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Böhmer AC, Hecker J, Schröder J, Gharahkhani P, May A, Gerges C, Anders M, Becker J, Hess T, Kreuser N, Thieme R, Noder T, Venerito M, Veits L, Schmidt T, Fuchs C, Izbicki JR, Hölscher AH, Dietrich A, Moulla Y, Lyros O, Lang H, Lorenz D, Schumacher B, Mayershofer R, Vashist Y, Ott K, Vieth M, Weismüller J, Moebus S, Knapp M, Neuhaus H, Rösch T, Ell C, Nöthen MM, Whiteman DC, Tomlinson I, Jankowski J, Fitzgerald RC, Palles C, Vaughan TL, Gockel I, Thrift AP, Fier H, Schumacher J. Shared Genetic Etiology of Obesity-Related Traits and Barrett's Esophagus/Adenocarcinoma: Insights from Genome-Wide Association Studies. Cancer Epidemiol Biomarkers Prev 2019; 29:427-433. [PMID: 31748258 DOI: 10.1158/1055-9965.epi-19-0374] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/09/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Obesity is a major risk factor for esophageal adenocarcinoma (EA) and its precursor Barrett's esophagus (BE). Research suggests that individuals with high genetic risk to obesity have a higher BE/EA risk. To facilitate understanding of biological factors that lead to progression from BE to EA, the present study investigated the shared genetic background of BE/EA and obesity-related traits. METHODS Cross-trait linkage disequilibrium score regression was applied to summary statistics from genome-wide association meta-analyses on BE/EA and on obesity traits. Body mass index (BMI) was used as a proxy for general obesity, and waist-to-hip ratio (WHR) for abdominal obesity. For single marker analyses, all genome-wide significant risk alleles for BMI and WHR were compared with summary statistics of the BE/EA meta-analyses. RESULTS Sex-combined analyses revealed a significant genetic correlation between BMI and BE/EA (rg = 0.13, P = 2 × 10-04) and a rg of 0.12 between WHR and BE/EA (P = 1 × 10-02). Sex-specific analyses revealed a pronounced genetic correlation between BMI and EA in females (rg = 0.17, P = 1.2 × 10-03), and WHR and EA in males (rg = 0.18, P = 1.51 × 10-02). On the single marker level, significant enrichment of concordant effects was observed for BMI and BE/EA risk variants (P = 8.45 × 10-03) and WHR and BE/EA risk variants (P = 2 × 10-02). CONCLUSIONS Our study provides evidence for sex-specific genetic correlations that might reflect specific biological mecha-nisms. The data demonstrate that shared genetic factors are particularly relevant in progression from BE to EA. IMPACT Our study quantifies the genetic correlation between BE/EA and obesity. Further research is now warranted to elucidate these effects and to understand the shared pathophysiology.
