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  • 1
    Publication Date: 2012-02-22
    Description: Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease-causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299548/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3299548/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacArthur, Daniel G -- Balasubramanian, Suganthi -- Frankish, Adam -- Huang, Ni -- Morris, James -- Walter, Klaudia -- Jostins, Luke -- Habegger, Lukas -- Pickrell, Joseph K -- Montgomery, Stephen B -- Albers, Cornelis A -- Zhang, Zhengdong D -- Conrad, Donald F -- Lunter, Gerton -- Zheng, Hancheng -- Ayub, Qasim -- DePristo, Mark A -- Banks, Eric -- Hu, Min -- Handsaker, Robert E -- Rosenfeld, Jeffrey A -- Fromer, Menachem -- Jin, Mike -- Mu, Xinmeng Jasmine -- Khurana, Ekta -- Ye, Kai -- Kay, Mike -- Saunders, Gary Ian -- Suner, Marie-Marthe -- Hunt, Toby -- Barnes, If H A -- Amid, Clara -- Carvalho-Silva, Denise R -- Bignell, Alexandra H -- Snow, Catherine -- Yngvadottir, Bryndis -- Bumpstead, Suzannah -- Cooper, David N -- Xue, Yali -- Romero, Irene Gallego -- 1000 Genomes Project Consortium -- Wang, Jun -- Li, Yingrui -- Gibbs, Richard A -- McCarroll, Steven A -- Dermitzakis, Emmanouil T -- Pritchard, Jonathan K -- Barrett, Jeffrey C -- Harrow, Jennifer -- Hurles, Matthew E -- Gerstein, Mark B -- Tyler-Smith, Chris -- 085532/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- BB/I02593X/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- RG/09/012/28096/British Heart Foundation/United Kingdom -- U54 HG003273/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2012 Feb 17;335(6070):823-8. doi: 10.1126/science.1215040.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Hinxton, UK. macarthur@atgu.mgh.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22344438" target="_blank"〉PubMed〈/a〉
    Keywords: Disease/genetics ; Gene Expression ; Gene Frequency ; *Genetic Variation ; *Genome, Human ; Humans ; Phenotype ; Polymorphism, Single Nucleotide ; Proteins/*genetics ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-11-07
    Description: Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491803/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491803/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jostins, Luke -- Ripke, Stephan -- Weersma, Rinse K -- Duerr, Richard H -- McGovern, Dermot P -- Hui, Ken Y -- Lee, James C -- Schumm, L Philip -- Sharma, Yashoda -- Anderson, Carl A -- Essers, Jonah -- Mitrovic, Mitja -- Ning, Kaida -- Cleynen, Isabelle -- Theatre, Emilie -- Spain, Sarah L -- Raychaudhuri, Soumya -- Goyette, Philippe -- Wei, Zhi -- Abraham, Clara -- Achkar, Jean-Paul -- Ahmad, Tariq -- Amininejad, Leila -- Ananthakrishnan, Ashwin N -- Andersen, Vibeke -- Andrews, Jane M -- Baidoo, Leonard -- Balschun, Tobias -- Bampton, Peter A -- Bitton, Alain -- Boucher, Gabrielle -- Brand, Stephan -- Buning, Carsten -- Cohain, Ariella -- Cichon, Sven -- D'Amato, Mauro -- De Jong, Dirk -- Devaney, Kathy L -- Dubinsky, Marla -- Edwards, Cathryn -- Ellinghaus, David -- Ferguson, Lynnette R -- Franchimont, Denis -- Fransen, Karin -- Gearry, Richard -- Georges, Michel -- Gieger, Christian -- Glas, Jurgen -- Haritunians, Talin -- Hart, Ailsa -- Hawkey, Chris -- Hedl, Matija -- Hu, Xinli -- Karlsen, Tom H -- Kupcinskas, Limas -- Kugathasan, Subra -- Latiano, Anna -- Laukens, Debby -- Lawrance, Ian C -- Lees, Charlie W -- Louis, Edouard -- Mahy, Gillian -- Mansfield, John -- Morgan, Angharad R -- Mowat, Craig -- Newman, William -- Palmieri, Orazio -- Ponsioen, Cyriel Y -- Potocnik, Uros -- Prescott, Natalie J -- Regueiro, Miguel -- Rotter, Jerome I -- Russell, Richard K -- Sanderson, Jeremy D -- Sans, Miquel -- Satsangi, Jack -- Schreiber, Stefan -- Simms, Lisa A -- Sventoraityte, Jurgita -- Targan, Stephan R -- Taylor, Kent D -- Tremelling, Mark -- Verspaget, Hein W -- De Vos, Martine -- Wijmenga, Cisca -- Wilson, David C -- Winkelmann, Juliane -- Xavier, Ramnik J -- Zeissig, Sebastian -- Zhang, Bin -- Zhang, Clarence K -- Zhao, Hongyu -- International IBD Genetics Consortium (IIBDGC) -- Silverberg, Mark S -- Annese, Vito -- Hakonarson, Hakon -- Brant, Steven R -- Radford-Smith, Graham -- Mathew, Christopher G -- Rioux, John D -- Schadt, Eric E -- Daly, Mark J -- Franke, Andre -- Parkes, Miles -- Vermeire, Severine -- Barrett, Jeffrey C -- Cho, Judy H -- 068545/Z/02/Wellcome Trust/United Kingdom -- 083948/Z/07/Z/Wellcome Trust/United Kingdom -- 085475/B/08/Z/Wellcome Trust/United Kingdom -- 085475/Z/08/Z/Wellcome Trust/United Kingdom -- 089120/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- AI062773/AI/NIAID NIH HHS/ -- CA141743/CA/NCI NIH HHS/ -- CZB/4/540/Chief Scientist Office/United Kingdom -- DK043351/DK/NIDDK NIH HHS/ -- DK062413/DK/NIDDK NIH HHS/ -- DK062420/DK/NIDDK NIH HHS/ -- DK062422/DK/NIDDK NIH HHS/ -- DK062423/DK/NIDDK NIH HHS/ -- DK062429/DK/NIDDK NIH HHS/ -- DK062429-S1/DK/NIDDK NIH HHS/ -- DK062431/DK/NIDDK NIH HHS/ -- DK062432/DK/NIDDK NIH HHS/ -- DK063491/DK/NIDDK NIH HHS/ -- DK076984/DK/NIDDK NIH HHS/ -- DK084554/DK/NIDDK NIH HHS/ -- DK83756/DK/NIDDK NIH HHS/ -- ETM/137/Chief Scientist Office/United Kingdom -- ETM/75/Chief Scientist Office/United Kingdom -- G0000934/British Heart Foundation/United Kingdom -- G0600329/Medical Research Council/United Kingdom -- G0800675/Medical Research Council/United Kingdom -- G0800759/Medical Research Council/United Kingdom -- G1002033/Medical Research Council/United Kingdom -- K23 DK097142/DK/NIDDK NIH HHS/ -- M01-RR00425/RR/NCRR NIH HHS/ -- P01 DK046763/DK/NIDDK NIH HHS/ -- P01DK046763/DK/NIDDK NIH HHS/ -- P30 DK043351/DK/NIDDK NIH HHS/ -- R01 CA141743/CA/NCI NIH HHS/ -- R01 DK055731/DK/NIDDK NIH HHS/ -- T32 GM007205/GM/NIGMS NIH HHS/ -- T32GM07205/GM/NIGMS NIH HHS/ -- U01 DK062418/DK/NIDDK NIH HHS/ -- U01 DK062420/DK/NIDDK NIH HHS/ -- U01 DK062422/DK/NIDDK NIH HHS/ -- U01 DK062429/DK/NIDDK NIH HHS/ -- U01 DK062431/DK/NIDDK NIH HHS/ -- U01 DK062432/DK/NIDDK NIH HHS/ -- UL1 TR000005/TR/NCATS NIH HHS/ -- UL1 TR000124/TR/NCATS NIH HHS/ -- UL1 TR000124-01/TR/NCATS NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2012 Nov 1;491(7422):119-24. doi: 10.1038/nature11582.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23128233" target="_blank"〉PubMed〈/a〉
    Keywords: Colitis, Ulcerative/genetics/immunology/microbiology/physiopathology ; Crohn Disease/genetics/immunology/microbiology/physiopathology ; Genetic Predisposition to Disease/*genetics ; Genome, Human/genetics ; *Genome-Wide Association Study ; Haplotypes/genetics ; *Host-Pathogen Interactions/genetics/immunology ; Humans ; Inflammatory Bowel Diseases/*genetics/immunology/*microbiology/physiopathology ; Mycobacterium/*immunology/pathogenicity ; Mycobacterium Infections/genetics/microbiology ; Mycobacterium tuberculosis/immunology/pathogenicity ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2013-05-24
    Description: Genome-wide association studies (GWAS) have identified common variants of modest-effect size at hundreds of loci for common autoimmune diseases; however, a substantial fraction of heritability remains unexplained, to which rare variants may contribute. To discover rare variants and test them for association with a phenotype, most studies re-sequence a small initial sample size and then genotype the discovered variants in a larger sample set. This approach fails to analyse a large fraction of the rare variants present in the entire sample set. Here we perform simultaneous amplicon-sequencing-based variant discovery and genotyping for coding exons of 25 GWAS risk genes in 41,911 UK residents of white European origin, comprising 24,892 subjects with six autoimmune disease phenotypes and 17,019 controls, and show that rare coding-region variants at known loci have a negligible role in common autoimmune disease susceptibility. These results do not support the rare-variant synthetic genome-wide-association hypothesis (in which unobserved rare causal variants lead to association detected at common tag variants). Many known autoimmune disease risk loci contain multiple, independently associated, common and low-frequency variants, and so genes at these loci are a priori stronger candidates for harbouring rare coding-region variants than other genes. Our data indicate that the missing heritability for common autoimmune diseases may not be attributable to the rare coding-region variant portion of the allelic spectrum, but perhaps, as others have proposed, may be a result of many common-variant loci of weak effect.