Shane McCarthy

Shane McCarthy

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Shane McCarthy

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Population-based identity-by-descent mapping combined with exome sequencing to detect rare risk variants for schizophrenia.

Am J Med Genet B Neuropsychiatr Genet 2019 Apr 23;180(3):223-231. Epub 2019 Feb 23.

Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition & Genomics (NICOG) Centre & NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland.

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http://dx.doi.org/10.1002/ajmg.b.32716DOI Listing
April 2019

Crumble: reference free lossy compression of sequence quality values.

Bioinformatics 2019 Jan;35(2):337-339

DNA Pipelines, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1093/bioinformatics/bty608DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330002PMC
January 2019

Altered DNA methylation associated with a translocation linked to major mental illness.

NPJ Schizophr 2018 Mar 19;4(1). Epub 2018 Mar 19.

Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, Western General Hospital, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK.

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http://dx.doi.org/10.1038/s41537-018-0047-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859082PMC
March 2018

A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease.

N Engl J Med 2018 03;378(12):1096-1106

From the Regeneron Genetics Center (N.S.A.-H., A.H.L., C.S., S. McCarthy, C.O., J.S.P., S.B., N.G., S. Mukherjee, A.E.L., E.D.F., J.P., I.B.B., A.R.S., J.G.R., J.D.O., O.G., T.M.T., A.B., F.E.D.) and Regeneron Pharmaceuticals (X. Cheng, Y.X., P.S., Y.L., D.E., S.Y.K., B.Z., W.O., A.J.M., G.D.Y., J.G.), Tarrytown, NY; the University of Texas Southwestern Medical Center at Dallas, Dallas (J.K., S.S., H.H.H., J.C.C.); and Geisinger Health System, Danville (G.C.W., A.N.S., M.D.S., X. Chu, J.Z.L., U.L.M., D.J.C., C.D.S., T.M.), and Perelman School of Medicine, University of Pennsylvania, Philadelphia (M.D.F., A.S., S.M.D., D.J.R.) - both in Pennsylvania.

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http://dx.doi.org/10.1056/NEJMoa1712191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6668033PMC
March 2018

BCFtools/csq: haplotype-aware variant consequences.

Bioinformatics 2017 Jul;33(13):2037-2039

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.

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http://dx.doi.org/10.1093/bioinformatics/btx100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870570PMC
July 2017

Genetic and Pharmacologic Inactivation of ANGPTL3 and Cardiovascular Disease.

N Engl J Med 2017 07 24;377(3):211-221. Epub 2017 May 24.

From Regeneron Genetics Center (F.E.D., C.O., C.S., O.G., S.M., C.V.V.H., S.B., L.H., A.L., J.P., N.S., A.J.M., J.D.O., J.G.R., A.R.S., I.B.B., T.M.T., G.D.Y., S.J.M., A. Baras) and Regeneron Pharmaceuticals (V.G., H.M.D., A.Z., W.S., N.S., A.J.M., S.H., A. Bouzelmat, R.Z., B.S., R.P., D.G., G.A.H., W.J.S., P.B., G.D.Y., S.J.M., J.G.) Tarrytown, NY; the Department of Medicine, Division of Translational Medicine and Human Genetics (R.L.D.), and Departments of Surgery (S.D.) and Genetics and Medicine (A.S., D.J.R.), Perelman School of Medicine, University of Pennsylvania, Philadelphia, and Geisinger Health System, Danville (J.B.L., M.F.M., M.D.R., H.L.K., D.H.L., D.J.C.) - both in Pennsylvania; the Division of Endocrinology and Metabolism, Department of Internal Medicine (W.H.H.S., I.-T.L.) and Cardiovascular Center (K.-W.L.), Taichung Veterans General Hospital, Institute of Medical Technology, National Chung-Hsing University (W.H.H.S.), School of Medicine, Chung Shan Medical University (I.-T.L.), and the Department of Medicine, China Medical University (K.-W.L.), Taichung, and School of Medicine, National Yang-Ming University (W.H.H.S., I.-T.L., K.-W.L.), and School of Medicine, National Defense Medical Center (W.H.H.S.), Taipei - all in Taiwan; Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA (X.G., J.I.R., Y.-D.I.C.); the Division of Cardiology, Department of Medicine, Molecular Physiology Institute, School of Medicine, Duke University, Durham, NC (W.E.K., S.H.S.); the Department of Clinical Biochemistry, Rigshospitalet (A.B.W., B.G.N., A.T.-H.), the Copenhagen General Population Study (B.G.N., A.T.-H.) and Department of Clinical Biochemistry (B.G.N.), Herlev and Gentofte Hospital, and the Copenhagen City Heart Study, Frederiksberg Hospital, Copenhagen University Hospital, and Faculty of Health and Medical Sciences, University of Copenhagen (B.G.N., A.T.-H.) - all in Copenhagen; and TNO Metabolic Health Research, Gaubius Laboratory, Leiden, the Netherlands (A.M.H., H.M.G.P.).

