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Nature Genetics

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https://www.readbyqxmd.com/read/28628109/truncating-mutations-in-rbm12-are-associated-with-psychosis
#1
Stacy Steinberg, Steinunn Gudmundsdottir, Gardar Sveinbjornsson, Jaana Suvisaari, Tiina Paunio, Minna Torniainen-Holm, Michael L Frigge, Gudrun A Jonsdottir, Johanna Huttenlocher, Sunna Arnarsdottir, Oddur Ingimarsson, Magnus Haraldsson, Thorarinn Tyrfingsson, Thorgeir E Thorgeirsson, Augustine Kong, Gudmundur L Norddahl, Daniel F Gudbjartsson, Engilbert Sigurdsson, Hreinn Stefansson, Kari Stefansson
Thus far, a handful of highly penetrant mutations conferring risk of psychosis have been discovered. Here we used whole-genome sequencing and long-range phasing to investigate an Icelandic kindred containing ten individuals with psychosis (schizophrenia, schizoaffective disorder or psychotic bipolar disorder). We found that all affected individuals carry RBM12 (RNA-binding-motif protein 12) c.2377G>T (P = 2.2 × 10(-4)), a nonsense mutation that results in the production of a truncated protein lacking a predicted RNA-recognition motif...
June 19, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28628108/germline-hypomorphic-card11-mutations-in-severe-atopic-disease
#2
Chi A Ma, Jeffrey R Stinson, Yuan Zhang, Jordan K Abbott, Michael A Weinreich, Pia J Hauk, Paul R Reynolds, Jonathan J Lyons, Celeste G Nelson, Elisa Ruffo, Batsukh Dorjbal, Salomé Glauzy, Natsuko Yamakawa, Swadhinya Arjunaraja, Kelsey Voss, Jennifer Stoddard, Julie Niemela, Yu Zhang, Sergio D Rosenzweig, Joshua J McElwee, Thomas DiMaggio, Helen F Matthews, Nina Jones, Kelly D Stone, Alejandro Palma, Matías Oleastro, Emma Prieto, Andrea R Bernasconi, Geronimo Dubra, Silvia Danielian, Jonathan Zaiat, Marcelo A Marti, Brian Kim, Megan A Cooper, Neil D Romberg, Eric Meffre, Erwin W Gelfand, Andrew L Snow, Joshua D Milner
Few monogenic causes for severe manifestations of common allergic diseases have been identified. Through next-generation sequencing on a cohort of patients with severe atopic dermatitis with and without comorbid infections, we found eight individuals, from four families, with novel heterozygous mutations in CARD11, which encodes a scaffolding protein involved in lymphocyte receptor signaling. Disease improved over time in most patients. Transfection of mutant CARD11 expression constructs into T cell lines demonstrated both loss-of-function and dominant-interfering activity upon antigen receptor-induced activation of nuclear factor-κB and mammalian target of rapamycin complex 1 (mTORC1)...
June 19, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28628107/identification-of-sequence-variants-influencing-immunoglobulin-levels
#3
Stefan Jonsson, Gardar Sveinbjornsson, Aitzkoa Lopez de Lapuente Portilla, Bhairavi Swaminathan, Rosina Plomp, Gillian Dekkers, Ram Ajore, Mina Ali, Arthur E H Bentlage, Evelina Elmér, Gudmundur I Eyjolfsson, Sigurjon A Gudjonsson, Urban Gullberg, Arnaldur Gylfason, Bjarni V Halldorsson, Markus Hansson, Hilma Holm, Åsa Johansson, Ellinor Johnsson, Aslaug Jonasdottir, Bjorn R Ludviksson, Asmundur Oddsson, Isleifur Olafsson, Sigurgeir Olafsson, Olof Sigurdardottir, Asgeir Sigurdsson, Lilja Stefansdottir, Gisli Masson, Patrick Sulem, Manfred Wuhrer, Anna-Karin Wihlborg, Gudmar Thorleifsson, Daniel F Gudbjartsson, Unnur Thorsteinsdottir, Gestur Vidarsson, Ingileif Jonsdottir, Björn Nilsson, Kari Stefansson
Immunoglobulins are the effector molecules of the adaptive humoral immune system. In a genome-wide association study of 19,219 individuals, we found 38 new variants and replicated 5 known variants associating with IgA, IgG or IgM levels or with composite immunoglobulin traits, accounted for by 32 loci. Variants at these loci also affect the risk of autoimmune diseases and blood malignancies and influence blood cell development. Notable associations include a rare variant at RUNX3 decreasing IgA levels by shifting isoform proportions (rs188468174[C>T]: P = 8...