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736321/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736321/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hunt, Karen A -- Mistry, Vanisha -- Bockett, Nicholas A -- Ahmad, Tariq -- Ban, Maria -- Barker, Jonathan N -- Barrett, Jeffrey C -- Blackburn, Hannah -- Brand, Oliver -- Burren, Oliver -- Capon, Francesca -- Compston, Alastair -- Gough, Stephen C L -- Jostins, Luke -- Kong, Yong -- Lee, James C -- Lek, Monkol -- MacArthur, Daniel G -- Mansfield, John C -- Mathew, Christopher G -- Mein, Charles A -- Mirza, Muddassar -- Nutland, Sarah -- Onengut-Gumuscu, Suna -- Papouli, Efterpi -- Parkes, Miles -- Rich, Stephen S -- Sawcer, Steven -- Satsangi, Jack -- Simmonds, Matthew J -- Trembath, Richard C -- Walker, Neil M -- Wozniak, Eva -- Todd, John A -- Simpson, Michael A -- Plagnol, Vincent -- van Heel, David A -- 068181/Wellcome Trust/United Kingdom -- 068545/Z/02/Wellcome Trust/United Kingdom -- 076113/C/04/Z/Wellcome Trust/United Kingdom -- 091157/Wellcome Trust/United Kingdom -- 100140/Wellcome Trust/United Kingdom -- CZB/4/540/Chief Scientist Office/United Kingdom -- ETM/137/Chief Scientist Office/United Kingdom -- ETM/75/Chief Scientist Office/United Kingdom -- G0000934/Medical Research Council/United Kingdom -- G0600329/Medical Research Council/United Kingdom -- G0601387/Medical Research Council/United Kingdom -- G0800759/Medical Research Council/United Kingdom -- G1001158/Medical Research Council/United Kingdom -- G1001158(95979)/Medical Research Council/United Kingdom -- JDRF 4-2001-1008/Wellcome Trust/United Kingdom -- WT061858/Wellcome Trust/United Kingdom -- England -- Nature. 2013 Jun 13;498(7453):232-5. doi: 10.1038/nature12170. Epub 2013 May 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23698362" target="_blank"〉PubMed〈/a〉
    Keywords: Autoimmune Diseases/*genetics ; European Continental Ancestry Group/genetics ; Exons/genetics ; Gene Frequency ; Genetic Predisposition to Disease/*genetics ; Genetic Variation/*genetics ; Genome-Wide Association Study ; Great Britain ; Humans ; Models, Genetic ; Mutation/genetics ; Open Reading Frames/*genetics ; Phenotype ; Sample Size
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-03-08
    Description: To systematically investigate the impact of immune stimulation upon regulatory variant activity, we exposed primary monocytes from 432 healthy Europeans to interferon-gamma (IFN-gamma) or differing durations of lipopolysaccharide and mapped expression quantitative trait loci (eQTLs). More than half of cis-eQTLs identified, involving hundreds of genes and associated pathways, are detected specifically in stimulated monocytes. Induced innate immune activity reveals multiple master regulatory trans-eQTLs including the major histocompatibility complex (MHC), coding variants altering enzyme and receptor function, an IFN-beta cytokine network showing temporal specificity, and an interferon regulatory factor 2 (IRF2) transcription factor-modulated network. Induced eQTL are significantly enriched for genome-wide association study loci, identifying context-specific associations to putative causal genes including CARD9, ATM, and IRF8. Thus, applying pathophysiologically relevant immune stimuli assists resolution of functional genetic variants.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064786/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064786/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fairfax, Benjamin P -- Humburg, Peter -- Makino, Seiko -- Naranbhai, Vivek -- Wong, Daniel -- Lau, Evelyn -- Jostins, Luke -- Plant, Katharine -- Andrews, Robert -- McGee, Chris -- Knight, Julian C -- 074318/Wellcome Trust/United Kingdom -- 088891/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 281824/European Research Council/International -- 98082/Medical Research Council/United Kingdom -- G1001708/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2014 Mar 7;343(6175):1246949. doi: 10.1126/science.1246949.