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Affiliation(s)
- Anne C Böhmer
- Institute of Human Genetics, University of Bonn, Bonn, Germany. .,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Julian Hecker
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Andrea May
- Department of Medicine II, Sana Klinikum, Offenbach, Germany
| | - Christian Gerges
- Department of Internal Medicine II, Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Mario Anders
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany.,Department of Gastroenterology and Interdisciplinary Endoscopy, Vivantes Wenckebach-Klinikum, Berlin, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - Timo Hess
- Center for Human Genetics, University Hospital Marburg, Marburg, Germany
| | - Nicole Kreuser
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - René Thieme
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Tania Noder
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Lothar Veits
- Institute of Pathology, Klinikum Bayreuth, Bayreuth, Germany
| | - Thomas Schmidt
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Claudia Fuchs
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Arnulf H Hölscher
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Arne Dietrich
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Yusef Moulla
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Orestis Lyros
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center, University of Mainz, Mainz, Germany
| | - Dietmar Lorenz
- Department of General, Visceral and Thoracic Surgery, Klinikum Darmstadt, Darmstadt, Germany
| | - Brigitte Schumacher
- Department of Internal Medicine and Gastroenterology, Elisabeth Hospital, Essen, Germany
| | | | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany.,Kantonsspital Aarau, Aarau, Switzerland
| | - Katja Ott
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany.,Department of General, Visceral and Thorax Surgery, RoMed Klinikum Rosenheim, Rosenheim, Germany
| | - Michael Vieth
- Institute of Pathology, Klinikum Bayreuth, Bayreuth, Germany
| | | | - Susanne Moebus
- Centre of Urban Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, University of Essen, Essen, Germany
| | - Michael Knapp
- Institute for Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
| | - Horst Neuhaus
- Department of Internal Medicine II, Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Thomas Rösch
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Ell
- Department of Medicine II, Sana Klinikum, Offenbach, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
| | - David C Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Janusz Jankowski
- University of Central Lancashire, Westlakes Science and Technology Park, Moor Row, United Kingdom.,Warwick Medical School, University of Warwick, Warwick, United Kingdom
| | - Rebecca C Fitzgerald
- Medical Research Council (MRC) Cancer Unit, Hutchison-MRC Research Centre and University of Cambridge, Cambridge, United Kingdom
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas L Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Aaron P Thrift
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.,Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Heide Fier
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Center for Human Genetics, University Hospital Marburg, Marburg, Germany
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2
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Schlauch D, Fier H, Lange C. Identification of genetic outliers due to sub-structure and cryptic relationships. Bioinformatics 2018; 33:1972-1979. [PMID: 28334167 DOI: 10.1093/bioinformatics/btx109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 02/21/2017] [Indexed: 01/29/2023] Open
Abstract
Motivation In order to minimize the effects of genetic confounding on the analysis of high-throughput genetic association studies, e.g. (whole-genome) sequencing (WGS) studies, genome-wide association studies (GWAS), etc., we propose a general framework to assess and to test formally for genetic heterogeneity among study subjects. As the approach fully utilizes the recent ancestor information captured by rare variants, it is especially powerful in WGS studies. Even for relatively moderate sample sizes, the proposed testing framework is able to identify study subjects that are genetically too similar, e.g. cryptic relationships, or that are genetically too different, e.g. population substructure. The approach is computationally fast, enabling the application to whole-genome sequencing data, and straightforward to implement. Results Simulation studies illustrate the overall performance of our approach. In an application to the 1000 Genomes Project, we outline an analysis/cleaning pipeline that utilizes our approach to formally assess whether study subjects are related and whether population substructure is present. In the analysis of the 1000 Genomes Project data, our approach revealed subjects that are most likely related, but had previously passed standard qc-filters. Availability and Implementation An implementation of our method, Similarity Test for Estimating Genetic Outliers (STEGO), is available in the R package stego from Github at https://github.com/dschlauch/stego . Contact dschlauch@fas.harvard.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Daniel Schlauch