June 19, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28628106/variants-in-the-fetal-genome-near-flt1-are-associated-with-risk-of-preeclampsia
#4
Ralph McGinnis, Valgerdur Steinthorsdottir, Nicholas O Williams, Gudmar Thorleifsson, Scott Shooter, Sigrun Hjartardottir, Suzannah Bumpstead, Lilja Stefansdottir, Lucy Hildyard, Jon K Sigurdsson, John P Kemp, Gabriela B Silva, Liv Cecilie V Thomsen, Tiina Jääskeläinen, Eero Kajantie, Sally Chappell, Noor Kalsheker, Ashley Moffett, Susan Hiby, Wai Kwong Lee, Sandosh Padmanabhan, Nigel A B Simpson, Vivien A Dolby, Eleonora Staines-Urias, Stephanie M Engel, Anita Haugan, Lill Trogstad, Gulnara Svyatova, Nodira Zakhidova, Dilbar Najmutdinova, Anna F Dominiczak, Håkon K Gjessing, Juan P Casas, Frank Dudbridge, James J Walker, Fiona Broughton Pipkin, Unnur Thorsteinsdottir, Reynir T Geirsson, Debbie A Lawlor, Ann-Charlotte Iversen, Per Magnus, Hannele Laivuori, Kari Stefansson, Linda Morgan
Preeclampsia, which affects approximately 5% of pregnancies, is a leading cause of maternal and perinatal death. The causes of preeclampsia remain unclear, but there is evidence for inherited susceptibility. Genome-wide association studies (GWAS) have not identified maternal sequence variants of genome-wide significance that replicate in independent data sets. We report the first GWAS of offspring from preeclamptic pregnancies and discovery of the first genome-wide significant susceptibility locus (rs4769613; P = 5...
June 19, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28628105/identification-of-liver-specific-enhancer-promoter-activity-in-the-3-untranslated-region-of-the-wild-type-aav2-genome
#5
Grant J Logan, Allison P Dane, Claus V Hallwirth, Christine M Smyth, Emilie E Wilkie, Anais K Amaya, Erhua Zhu, Neeta Khandekar, Samantha L Ginn, Sophia H Y Liao, Sharon C Cunningham, Natsuki Sasaki, Martí Cabanes-Creus, Patrick P L Tam, David W Russell, Leszek Lisowski, Ian E Alexander
Vectors based on adeno-associated virus type 2 (AAV2) are powerful tools for gene transfer and genome editing applications. The level of interest in this system has recently surged in response to reports of therapeutic efficacy in human clinical trials, most notably for those in patients with hemophilia B (ref. 3). Understandably, a recent report drawing an association between AAV2 integration events and human hepatocellular carcinoma (HCC) has generated controversy about the causal or incidental nature of this association and the implications for AAV vector safety...
