Rubin, Gautam Shankar, Xiaomin Bao, Howard Y Chang, Paul A Khavari, Anthony E Oro
Human embryonic stem cell (hESC) differentiation promises advances in regenerative medicine1-3 , yet conversion of hESCs into transplantable cells or tissues remains poorly understood. Using our keratinocyte differentiation system, we employ a multi-dimensional genomics approach to interrogate the contributions of inductive morphogens retinoic acid and bone morphogenetic protein 4 (BMP4) and the epidermal master regulator p63 (encoded by TP63)4,5 during surface ectoderm commitment. In contrast to other master regulators6-9 , p63 effects major transcriptional changes only after morphogens alter chromatin accessibility, establishing an epigenetic landscape for p63 to modify...
November 5, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30397334/whole-genome-sequencing-of-175-mongolians-uncovers-population-specific-genetic-architecture-and-gene-flow-throughout-north-and-east-asia
#15
Haihua Bai, Xiaosen Guo, Narisu Narisu, Tianming Lan, Qizhu Wu, Yanping Xing, Yong Zhang, Stephen R Bond, Zhili Pei, Yanru Zhang, Dandan Zhang, Jirimutu Jirimutu, Dong Zhang, Xukui Yang, Morigenbatu Morigenbatu, Li Zhang, Bingyi Ding, Baozhu Guan, Junwei Cao, Haorong Lu, Yiyi Liu, Wangsheng Li, Ningxin Dang, Mingyang Jiang, Shenyuan Wang, Huixin Xu, Dingzhu Wang, Chunxia Liu, Xin Luo, Ying Gao, Xueqiong Li, Zongze Wu, Liqing Yang, Fanhua Meng, Xiaolian Ning, Hashenqimuge Hashenqimuge, Kaifeng Wu, Bo Wang, Suyalatu Suyalatu, Yingchun Liu, Chen Ye, Huiguang Wu, Kalle Leppälä, Lu Li, Lin Fang, Yujie Chen, Wenhao Xu, Tao Li, Xin Liu, Xun Xu, Christopher R Gignoux, Huanming Yang, Lawrence C Brody, Jun Wang, Karsten Kristiansen, Burenbatu Burenbatu, Huanmin Zhou, Ye Yin
The genetic variation in Northern Asian populations is currently undersampled. To address this, we generated a new genetic variation reference panel by whole-genome sequencing of 175 ethnic Mongolians, representing six tribes. The cataloged variation in the panel shows strong population stratification among these tribes, which correlates with the diverse demographic histories in the region. Incorporating our results with the 1000 Genomes Project panel identifies derived alleles shared between Finns and Mongolians/Siberians, suggesting that substantial gene flow between northern Eurasian populations has occurred in the past...
November 5, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30397333/comparative-genomics-of-the-major-parasitic-worms
#16
(no author information available yet)
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed...
November 5, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30390058/author-correction-a-genome-wide-cross-trait-analysis-from-uk-biobank-highlights-the-shared-genetic-architecture-of-asthma-and-allergic-diseases
#17
Zhaozhong Zhu, Phil H Lee, Mark D Chaffin, Wonil Chung, Po-Ru Loh, Quan Lu, David C Christiani, Liming Liang
In the version of this article originally published, there were two errors in the text of the second paragraph of the Methods section. In the sentence "To identify genetic variants that contribute to doctor-diagnosed asthma and allergic diseases (detailed phenotype information described in the Supplementary Note) and link them with other conditions, we performed GWASs using phenotype measures in UK Biobank participants (N = 487,409)" the number of participants should have been 150,509. In the sentence "Thus, a total of 110,361 European descendants with high-quality genotyping and complete phenotype/covariate data were used for these analyses, including 25,685 allergic diseases subjects (hay fever/allergic rhinitis or eczema, without doctor-diagnosed asthma), 14,085 asthma subjects and 76,768 controls for the analysis" the phrase "without doctor-diagnosed asthma" should have read "some with doctor-diagnosed asthma...
November 2, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30390057/author-correction-discovery-and-refinement-of-genetic-loci-associated-with-cardiometabolic-risk-using-dense-imputation-maps
#18
Valentina Iotchkova, Jie Huang, John A Morris, Deepti Jain, Caterina Barbieri, Klaudia Walter, Josine L Min, Lu Chen, William Astle, Massimilian Cocca, Patrick Deelen, Heather Elding, Aliki-Eleni Farmaki, Christopher S Franklin, Mattias Franberg, Tom R Gaunt, Albert Hofman, Tao Jiang, Marcus E Kleber, Genevieve Lachance, Jian'an Luan, Giovanni Malerba, Angela Matchan, Daniel Mead, Yasin Memari, Ioanna Ntalla, Kalliope Panoutsopoulou, Raha Pazoki, John R B Perry, Fernando Rivadeneira, Maria Sabater-Lleal, Bengt Sennblad, So-Youn Shin, Lorraine Southam, Michela Traglia, Freerk van Dijk, Elisabeth M van Leeuwen, Gianluigi Zaza, Weihua Zhang, Najaf Amin, Adam Butterworth, John C Chambers, George Dedoussis, Abbas Dehghan, Oscar H Franco, Lude Franke, Mattia Frontini, Giovanni Gambaro, Paolo Gasparini, Anders Hamsten, Aaron Isaacs, Jaspal S Kooner, Charles Kooperberg, Claudia Langenberg, Winfried Marz, Robert A Scott, Morris A Swertz, Daniela Toniolo, Andre G Uitterlinden, Cornelia M van Duijn, Hugh Watkins, Eleftheria Zeggini, Mathew T Maurano, Nicholas J Timpson, Alexander P Reiner, Paul L Auer, Nicole Soranzo
In the version of the article published, the surname of author Aaron Isaacs is misspelled as Issacs.
November 2, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30374075/neutral-tumor-evolution
#19
LETTER
Maxime Tarabichi, Iñigo Martincorena, Moritz Gerstung, Armand M Leroi, Florian Markowetz, Paul T Spellman, Quaid D Morris, Ole Christian Lingjærde, David C Wedge, Peter Van Loo
No abstract text is available yet for this article.
October 29, 2018: Nature Genetics
https://www.readbyqxmd.com/read/30374074/distinguishing-genetic-correlation-from-causation-across-52-diseases-and-complex-traits
#20
Luke J O'Connor, Alkes L Price
Mendelian randomization, a method to infer causal relationships, is confounded by genetic correlations reflecting shared etiology. We developed a model in which a latent causal variable mediates the genetic correlation; trait 1 is partially genetically causal for trait 2 if it is strongly genetically correlated with the latent causal variable, quantified using the genetic causality proportion. We fit this model using mixed fourth moments [Formula: see text] and [Formula: see text] of marginal effect sizes for each trait; if trait 1 is causal for trait 2, then SNPs affecting trait 1 (large [Formula: see text]) will have correlated effects on trait 2 (large α1 α2 ), but not vice versa...
October 29, 2018: Nature Genetics
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