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Heide Fier
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA.,Department of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - Christoph Lange
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA 02115, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
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3
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Altmüller J, Haenisch B, Kawalia A, Menzen M, Nöthen MM, Fier H, Molderings GJ. Mutational profiling in the peripheral blood leukocytes of patients with systemic mast cell activation syndrome using next-generation sequencing. Immunogenetics 2017; 69:359-369. [DOI: 10.1007/s00251-017-0981-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/26/2017] [Indexed: 02/07/2023]
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4
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Forstner AJ, Hecker J, Hofmann A, Maaser A, Reinbold CS, Mühleisen TW, Leber M, Strohmaier J, Degenhardt F, Treutlein J, Mattheisen M, Schumacher J, Streit F, Meier S, Herms S, Hoffmann P, Lacour A, Witt SH, Reif A, Müller-Myhsok B, Lucae S, Maier W, Schwarz M, Vedder H, Kammerer-Ciernioch J, Pfennig A, Bauer M, Hautzinger M, Moebus S, Schenk LM, Fischer SB, Sivalingam S, Czerski PM, Hauser J, Lissowska J, Szeszenia-Dabrowska N, Brennan P, McKay JD, Wright A, Mitchell PB, Fullerton JM, Schofield PR, Montgomery GW, Medland SE, Gordon SD, Martin NG, Krasnov V, Chuchalin A, Babadjanova G, Pantelejeva G, Abramova LI, Tiganov AS, Polonikov A, Khusnutdinova E, Alda M, Cruceanu C, Rouleau GA, Turecki G, Laprise C, Rivas F, Mayoral F, Kogevinas M, Grigoroiu-Serbanescu M, Becker T, Schulze TG, Rietschel M, Cichon S, Fier H, Nöthen MM. Identification of shared risk loci and pathways for bipolar disorder and schizophrenia. PLoS One 2017; 12:e0171595. [PMID: 28166306 PMCID: PMC5293228 DOI: 10.1371/journal.pone.0171595] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/23/2017] [Indexed: 12/21/2022] Open
Abstract
Bipolar disorder (BD) is a highly heritable neuropsychiatric disease characterized by recurrent episodes of mania and depression. BD shows substantial clinical and genetic overlap with other psychiatric disorders, in particular schizophrenia (SCZ). The genes underlying this etiological overlap remain largely unknown. A recent SCZ genome wide association study (GWAS) by the Psychiatric Genomics Consortium identified 128 independent genome-wide significant single nucleotide polymorphisms (SNPs). The present study investigated whether these SCZ-associated SNPs also contribute to BD development through the performance of association testing in a large BD GWAS dataset (9747 patients, 14278 controls). After re-imputation and correction for sample overlap, 22 of 107 investigated SCZ SNPs showed nominal association with BD. The number of shared SCZ-BD SNPs was significantly higher than expected (p = 1.46x10-8). This provides further evidence that SCZ-associated loci contribute to the development of BD. Two SNPs remained significant after Bonferroni correction. The most strongly associated SNP was located near TRANK1, which is a reported genome-wide significant risk gene for BD. Pathway analyses for all shared SCZ-BD SNPs revealed 25 nominally enriched gene-sets, which showed partial overlap in terms of the underlying genes. The enriched gene-sets included calcium- and glutamate signaling, neuropathic pain signaling in dorsal horn neurons, and calmodulin binding. The present data provide further insights into shared risk loci and disease-associated pathways for BD and SCZ. This may suggest new research directions for the treatment and prevention of these two major psychiatric disorders.
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Affiliation(s)
- Andreas J. Forstner
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Department of Psychiatry (UPK), University of Basel, Basel, Switzerland
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Julian Hecker
- Institute for Genomics Mathematics, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Institute of Medical Microbiology, Immunology and Parasitology, University of Bonn, Bonn, Germany
| | - Anna Maaser
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Céline S. Reinbold
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Thomas W. Mühleisen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
| | - Markus Leber
- Department of Psychiatry & Psychotherapy, University of Cologne, Cologne, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/University of Heidelberg, Mannheim, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/University of Heidelberg, Mannheim, Germany
| | - Manuel Mattheisen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Biomedicine and Centre for integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - Johannes Schumacher
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/University of Heidelberg, Mannheim, Germany
| | - Sandra Meier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/University of Heidelberg, Mannheim, Germany
- The Lundbeck Foundation Initiative for integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
- National Centre Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - André Lacour
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/University of Heidelberg, Mannheim, Germany
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt am Main, Frankfurt am Main, Germany