June 19, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28604732/meta-analysis-of-five-genome-wide-association-studies-identifies-multiple-new-loci-associated-with-testicular-germ-cell-tumor
#6
Zhaoming Wang, Katherine A McGlynn, Ewa Rajpert-De Meyts, D Timothy Bishop, Charles C Chung, Marlene D Dalgaard, Mark H Greene, Ramneek Gupta, Tom Grotmol, Trine B Haugen, Robert Karlsson, Kevin Litchfield, Nandita Mitra, Kasper Nielsen, Louise C Pyle, Stephen M Schwartz, Vésteinn Thorsson, Saran Vardhanabhuti, Fredrik Wiklund, Clare Turnbull, Stephen J Chanock, Peter A Kanetsky, Katherine L Nathanson
The international Testicular Cancer Consortium (TECAC) combined five published genome-wide association studies of testicular germ cell tumor (TGCT; 3,558 cases and 13,970 controls) to identify new susceptibility loci. We conducted a fixed-effects meta-analysis, including, to our knowledge, the first analysis of the X chromosome. Eight new loci mapping to 2q14.2, 3q26.2, 4q35.2, 7q36.3, 10q26.13, 15q21.3, 15q22.31, and Xq28 achieved genome-wide significance (P < 5 × 10(-8)). Most loci harbor biologically plausible candidate genes...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28604731/genome-wide-association-analysis-of-insomnia-complaints-identifies-risk-genes-and-genetic-overlap-with-psychiatric-and-metabolic-traits
#7
Anke R Hammerschlag, Sven Stringer, Christiaan A de Leeuw, Suzanne Sniekers, Erdogan Taskesen, Kyoko Watanabe, Tessa F Blanken, Kim Dekker, Bart H W Te Lindert, Rick Wassing, Ingileif Jonsdottir, Gudmar Thorleifsson, Hreinn Stefansson, Thorarinn Gislason, Klaus Berger, Barbara Schormair, Juergen Wellmann, Juliane Winkelmann, Kari Stefansson, Konrad Oexle, Eus J W Van Someren, Danielle Posthuma
Persistent insomnia is among the most frequent complaints in general practice. To identify genetic factors for insomnia complaints, we performed a genome-wide association study (GWAS) and a genome-wide gene-based association study (GWGAS) in 113,006 individuals. We identify three loci and seven genes associated with insomnia complaints, with the associations for one locus and five genes supported by joint analysis with an independent sample (n = 7,565). Our top association (MEIS1, P < 5 × 10(-8)) has previously been implicated in restless legs syndrome (RLS)...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28604730/large-scale-association-analysis-identifies-new-lung-cancer-susceptibility-loci-and-heterogeneity-in-genetic-susceptibility-across-histological-subtypes
#8
James D McKay, Rayjean J Hung, Younghun Han, Xuchen Zong, Robert Carreras-Torres, David C Christiani, Neil E Caporaso, Mattias Johansson, Xiangjun Xiao, Yafang Li, Jinyoung Byun, Alison Dunning, Karen A Pooley, David C Qian, Xuemei Ji, Geoffrey Liu, Maria N Timofeeva, Stig E Bojesen, Xifeng Wu, Loic Le Marchand, Demetrios Albanes, Heike Bickeböller, Melinda C Aldrich, William S Bush, Adonina Tardon, Gad Rennert, M Dawn Teare, John K Field, Lambertus A Kiemeney, Philip Lazarus, Aage Haugen, Stephen Lam, Matthew B Schabath, Angeline S Andrew, Hongbing Shen, Yun-Chul Hong, Jian-Min Yuan, Pier Alberto Bertazzi, Angela C Pesatori, Yuanqing Ye, Nancy Diao, Li Su, Ruyang Zhang, Yonathan Brhane, Natasha Leighl, Jakob S Johansen, Anders Mellemgaard, Walid Saliba, Christopher A Haiman, Lynne R Wilkens, Ana Fernandez-Somoano, Guillermo Fernandez-Tardon, Henricus F M van der Heijden, Jin Hee Kim, Juncheng Dai, Zhibin Hu, Michael P A Davies, Michael W Marcus, Hans Brunnström, Jonas Manjer, Olle Melander, David C Muller, Kim Overvad, Antonia Trichopoulou, Rosario Tumino, Jennifer A Doherty, Matt P Barnett, Chu Chen, Gary E Goodman, Angela Cox, Fiona Taylor, Penella Woll, Irene