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24604202" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Antigens, CD14/immunology ; Aryl Hydrocarbon Hydroxylases/genetics ; Basic-Leucine Zipper Transcription Factors/genetics ; CARD Signaling Adaptor Proteins/genetics ; Chromosome Mapping ; Crohn Disease/epidemiology/*genetics ; Cytochrome P-450 CYP1B1 ; Female ; Gene Expression Regulation/*immunology ; *Genetic Predisposition to Disease ; Genetic Variation ; Genome-Wide Association Study ; Humans ; Immunity, Innate/*genetics ; Indoleamine-Pyrrole 2,3,-Dioxygenase/genetics ; Interferon Regulatory Factor-2/genetics ; Interferon Regulatory Factors/genetics ; Interferon-gamma/pharmacology ; Male ; Middle Aged ; Monocytes/drug effects/*immunology ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Receptors, Purinergic P2/genetics ; Young Adult
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Manuel A. Rivas; Daniel Graham; Patrick Sulem; Christine Stevens; A. Nicole Desch; Philippe Goyette; Daniel Gudbjartsson; Ingileif Jonsdottir; Unnur Thorsteinsdottir; Frauke Degenhardt; Sören Mucha; Mitja I. Kurki; Dalin Li; Mauro D’Amato; Vito Annese; Severine Vermeire; Rinse K. Weersma; Jonas Halfvarson; Paulina Paavola-Sakki; Maarit Lappalainen; Monkol Lek; Beryl Cummings; Taru Tukiainen; Talin Haritunians; Leena Halme; Lotta L. E. Koskinen; Ashwin N. Ananthakrishnan; Yang Luo; Graham A. Heap; Marijn C. Visschedijk; UK IBD Genetics Consortium; J. Barrett; K. de Lange; C. Edwards; A. Hart; C. Hawkey; L. Jostins; N. Kennedy; C. Lamb; J. Lee; C. Lees; J. Mansfield; C. Mathew; C. Mowatt; W. Newman; E. Nimmo; M. Parkes; M. Pollard; N. Prescott; J. Randall; D. Rice; J. Satsangi; A. Simmons; M. Tremelling; H. Uhlig; D. Wilson; NIDDK IBD Genetics Consortium; C. Abraham; J.P. Achkar; A. Bitton; G. Boucher; K. Croitoru; P. Fleshner; J. Glas; S. Kugathasan; J. V. Limbergen; R. Milgrom; D. Proctor; M. Regueiro; P. L. Schumm; Y. Sharma; J. M. Stempak; S. R. Targan; M. H. Wang; Daniel G. Mac; Arthur; Benjamin M. Neale; Tariq Ahmad; Carl A. Anderson; Steven R. Brant; Richard H. Duerr; Mark S. Silverberg; Judy H. Cho; Aarno Palotie; Päivi Saavalainen; Kimmo Kontula; Martti FärkkiläDermot P. B. McGovern; Andre Franke; Kari Stefansson; John D. Rioux; Ramnik J. Xavier; Mark J. Daly
    Springer Nature
    Publication Date: 2016-09-14
    Description: Erratum: A protein-truncating R179X variant in 〈i〉RNF186〈/i〉 confers protection against ulcerative colitis Nature Communications, Published online: 13 September 2016; doi:10.1038/ncomms12869
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 6
    Publication Date: 2012-04-12
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 7
  • 8
    Publication Date: 2016-06-16
    Description: Motivation : For many classes of disease the same genetic risk variants underly many related phenotypes or disease subtypes. Multinomial logistic regression provides an attractive framework to analyze multi-category phenotypes, and explore the genetic relationships between these phenotype categories. We introduce Trinculo, a program that implements a wide range of multinomial analyses in a single fast package that is designed to be easy to use by users of standard genome-wide association study software. Availability and implementation : An open source C implementation, with code and binaries for Linux and Mac OSX, is available for download at http://sourceforge.net/projects/trinculo Supplementary information: Supplementary data are available at Bioinformatics online. Contact : lj4@well.ox.ac.uk
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 9
    Publication Date: 2012-05-02
    Description: Kogan et al. recently reported an association between an intronic variant in the oxytocin receptor gene, OXTR, and perceived prosociality (1). The significance of this association is described as P 〈 0.001, but the reported t statistic corresponds to P = 3.2 × 10−16. This level of significance is striking given the small number of genotyped individuals (N = 23) compared with other studies of complex trait genetics (2, 3). We show that this highly significant P value is a result of a misapplication of the statistical technique of hierarchical linear models (HLMs), and that the P value under an...
    Keywords: Letters
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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