| | - Bertram Müller-Myhsok
- Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- University of Liverpool, Institute of Translational Medicine, Liverpool, United Kingdom
| | | | - Wolfgang Maier
- Department of Psychiatry, University of Bonn, Bonn, Germany
| | | | | | | | - Andrea Pfennig
- Department of Psychiatry and Psychotherapy, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Michael Bauer
- Department of Psychiatry and Psychotherapy, University Hospital Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Martin Hautzinger
- Department of Psychology, Clinical Psychology and Psychotherapy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry and Epidemiology, University Duisburg-Essen, Essen, Germany
| | - Lorena M. Schenk
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Sascha B. Fischer
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Sugirthan Sivalingam
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Piotr M. Czerski
- Laboratory of Psychiatric Genetics, Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Hauser
- Laboratory of Psychiatric Genetics, Department of Psychiatry, Poznan University of Medical Sciences, Poznan, Poland
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology Warsaw, Warsaw, Poland
| | | | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - James D. McKay
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Adam Wright
- School of Psychiatry, University of New South Wales, Randwick, Australia
- Black Dog Institute, Prince of Wales Hospital, Randwick, Australia
| | - Philip B. Mitchell
- School of Psychiatry, University of New South Wales, Randwick, Australia
- Black Dog Institute, Prince of Wales Hospital, Randwick, Australia
| | - Janice M. Fullerton
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Peter R. Schofield
- Neuroscience Research Australia, Sydney, Australia
- School of Medical Sciences Faculty of Medicine, University of New South Wales, Sydney, Australia
| | | | - Sarah E. Medland
- Queensland Institute of Medical Research (QIMR), Brisbane, Australia
| | - Scott D. Gordon
- Queensland Institute of Medical Research (QIMR), Brisbane, Australia
| | | | - Valery Krasnov
- Moscow Research Institute of Psychiatry, Moscow, Russian Federation
| | - Alexander Chuchalin
- Institute of Pulmonology, Russian State Medical University, Moscow, Russian Federation
| | - Gulja Babadjanova
- Institute of Pulmonology, Russian State Medical University, Moscow, Russian Federation
| | - Galina Pantelejeva
- Russian Academy of Medical Sciences, Mental Health Research Center, Moscow, Russian Federation
| | - Lilia I. Abramova
- Russian Academy of Medical Sciences, Mental Health Research Center, Moscow, Russian Federation
| | - Alexander S. Tiganov
- Russian Academy of Medical Sciences, Mental Health Research Center, Moscow, Russian Federation
| | - Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation
- Research Institute for Genetic and Molecular Epidemiology, Kursk State Medical University, Kursk, Russian Federation
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russian Federation
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Russian Federation
| | - Martin Alda
- Department of Psychiatry, Dalhousie University, Halifax, Canada
- National Institute of Mental Health, Klecany, Czech Republic
| | - Cristiana Cruceanu
- Montreal Neurological Institute, McGill University, Montreal, Canada
- Department of Human Genetics, McGill University, Montreal, Canada
- McGill Group for Suicide Studies & Douglas Research Institute, Montreal, Canada
| | - Guy A. Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Gustavo Turecki
- Department of Human Genetics, McGill University, Montreal, Canada
- McGill Group for Suicide Studies & Douglas Research Institute, Montreal, Canada
- Department of Psychiatry, McGill University, Montreal, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi (UQAC), Saguenay, Canada
| | - Fabio Rivas
- Department of Psychiatry, Hospital Regional Universitario, Biomedical Institute of Malaga, Malaga, Spain
| | - Fermin Mayoral
- Department of Psychiatry, Hospital Regional Universitario, Biomedical Institute of Malaga, Malaga, Spain
| | - Manolis Kogevinas
- Center for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
| | - Maria Grigoroiu-Serbanescu
- Biometric Psychiatric Genetics Research Unit, Alexandru Obregia Clinical Psychiatric Hospital, Bucharest, Romania
| | - Tim Becker
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Institute for Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Thomas G. Schulze
- Institute of Psychiatric Phenomics and Genomics, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/University of Heidelberg, Mannheim, Germany
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
| | - Heide Fier
- Institute for Genomics Mathematics, University of Bonn, Bonn, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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5
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Basmanav FB, Forstner AJ, Fier H, Herms S, Meier S, Degenhardt F, Hoffmann P, Barth S, Fricker N, Strohmaier J, Witt SH, Ludwig M, Schmael C, Moebus S, Maier W, Mössner R, Rujescu D, Rietschel M, Lange C, Nöthen MM, Cichon S. Investigation of the role of TCF4 rare sequence variants in schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2015; 168B:354-62. [PMID: 26010163 DOI: 10.1002/ajmg.b.32318] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 04/13/2015] [Indexed: 12/20/2022]