Brüske, H-Erich Wichmann, Judith Manz, Thomas R Muley, Angela Risch, Albert Rosenberger, Kjell Grankvist, Mikael Johansson, Frances A Shepherd, Ming-Sound Tsao, Susanne M Arnold, Eric B Haura, Ciprian Bolca, Ivana Holcatova, Vladimir Janout, Milica Kontic, Jolanta Lissowska, Anush Mukeria, Simona Ognjanovic, Tadeusz M Orlowski, Ghislaine Scelo, Beata Swiatkowska, David Zaridze, Per Bakke, Vidar Skaug, Shanbeh Zienolddiny, Eric J Duell, Lesley M Butler, Woon-Puay Koh, Yu-Tang Gao, Richard S Houlston, John McLaughlin, Victoria L Stevens, Philippe Joubert, Maxime Lamontagne, David C Nickle, Ma'en Obeidat, Wim Timens, Bin Zhu, Lei Song, Linda Kachuri, María Soler Artigas, Martin D Tobin, Louise V Wain, Thorunn Rafnar, Thorgeir E Thorgeirsson, Gunnar W Reginsson, Kari Stefansson, Dana B Hancock, Laura J Bierut, Margaret R Spitz, Nathan C Gaddis, Sharon M Lutz, Fangyi Gu, Eric O Johnson, Ahsan Kamal, Claudio Pikielny, Dakai Zhu, Sara Lindströem, Xia Jiang, Rachel F Tyndale, Georgia Chenevix-Trench, Jonathan Beesley, Yohan Bossé, Stephen Chanock, Paul Brennan, Maria Teresa Landi, Christopher I Amos
Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28604729/dnmt-and-hdac-inhibitors-induce-cryptic-transcription-start-sites-encoded-in-long-terminal-repeats
#9
David Brocks, Christopher R Schmidt, Michael Daskalakis, Hyo Sik Jang, Nakul M Shah, Daofeng Li, Jing Li, Bo Zhang, Yiran Hou, Sara Laudato, Daniel B Lipka, Johanna Schott, Holger Bierhoff, Yassen Assenov, Monika Helf, Alzbeta Ressnerova, Md Saiful Islam, Anders M Lindroth, Simon Haas, Marieke Essers, Charles D Imbusch, Benedikt Brors, Ina Oehme, Olaf Witt, Michael Lübbert, Jan-Philipp Mallm, Karsten Rippe, Rainer Will, Dieter Weichenhan, Georg Stoecklin, Clarissa Gerhäuser, Christopher C Oakes, Ting Wang, Christoph Plass
Several mechanisms of action have been proposed for DNA methyltransferase and histone deacetylase inhibitors (DNMTi and HDACi), primarily based on candidate-gene approaches. However, less is known about their genome-wide transcriptional and epigenomic consequences. By mapping global transcription start site (TSS) and chromatin dynamics, we observed the cryptic transcription of thousands of treatment-induced non-annotated TSSs (TINATs) following DNMTi and HDACi treatment. The resulting transcripts frequently splice into protein-coding exons and encode truncated or chimeric ORFs translated into products with predicted abnormal or immunogenic functions...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28604728/identification-of-19-new-risk-loci-and-potential-regulatory-mechanisms-influencing-susceptibility-to-testicular-germ-cell-tumor
#10
Kevin Litchfield, Max Levy, Giulia Orlando, Chey Loveday, Philip J Law, Gabriele Migliorini, Amy Holroyd, Peter Broderick, Robert Karlsson, Trine B Haugen, Wenche Kristiansen, Jérémie Nsengimana, Kerry Fenwick, Ioannis Assiotis, ZSofia Kote-Jarai, Alison M Dunning, Kenneth Muir, Julian Peto, Rosalind Eeles, Douglas F Easton, Darshna Dudakia, Nick Orr, Nora Pashayan, D Timothy Bishop, Alison Reid, Robert A Huddart, Janet Shipley, Tom Grotmol, Fredrik Wiklund, Richard S Houlston, Clare Turnbull
Genome-wide association studies (GWAS) have transformed understanding of susceptibility to testicular germ cell tumors (TGCTs), but much of the heritability remains unexplained. Here we report a new GWAS, a meta-analysis with previous GWAS and a replication series, totaling 7,319 TGCT cases and 23,082 controls. We identify 19 new TGCT risk loci, roughly doubling the number of known TGCT risk loci to 44. By performing in situ Hi-C in TGCT cells, we provide evidence for a network of physical interactions among all 44 TGCT risk SNPs and candidate causal genes...