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http://dx.doi.org/10.1056/NEJMoa1612790DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5800308PMC
July 2017

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Authors:
Ioanna Tachmazidou Dániel Süveges Josine L Min Graham R S Ritchie Julia Steinberg Klaudia Walter Valentina Iotchkova Jeremy Schwartzentruber Jie Huang Yasin Memari Shane McCarthy Andrew A Crawford Cristina Bombieri Massimiliano Cocca Aliki-Eleni Farmaki Tom R Gaunt Pekka Jousilahti Marjolein N Kooijman Benjamin Lehne Giovanni Malerba Satu Männistö Angela Matchan Carolina Medina-Gomez Sarah J Metrustry Abhishek Nag Ioanna Ntalla Lavinia Paternoster Nigel W Rayner Cinzia Sala William R Scott Hashem A Shihab Lorraine Southam Beate St Pourcain Michela Traglia Katerina Trajanoska Gialuigi Zaza Weihua Zhang María S Artigas Narinder Bansal Marianne Benn Zhongsheng Chen Petr Danecek Wei-Yu Lin Adam Locke Jian'an Luan Alisa K Manning Antonella Mulas Carlo Sidore Anne Tybjaerg-Hansen Anette Varbo Magdalena Zoledziewska Chris Finan Konstantinos Hatzikotoulas Audrey E Hendricks John P Kemp Alireza Moayyeri Kalliope Panoutsopoulou Michal Szpak Scott G Wilson Michael Boehnke Francesco Cucca Emanuele Di Angelantonio Claudia Langenberg Cecilia Lindgren Mark I McCarthy Andrew P Morris Børge G Nordestgaard Robert A Scott Martin D Tobin Nicholas J Wareham Paul Burton John C Chambers George Davey Smith George Dedoussis Janine F Felix Oscar H Franco Giovanni Gambaro Paolo Gasparini Christopher J Hammond Albert Hofman Vincent W V Jaddoe Marcus Kleber Jaspal S Kooner Markus Perola Caroline Relton Susan M Ring Fernando Rivadeneira Veikko Salomaa Timothy D Spector Oliver Stegle Daniela Toniolo André G Uitterlinden Inês Barroso Celia M T Greenwood John R B Perry Brian R Walker Adam S Butterworth Yali Xue Richard Durbin Kerrin S Small Nicole Soranzo Nicholas J Timpson Eleftheria Zeggini

Am J Hum Genet 2017 Jun 25;100(6):865-884. Epub 2017 May 25.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2017.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473732PMC
June 2017

Divergent Levels of Marker Chromosomes in an hiPSC-Based Model of Psychosis.

Stem Cell Reports 2017 03 16;8(3):519-528. Epub 2017 Feb 16.

Departments of Neuroscience, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2017.01.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5355568PMC
March 2017

A reference panel of 64,976 haplotypes for genotype imputation.

Authors:
Shane McCarthy Sayantan Das Warren Kretzschmar Olivier Delaneau Andrew R Wood Alexander Teumer Hyun Min Kang Christian Fuchsberger Petr Danecek Kevin Sharp Yang Luo Carlo Sidore Alan Kwong Nicholas Timpson Seppo Koskinen Scott Vrieze Laura J Scott He Zhang Anubha Mahajan Jan Veldink Ulrike Peters Carlos Pato Cornelia M van Duijn Christopher E Gillies Ilaria Gandin Massimo Mezzavilla Arthur Gilly Massimiliano Cocca Michela Traglia Andrea Angius Jeffrey C Barrett Dorrett Boomsma Kari Branham Gerome Breen Chad M Brummett Fabio Busonero Harry Campbell Andrew Chan Sai Chen Emily Chew Francis S Collins Laura J Corbin George Davey Smith George Dedoussis Marcus Dorr Aliki-Eleni Farmaki Luigi Ferrucci Lukas Forer Ross M Fraser Stacey Gabriel Shawn Levy Leif Groop Tabitha Harrison Andrew Hattersley Oddgeir L Holmen Kristian Hveem Matthias Kretzler James C Lee Matt McGue Thomas Meitinger David Melzer Josine L Min Karen L Mohlke John B Vincent Matthias Nauck Deborah Nickerson Aarno Palotie Michele Pato Nicola Pirastu Melvin McInnis J Brent Richards Cinzia Sala Veikko Salomaa David Schlessinger Sebastian Schoenherr P Eline Slagboom Kerrin Small Timothy Spector Dwight Stambolian Marcus Tuke Jaakko Tuomilehto Leonard H Van den Berg Wouter Van Rheenen Uwe Volker Cisca Wijmenga Daniela Toniolo Eleftheria Zeggini Paolo Gasparini Matthew G Sampson James F Wilson Timothy Frayling Paul I W de Bakker Morris A Swertz Steven McCarroll Charles Kooperberg Annelot Dekker David Altshuler Cristen Willer William Iacono Samuli Ripatti Nicole Soranzo Klaudia Walter Anand Swaroop Francesco Cucca Carl A Anderson Richard M Myers Michael Boehnke Mark I McCarthy Richard Durbin

Nat Genet 2016 10 22;48(10):1279-83. Epub 2016 Aug 22.

Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/ng.3643DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388176PMC
October 2016

Deep Roots for Aboriginal Australian Y Chromosomes.

Curr Biol 2016 Mar 25;26(6):809-13. Epub 2016 Feb 25.

The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2016.01.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819516PMC
March 2016

Whole-genome sequencing identifies EN1 as a determinant of bone density and fracture.

Authors:
Hou-Feng Zheng Vincenzo Forgetta Yi-Hsiang Hsu Karol Estrada Alberto Rosello-Diez Paul J Leo Chitra L Dahia Kyung Hyun Park-Min Jonathan H Tobias Charles Kooperberg Aaron Kleinman Unnur Styrkarsdottir Ching-Ti Liu Charlotta Uggla Daniel S Evans Carrie M Nielson Klaudia Walter Ulrika Pettersson-Kymmer Shane McCarthy Joel Eriksson Tony Kwan Mila Jhamai Katerina Trajanoska Yasin Memari Josine Min Jie Huang Petr Danecek Beth Wilmot Rui Li Wen-Chi Chou Lauren E Mokry Alireza Moayyeri Melina Claussnitzer Chia-Ho Cheng Warren Cheung Carolina Medina-Gómez Bing Ge Shu-Huang Chen Kwangbom Choi Ling Oei James Fraser Robert Kraaij Matthew A Hibbs Celia L Gregson Denis Paquette Albert Hofman Carl Wibom Gregory J Tranah Mhairi Marshall Brooke B Gardiner Katie Cremin Paul Auer Li Hsu Sue Ring Joyce Y Tung Gudmar Thorleifsson Anke W Enneman Natasja M van Schoor Lisette C P G M de Groot Nathalie van der Velde Beatrice Melin John P Kemp Claus Christiansen Adrian Sayers Yanhua Zhou Sophie Calderari Jeroen van Rooij Chris Carlson Ulrike Peters Soizik Berlivet Josée Dostie Andre G Uitterlinden Stephen R Williams Charles Farber Daniel Grinberg Andrea Z LaCroix Jeff Haessler Daniel I Chasman Franco Giulianini Lynda M Rose Paul M Ridker John A Eisman Tuan V Nguyen Jacqueline R Center Xavier Nogues Natalia Garcia-Giralt Lenore L Launer Vilmunder Gudnason Dan Mellström Liesbeth Vandenput Najaf Amin Cornelia M van Duijn Magnus K Karlsson Östen Ljunggren Olle Svensson Göran Hallmans François Rousseau Sylvie Giroux Johanne Bussière Pascal P Arp Fjorda Koromani Richard L Prince Joshua R Lewis Bente L Langdahl A Pernille Hermann Jens-Erik B Jensen Stephen Kaptoge Kay-Tee Khaw Jonathan Reeve Melissa M Formosa Angela Xuereb-Anastasi Kristina Åkesson Fiona E McGuigan Gaurav Garg Jose M Olmos Maria T Zarrabeitia Jose A Riancho Stuart H Ralston Nerea Alonso Xi Jiang David Goltzman Tomi Pastinen Elin Grundberg Dominique Gauguier Eric S Orwoll David Karasik George Davey-Smith Albert V Smith Kristin Siggeirsdottir Tamara B Harris M Carola Zillikens Joyce B J van Meurs Unnur Thorsteinsdottir Matthew T Maurano Nicholas J Timpson Nicole Soranzo Richard Durbin Scott G Wilson Evangelia E Ntzani Matthew A Brown Kari Stefansson David A Hinds Tim Spector L Adrienne Cupples Claes Ohlsson Celia M T Greenwood Rebecca D Jackson David W Rowe Cynthia A Loomis David M Evans Cheryl L Ackert-Bicknell Alexandra L Joyner Emma L Duncan Douglas P Kiel Fernando Rivadeneira J Brent Richards

Nature 2015 Oct 14;526(7571):112-7. Epub 2015 Sep 14.

Departments of Medicine, Human Genetics, Epidemiology and Biostatistics, McGill University, Montréal H3A 1A2, Canada.

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http://dx.doi.org/10.1038/nature14878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755714PMC
October 2015

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

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http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

Unlocking the treasure trove: from genes to schizophrenia biology.