Abstract
Transcription factor 4 (TCF4) is one of the most robust of all reported schizophrenia risk loci and is supported by several genetic and functional lines of evidence. While numerous studies have implicated common genetic variation at TCF4 in schizophrenia risk, the role of rare, small-sized variants at this locus-such as single nucleotide variants and short indels which are below the resolution of chip-based arrays requires further exploration. The aim of the present study was to investigate the association between rare TCF4 sequence variants and schizophrenia. Exon-targeted resequencing was performed in 190 German schizophrenia patients. Six rare variants at the coding exons and flanking sequences of the TCF4 gene were identified, including two missense variants and one splice site variant. These six variants were then pooled with nine additional rare variants identified in 379 European participants of the 1000 Genomes Project, and all 15 variants were genotyped in an independent German sample (n = 1,808 patients; n = 2,261 controls). These data were then analyzed using six statistical methods developed for the association analysis of rare variants. No significant association (P < 0.05) was found. However, the results from our association and power analyses suggest that further research into the possible involvement of rare TCF4 sequence variants in schizophrenia risk is warranted by the assessment of larger cohorts with higher statistical power to identify rare variant associations.
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Affiliation(s)
- F Buket Basmanav
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Heide Fier
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany.,Department of Genomic Mathematics, University of Bonn, Bonn, Germany
| | - Stefan Herms
- Department of Genomics, Life and Brain Center, Bonn, Germany.,Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Sandra Meier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany.,National Center for Register-Based Research, Aarhus University, Aarhus, Denmark
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany.,Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Neuroscience and Medicine INM-1, Research Center Juelich, Juelich, Germany
| | - Sandra Barth
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Nadine Fricker
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Christine Schmael
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Susanne Moebus
- Centre of Urban Epidemiology, Institute of Medical Informatics, Biometry and Epidemiology, Essen, Germany
| | - Wolfgang Maier
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Rainald Mössner
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany.,Department of Psychiatry, University of Tübingen
| | - Dan Rujescu
- Department of Psychiatry, University of Halle, Halle, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim/Heidelberg University, Mannheim, Germany
| | - Christoph Lange
- Department of Genomic Mathematics, University of Bonn, Bonn, Germany.,German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany.,Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life and Brain Center, Bonn, Germany.,Division of Medical Genetics, University Hospital Basel and Department of Biomedicine, University of Basel, Basel, Switzerland.,Institute of Neuroscience and Medicine INM-1, Research Center Juelich, Juelich, Germany
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6
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Yip WK, Fier H, DeMeo DL, Aryee M, Laird N, Lange C. A novel method for detecting association between DNA methylation and diseases using spatial information. Genet Epidemiol 2014; 38:714-21. [PMID: 25250875 DOI: 10.1002/gepi.21851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/19/2014] [Accepted: 07/29/2014] [Indexed: 12/22/2022]
Abstract
DNA methylation may represent an important contributor to the missing heritability described in complex trait genetics. However, technology to measure DNA methylation has outpaced statistical methods for analysis. Taking advantage of the recent finding that methylated sites cluster together, we propose a Spatial Clustering Method (SCM) to detect differentially methylated regions (DMRs) in the genome in case and control studies using spatial location information. This new method compares the distribution of distances in cases and controls between DNA methylation marks in the genomic region of interest. A statistic is computed based on these distances. Proper type I error rate is maintained and statistical significance is evaluated using permutation test. The effectiveness of the SCM we propose is evaluated by a simulation study. By simulating a simple disease model, we demonstrate that SCM has good power to detect DMRs associated with the disease. Finally, we applied the SCM to an exploratory analysis of chromosome 14 from a colorectal cancer data set and identified statistically significant genomic regions. Identification of these regions should lead to a better understanding of methylated sites and their contribution to disease. The SCM can be used as a reliable statistical method for the identification of DMRs associated with disease states in exploratory epigenetic analyses.