June 12, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28581503/between-region-genetic-divergence-reflects-the-mode-and-tempo-of-tumor-evolution
#11
Ruping Sun, Zheng Hu, Andrea Sottoriva, Trevor A Graham, Arbel Harpak, Zhicheng Ma, Jared M Fischer, Darryl Shibata, Christina Curtis
Given the implications of tumor dynamics for precision medicine, there is a need to systematically characterize the mode of evolution across diverse solid tumor types. In particular, methods to infer the role of natural selection within established human tumors are lacking. By simulating spatial tumor growth under different evolutionary modes and examining patterns of between-region subclonal genetic divergence from multiregion sequencing (MRS) data, we demonstrate that it is feasible to distinguish tumors driven by strong positive subclonal selection from those evolving neutrally or under weak selection, as the latter fail to dramatically alter subclonal composition...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28581502/genome-wide-characterization-of-mammalian-promoters-with-distal-enhancer-functions
#12
Lan T M Dao, Ariel O Galindo-Albarrán, Jaime A Castro-Mondragon, Charlotte Andrieu-Soler, Alejandra Medina-Rivera, Charbel Souaid, Guillaume Charbonnier, Aurélien Griffon, Laurent Vanhille, Tharshana Stephen, Jaafar Alomairi, David Martin, Magali Torres, Nicolas Fernandez, Eric Soler, Jacques van Helden, Denis Puthier, Salvatore Spicuglia
Gene expression in mammals is precisely regulated by the combination of promoters and gene-distal regulatory regions, known as enhancers. Several studies have suggested that some promoters might have enhancer functions. However, the extent of this type of promoters and whether they actually function to regulate the expression of distal genes have remained elusive. Here, by exploiting a high-throughput enhancer reporter assay, we unravel a set of mammalian promoters displaying enhancer activity. These promoters have distinct genomic and epigenomic features and frequently interact with other gene promoters...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28581501/genomic-analyses-in-cotton-identify-signatures-of-selection-and-loci-associated-with-fiber-quality-and-yield-traits
#13
Lei Fang, Qiong Wang, Yan Hu, Yinhua Jia, Jiedan Chen, Bingliang Liu, Zhiyuan Zhang, Xueying Guan, Shuqi Chen, Baoliang Zhou, Gaofu Mei, Junling Sun, Zhaoe Pan, Shoupu He, Songhua Xiao, Weijun Shi, Wenfang Gong, Jianguang Liu, Jun Ma, Caiping Cai, Xiefei Zhu, Wangzhen Guo, Xiongming Du, Tianzhen Zhang
Upland cotton (Gossypium hirsutum) is the most important natural fiber crop in the world. The overall genetic diversity among cultivated species of cotton and the genetic changes that occurred during their improvement are poorly understood. Here we report a comprehensive genomic assessment of modern improved upland cotton based on the genome-wide resequencing of 318 landraces and modern improved cultivars or lines. We detected more associated loci for lint yield than for fiber quality, which suggests that lint yield has stronger selection signatures than other traits...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28581500/hyperactivation-of-hush-complex-function-by-charcot-marie-tooth-disease-mutation-in-morc2
#14
Iva A Tchasovnikarova, Richard T Timms, Christopher H Douse, Rhys C Roberts, Gordon Dougan, Robert E Kingston, Yorgo Modis, Paul J Lehner
Dominant mutations in the MORC2 gene have recently been shown to cause axonal Charcot-Marie-Tooth (CMT) disease, but the cellular function of MORC2 is poorly understood. Here, through a genome-wide CRISPR-Cas9-mediated forward genetic screen, we identified MORC2 as an essential gene required for epigenetic silencing by the HUSH complex. HUSH recruits MORC2 to target sites in heterochromatin. We exploited a new method, differential viral accessibility (DIVA), to show that loss of MORC2 results in chromatin decompaction at these target loci, which is concomitant with a loss of H3K9me3 deposition and transcriptional derepression...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28581499/high-quality-de-novo-assembly-of-the-apple-genome-and-methylome-dynamics-of-early-fruit-development
#15
Nicolas Daccord, Jean-Marc Celton, Gareth Linsmith, Claude Becker, Nathalie Choisne, Elio Schijlen, Henri van de Geest, Luca Bianco, Diego Micheletti, Riccardo Velasco, Erica Adele Di Pierro, Jérôme Gouzy, D Jasper G Rees, Philippe Guérif, Hélène Muranty, Charles-Eric Durel, François Laurens, Yves Lespinasse, Sylvain Gaillard, Sébastien Aubourg, Hadi Quesneville, Detlef Weigel, Eric van de Weg, Michela Troggio, Etienne Bucher
Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago...