Schizophr Bull 2014 May 27;40(3):492-6. Epub 2014 Mar 27.

*To whom correspondence should be addressed; Department of Psychiatry & Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland; tel: +353-1-8962467, fax: +353-1-8963405, e-mail:

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http://dx.doi.org/10.1093/schbul/sbu042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984532PMC
May 2014

A calibrated human Y-chromosomal phylogeny based on resequencing.

Genome Res 2013 Feb 4;23(2):388-95. Epub 2012 Oct 4.

The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom.

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http://genome.cshlp.org/cgi/doi/10.1101/gr.143198.112
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http://dx.doi.org/10.1101/gr.143198.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3561879PMC
February 2013

When does the non-variational nature of second-order Møller-Plesset energies manifest itself? All-electron correlation energies for open-shell atoms from K to Br.

J Chem Phys 2012 Feb;136(5):054107

Department of Chemistry, University of New Brunswick, Fredericton, New Brunswick E3B 5A3, Canada.

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http://aip.scitation.org/doi/10.1063/1.3679969
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http://dx.doi.org/10.1063/1.3679969DOI Listing
February 2012

Modelling schizophrenia using human induced pluripotent stem cells.

Nature 2011 May 13;473(7346):221-5. Epub 2011 Apr 13.

Salk Institute for Biological Studies, Laboratory of Genetics, 10010 North Torrey Pines Road, La Jolla California 92037, USA.

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http://dx.doi.org/10.1038/nature09915DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3392969PMC
May 2011

Accurate all-electron correlation energies for the closed-shell atoms from Ar to Rn and their relationship to the corresponding MP2 correlation energies.

J Chem Phys 2011 Jan;134(4):044102

Department of Chemistry, University of New Brunswick, Fredericton, New Brunswick E3B 5A3, Canada.

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http://aip.scitation.org/doi/10.1063/1.3547262
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http://dx.doi.org/10.1063/1.3547262DOI Listing
January 2011

Genetic polymorphisms of glutathione S-transferase genes GSTP1, GSTM1, and GSTT1 and risk of esophageal and gastric cardia cancers.

Cancer Causes Control 2009 Dec 18;20(10):2031-8. Epub 2009 Jul 18.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Box 281, 171 77 Stockholm, Sweden.

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http://link.springer.com/10.1007/s10552-009-9399-7
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http://dx.doi.org/10.1007/s10552-009-9399-7DOI Listing
December 2009

Toward improved density functionals for the correlation energy.

J Chem Phys 2009 Oct;131(13):134109

Department of Chemistry, University of New Brunswick, Fredericton, New Brunswick E3B 5A3, Canada.

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http://aip.scitation.org/doi/10.1063/1.3243845
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http://dx.doi.org/10.1063/1.3243845DOI Listing
October 2009

Nonlocal Wigner-like correlation energy density functional: parametrization and tests on two-electron systems.

J Chem Phys 2007 Jul;127(2):024101

Physikalische Chemie, Universität des Saarlandes, 66123 Saarbrücken, Germany.

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http://dx.doi.org/10.1063/1.2747242DOI Listing
July 2007

Complex HTR2C linkage disequilibrium and promoter associations with body mass index and serum leptin.

Hum Genet 2005 Oct 14;117(6):545-57. Epub 2005 Jul 14.

Center for Genomics and Bioinformatics, Karolinska Institutet, Berzelius Väg 35, 17177 Stockholm, Sweden.

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http://dx.doi.org/10.1007/s00439-005-1328-6DOI Listing
October 2005

MAOA haplotypes associated with thrombocyte-MAO activity.

BMC Genet 2005 Sep 20;6:46. Epub 2005 Sep 20.

Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1186/1471-2156-6-46DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1249565PMC
September 2005

Mutation screening of a haplotype block around the insulin degrading enzyme gene and association with Alzheimer's disease.

Am J Med Genet B Neuropsychiatr Genet 2005 Jul;136B(1):69-71

Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden.

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http://dx.doi.org/10.1002/ajmg.b.30172DOI Listing
July 2005

Serotonin receptor 2C (HTR2C) and schizophrenia: examination of possible medication and genetic influences on expression levels.

Am J Med Genet B Neuropsychiatr Genet 2005 Apr;134B(1):84-9

Department of Evolution, Genomics and Systematics, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1002/ajmg.b.30151DOI Listing
April 2005

Analysis of 5-hydroxytryptamine 2c receptor gene promoter variants as alcohol-dependence risk factors.

Alcohol Alcohol 2004 Sep-Oct;39(5):380-5. Epub 2004 Aug 10.

Center for Genomics and Bioinformatics, Karolinska Institutet, Stockholm, Sweden.

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http://dx.doi.org/10.1093/alcalc/agh086DOI Listing
December 2004