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Affiliation(s)
- Wai-Ki Yip
- Harvard University, Boston, Massachusetts, United States of America
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7
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Al Chawa T, Ludwig KU, Fier H, Pötzsch B, Reich RH, Schmidt G, Braumann B, Daratsianos N, Böhmer AC, Schuencke H, Alblas M, Fricker N, Hoffmann P, Knapp M, Lange C, Nöthen MM, Mangold E. Nonsyndromic cleft lip with or without cleft palate: Increased burden of rare variants within Gremlin-1, a component of the bone morphogenetic protein 4 pathway. ACTA ACUST UNITED AC 2014; 100:493-8. [PMID: 24706492 DOI: 10.1002/bdra.23244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/20/2014] [Accepted: 03/10/2014] [Indexed: 11/11/2022]
Abstract
BACKGROUND The genes Gremlin-1 (GREM1) and Noggin (NOG) are components of the bone morphogenetic protein 4 pathway, which has been implicated in craniofacial development. Both genes map to recently identified susceptibility loci (chromosomal region 15q13, 17q22) for nonsyndromic cleft lip with or without cleft palate (nsCL/P). The aim of the present study was to determine whether rare variants in either gene are implicated in nsCL/P etiology. METHODS The complete coding regions, untranslated regions, and splice sites of GREM1 and NOG were sequenced in 96 nsCL/P patients and 96 controls of Central European ethnicity. Three burden and four nonburden tests were performed. Statistically significant results were followed up in a second case-control sample (n = 96, respectively). For rare variants observed in cases, segregation analyses were performed. RESULTS In NOG, four rare sequence variants (minor allele frequency < 1%) were identified. Here, burden and nonburden analyses generated nonsignificant results. In GREM1, 33 variants were identified, 15 of which were rare. Of these, five were novel. Significant p-values were generated in three nonburden analyses. Segregation analyses revealed incomplete penetrance for all variants investigated. CONCLUSION Our study did not provide support for NOG being the causal gene at 17q22. However, the observation of a significant excess of rare variants in GREM1 supports the hypothesis that this is the causal gene at chr. 15q13. Because no single causal variant was identified, future sequencing analyses of GREM1 should involve larger samples and the investigation of regulatory elements.
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Affiliation(s)
- Taofik Al Chawa
- Institute of Human Genetics, University of Bonn, Bonn, Germany; Klinikverbund St. Antonius und St. Josef, Wuppertal, Germany; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
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8
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Qiao D, Cho MH, Fier H, Bakke PS, Gulsvik A, Silverman EK, Lange C. On the simultaneous association analysis of large genomic regions: a massive multi-locus association test. ACTA ACUST UNITED AC 2013; 30:157-64. [PMID: 24262215 DOI: 10.1093/bioinformatics/btt654] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MOTIVATION For samples of unrelated individuals, we propose a general analysis framework in which hundred thousands of genetic loci can be tested simultaneously for association with complex phenotypes. The approach is built on spatial-clustering methodology, assuming that genetic loci that are associated with the target phenotype cluster in certain genomic regions. In contrast to standard methodology for multilocus analysis, which has focused on the dimension reduction of the data, our multilocus association-clustering test profits from the availability of large numbers of genetic loci by detecting clusters of loci that are associated with the phenotype. RESULTS The approach is computationally fast and powerful, enabling the simultaneous association testing of large genomic regions. Even the entire genome or certain chromosomes can be tested simultaneously. Using simulation studies, the properties of the approach are evaluated. In an application to a genome-wide association study for chronic obstructive pulmonary disease, we illustrate the practical relevance of the proposed method by simultaneously testing all genotyped loci of the genome-wide association study and by testing each chromosome individually. Our findings suggest that statistical methodology that incorporates spatial-clustering information will be especially useful in whole-genome sequencing studies in which millions or billions of base pairs are recorded and grouped by genomic regions or genes, and are tested jointly for association. AVAILABILITY AND IMPLEMENTATION Implementation of the approach is available upon request.