June 5, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28553959/biallelic-trip13-mutations-predispose-to-wilms-tumor-and-chromosome-missegregation
#16
Shawn Yost, Bas de Wolf, Sandra Hanks, Anna Zachariou, Chiara Marcozzi, Matthew Clarke, Richarda M de Voer, Banafsheh Etemad, Esther Uijttewaal, Emma Ramsay, Harriet Wylie, Anna Elliott, Susan Picton, Audrey Smith, Sarah Smithson, Sheila Seal, Elise Ruark, Gunnar Houge, Jonathon Pines, Geert J P L Kops, Nazneen Rahman
Through exome sequencing, we identified six individuals with biallelic loss-of-function mutations in TRIP13. All six developed Wilms tumor. Constitutional mosaic aneuploidies, microcephaly, developmental delay and seizures, which are features of mosaic variegated aneuploidy (MVA) syndrome, were more variably present. Through functional studies, we show that TRIP13-mutant patient cells have no detectable TRIP13 and have substantial impairment of the spindle assembly checkpoint (SAC), leading to a high rate of chromosome missegregation...
May 29, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28553958/polygenic-burdens-on-cell-specific-pathways-underlie-the-risk-of-rheumatoid-arthritis
#17
Kazuyoshi Ishigaki, Yuta Kochi, Akari Suzuki, Yumi Tsuchida, Haruka Tsuchiya, Shuji Sumitomo, Kensuke Yamaguchi, Yasuo Nagafuchi, Shinichiro Nakachi, Rika Kato, Keiichi Sakurai, Hirofumi Shoda, Katsunori Ikari, Atsuo Taniguchi, Hisashi Yamanaka, Fuyuki Miya, Tatsuhiko Tsunoda, Yukinori Okada, Yukihide Momozawa, Yoichiro Kamatani, Ryo Yamada, Michiaki Kubo, Keishi Fujio, Kazuhiko Yamamoto
Recent evidence suggests that a substantial portion of complex disease risk alleles modify gene expression in a cell-specific manner. To identify candidate causal genes and biological pathways of immune-related complex diseases, we conducted expression quantitative trait loci (eQTL) analysis on five subsets of immune cells (CD4(+) T cells, CD8(+) T cells, B cells, natural killer (NK) cells and monocytes) and unfractionated peripheral blood from 105 healthy Japanese volunteers. We developed a three-step analytical pipeline comprising (i) prediction of individual gene expression using our eQTL database and public epigenomic data, (ii) gene-level association analysis and (iii) prediction of cell-specific pathway activity by integrating the direction of eQTL effects...
May 29, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28553957/genetic-association-study-of-exfoliation-syndrome-identifies-a-protective-rare-variant-at-loxl1-and-five-new-susceptibility-loci
#18
Tin Aung, Mineo Ozaki, Mei Chin Lee, Ursula Schlötzer-Schrehardt, Gudmar Thorleifsson, Takanori Mizoguchi, Robert P Igo, Aravind Haripriya, Susan E Williams, Yury S Astakhov, Andrew C Orr, Kathryn P Burdon, Satoko Nakano, Kazuhiko Mori, Khaled Abu-Amero, Michael Hauser, Zheng Li, Gopalakrishnan Prakadeeswari, Jessica N Cooke Bailey, Alina Popa Cherecheanu, Jae H Kang, Sarah Nelson, Ken Hayashi, Shin-Ichi Manabe, Shigeyasu Kazama, Tomasz Zarnowski, Kenji Inoue, Murat Irkec, Miguel Coca-Prados, Kazuhisa Sugiyama, Irma Järvelä, Patricio Schlottmann, S Fabian Lerner, Hasnaa Lamari, Yildirim Nilgün, Mukharram Bikbov, Ki Ho Park, Soon Cheol Cha, Kenji Yamashiro, Juan C Zenteno, Jost B Jonas, Rajesh S Kumar, Shamira A Perera, Anita S Y Chan, Nino Kobakhidze, Ronnie George, Lingam Vijaya, Tan Do, Deepak P Edward, Lourdes de Juan Marcos, Mohammad Pakravan, Sasan Moghimi, Ryuichi Ideta, Daniella Bach-Holm, Per Kappelgaard, Barbara Wirostko, Samuel Thomas, Daniel Gaston, Karen Bedard, Wenda L Greer, Zhenglin Yang, Xueyi Chen, Lulin Huang, Jinghong Sang, Hongyan Jia, Liyun Jia, Chunyan Qiao, Hui Zhang, Xuyang Liu, Bowen Zhao, Ya-Xing Wang, Liang Xu, Stéphanie Leruez, Pascal Reynier, George Chichua, Sergo Tabagari, Steffen Uebe, Matthias Zenkel, Daniel Berner, Georg Mossböck, Nicole Weisschuh, Ursula Hoja, Ulrich-Christoph Welge-Luessen, Christian Mardin, Panayiota Founti, Anthi Chatzikyriakidou, Theofanis Pappas, Eleftherios Anastasopoulos, Alexandros Lambropoulos, Arkasubhra Ghosh, Rohit Shetty, Natalia Porporato, Vijayan Saravanan, Rengaraj Venkatesh, Chandrashekaran Shivkumar, Narendran Kalpana, Sripriya Sarangapani, Mozhgan R Kanavi, Afsaneh Naderi Beni, Shahin Yazdani, Alireza Lashay, Homa Naderifar, Nassim Khatibi, Antonio Fea, Carlo Lavia, Laura Dallorto, Teresa Rolle, Paolo Frezzotti, Daniela Paoli, Erika Salvi, Paolo Manunta, Yosai Mori, Kazunori Miyata, Tomomi Higashide, Etsuo Chihara, Satoshi Ishiko, Akitoshi Yoshida, Masahide Yanagi, Yoshiaki Kiuchi, Tsutomu Ohashi, Toshiya Sakurai, Takako Sugimoto, Hideki Chuman, Makoto Aihara, Masaru Inatani, Masahiro Miyake, Norimoto Gotoh, Fumihiko Matsuda, Nagahisa Yoshimura, Yoko Ikeda, Morio Ueno, Chie Sotozono, Jin Wook Jeoung, Min Sagong, Kyu Hyung Park, Jeeyun Ahn, Marisa Cruz-Aguilar, Sidi M Ezzouhairi, Abderrahman Rafei, Yaan Fun Chong, Xiao Yu Ng, Shuang Ru Goh, Yueming Chen, Victor H K Yong, Muhammad Imran Khan, Olusola O Olawoye, Adeyinka O Ashaye, Idakwo Ugbede, Adeola Onakoya, Nkiru Kizor-Akaraiwe, Chaiwat Teekhasaenee, Yanin Suwan, Wasu Supakontanasan, Suhanya Okeke, Nkechi J Uche, Ifeoma Asimadu, Humaira Ayub, Farah Akhtar, Ewa Kosior-Jarecka, Urszula Lukasik, Ignacio Lischinsky, Vania Castro, Rodolfo Perez Grossmann, Gordana Sunaric Megevand, Sylvain Roy, Edward Dervan, Eoin Silke, Aparna Rao, Priti Sahay, Pablo Fornero, Osvaldo Cuello, Delia Sivori, Tamara Zompa, Richard A Mills, Emmanuelle Souzeau, Paul Mitchell, Jie Jin Wang, Alex W Hewitt, Michael Coote, Jonathan G Crowston, Sergei Y Astakhov, Eugeny L Akopov, Anton Emelyanov, Vera Vysochinskaya, Gyulli Kazakbaeva, Rinat Fayzrakhmanov, Saleh A Al-Obeidan, Ohoud Owaidhah, Leyla Ali Aljasim, Balram Chowbay, Jia Nee Foo, Raphael Q Soh, Kar Seng Sim, Zhicheng Xie, Augustine W O Cheong, Shi Qi Mok, Hui Meng Soo, Xiao Yin Chen, Su Qin Peh, Khai Koon Heng, Rahat Husain, Su-Ling Ho, Axel M Hillmer, Ching-Yu Cheng, Francisco A Escudero-Domínguez, Rogelio González-Sarmiento, Frederico Martinon-Torres, Antonio Salas, Kessara Pathanapitoon, Linda Hansapinyo, Boonsong Wanichwecharugruang, Naris Kitnarong, Anavaj Sakuntabhai, Hip X Nguyn, Giang T T Nguyn, Trình V Nguyn, Werner Zenz, Alexander Binder, Daniela S Klobassa, Martin L Hibberd, Sonia Davila, Stefan Herms, Markus M Nöthen, Susanne Moebus, Robyn M Rautenbach, Ari Ziskind, Trevor R Carmichael, Michele Ramsay, Lydia Álvarez, Montserrat García, Héctor González-Iglesias, Pedro P Rodríguez-Calvo, Luis Fernández-Vega Cueto, Çilingir Oguz, Nevbahar Tamcelik, Eray Atalay, Bilge Batu, Dilek Aktas, Burcu Kasım, M Roy Wilson, Anne L Coleman, Yutao Liu, Pratap Challa, Leon Herndon, Rachel W Kuchtey, John Kuchtey, Karen Curtin, Craig J Chaya, Alan Crandall, Linda M Zangwill, Tien Yin Wong, Masakazu Nakano, Shigeru Kinoshita, Anneke I den Hollander, Eija Vesti, John H Fingert, Richard K Lee, Arthur J Sit, Bradford J Shingleton, Ningli Wang, Daniele Cusi, Raheel Qamar, Peter Kraft, Margaret A Pericak-Vance, Soumya Raychaudhuri, Steffen Heegaard, Tero Kivelä, André Reis, Friedrich E Kruse, Robert N Weinreb, Louis R Pasquale, Jonathan L Haines, Unnur Thorsteinsdottir, Fridbert Jonasson, R Rand Allingham, Dan Milea, Robert Ritch, Toshiaki Kubota, Kei Tashiro, Eranga N Vithana, Shazia Micheal, Fotis Topouzis, Jamie E Craig, Michael Dubina, Periasamy Sundaresan, Kari Stefansson, Janey L Wiggs, Francesca Pasutto, Chiea Chuen Khor
Exfoliation syndrome (XFS) is the most common known risk factor for secondary glaucoma and a major cause of blindness worldwide. Variants in two genes, LOXL1 and CACNA1A, have previously been associated with XFS. To further elucidate the genetic basis of XFS, we collected a global sample of XFS cases to refine the association at LOXL1, which previously showed inconsistent results across populations, and to identify new variants associated with XFS. We identified a rare protective allele at LOXL1 (p.Phe407, odds ratio (OR) = 25, P = 2...
May 29, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28530678/the-complex-genetics-of-hypoplastic-left-heart-syndrome
#19
Xiaoqin Liu, Hisato Yagi, Shazina Saeed, Abha S Bais, George C Gabriel, Zhaohan Chen, Kevin A Peterson, You Li, Molly C Schwartz, William T Reynolds, Manush Saydmohammed, Brian Gibbs, Yijen Wu, William Devine, Bishwanath Chatterjee, Nikolai T Klena, Dennis Kostka, Karen L de Mesy Bentley, Madhavi K Ganapathiraju, Phillip Dexheimer, Linda Leatherbury, Omar Khalifa, Anchit Bhagat, Maliha Zahid, William Pu, Simon Watkins, Paul Grossfeld, Stephen A Murray, George A Porter, Michael Tsang, Lisa J Martin, D Woodrow Benson, Bruce J Aronow, Cecilia W Lo
Congenital heart disease (CHD) affects up to 1% of live births. Although a genetic etiology is indicated by an increased recurrence risk, sporadic occurrence suggests that CHD genetics is complex. Here, we show that hypoplastic left heart syndrome (HLHS), a severe CHD, is multigenic and genetically heterogeneous. Using mouse forward genetics, we report what is, to our knowledge, the first isolation of HLHS mutant mice and identification of genes causing HLHS. Mutations from seven HLHS mouse lines showed multigenic enrichment in ten human chromosome regions linked to HLHS...
May 22, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28530677/whole-genome-resequencing-of-292-pigeonpea-accessions-identifies-genomic-regions-associated-with-domestication-and-agronomic-traits
#20
Rajeev K Varshney, Rachit K Saxena, Hari D Upadhyaya, Aamir W Khan, Yue Yu, Changhoon Kim, Abhishek Rathore, Dongseon Kim, Jihun Kim, Shaun An, Vinay Kumar, Ghanta Anuradha, Kalinati Narasimhan Yamini, Wei Zhang, Sonnappa Muniswamy, Jong-So Kim, R Varma Penmetsa, Eric von Wettberg, Swapan K Datta
Pigeonpea (Cajanus cajan), a tropical grain legume with low input requirements, is expected to continue to have an important role in supplying food and nutritional security in developing countries in Asia, Africa and the tropical Americas. From whole-genome resequencing of 292 Cajanus accessions encompassing breeding lines, landraces and wild species, we characterize genome-wide variation. On the basis of a scan for selective sweeps, we find several genomic regions that were likely targets of domestication and breeding...
May 22, 2017: Nature Genetics
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