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Affiliation(s)
- Dandi Qiao
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 20115, USA, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Department of Genomic Mathematics, University of Bonn, 53113 Bonn, Germany and Department of Thoracic Medicine, Haukeland University Hospital and Section for Respiratory Medicine Institute of Medicine, University of Bergen, 5006 Bergen, Norway
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9
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Nasser E, Mangold E, Tradowsky DC, Fier H, Becker J, Boehmer AC, Herberz R, Fricker N, Barth S, Wahle P, Nowak S, Reutter H, Reich RH, Lauster C, Braumann B, Kreusch T, Hemprich A, Pötzsch B, Hoffmann P, Kramer FJ, Knapp M, Lange C, Nöthen MM, Ludwig KU. Resequencing of VAX1 in patients with nonsyndromic cleft lip with or without cleft palate. ACTA ACUST UNITED AC 2012; 94:925-33. [PMID: 23081944 DOI: 10.1002/bdra.23078] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/16/2012] [Accepted: 08/02/2012] [Indexed: 11/11/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common of all congenital anomalies, and has a multifactorial etiology involving both environmental and genetic factors. Recent genome-wide association studies (GWAS) identified strong association between a locus on chromosome 10q25.3 and NSCL/P in European samples. One gene at 10q25.3, the ventral anterior homeobox 1 (VAX1) gene, is considered a strong candidate gene for craniofacial malformations. The purpose of the present study was to provide further evidence that VAX1 is the causal gene at the 10q25.3 locus through identification of an excess of rare mutations in patients with NSCL/P. METHODS The 5'UTR, complete coding regions, and adjacent splice sites of the two known VAX1 isoforms were sequenced in 384 patients with NSCL/P and 384 controls of Central European descent. Observed variants were investigated with respect to familial cosegregation or de novo occurrence, and in silico analyses were performed to identify putative effects on the transcript or protein level. RESULTS Eighteen single-base variants were found, 15 of them rare and previously unreported. In the long VAX1 isoform, predicted functionally relevant variants were observed more often in NSCL/P cases, although this difference was not significant (p = 0.17). Analysis of family members demonstrated incomplete cosegregation in most pedigrees. CONCLUSION Our data do not support the hypothesis that highly penetrant rare variants in VAX1 are a cause of NSCL/P. To determine whether VAX1 is the causative gene at 10q25.3 further research, in particular into the biologic function of its long isoform, is warranted. Birth Defects Research (Part A), 2012.
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Affiliation(s)
- Entessar Nasser
- Institute of Human Genetics, University of Bonn, Bonn, Germany; Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany
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Fier H, Won S, Prokopenko D, AlChawa T, Ludwig KU, Fimmers R, Silverman EK, Pagano M, Mangold E, Lange C. 'Location, Location, Location': a spatial approach for rare variant analysis and an application to a study on non-syndromic cleft lip with or without cleft palate. Bioinformatics 2012; 28:3027-33. [PMID: 23044548 PMCID: PMC3516147 DOI: 10.1093/bioinformatics/bts568] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Motivation: For the analysis of rare variants in sequence data, numerous approaches have been suggested. Fixed and flexible threshold approaches collapse the rare variant information of a genomic region into a test statistic with reduced dimensionality. Alternatively, the rare variant information can be combined in statistical frameworks that are based on suitable regression models, machine learning, etc. Although the existing approaches provide powerful tests that can incorporate information on allele frequencies and prior biological knowledge, differences in the spatial clustering of rare variants between cases and controls cannot be incorporated. Based on the assumption that deleterious variants and protective variants cluster or occur in different parts of the genomic region of interest, we propose a testing strategy for rare variants that builds on spatial cluster methodology and that guides the identification of the biological relevant segments of the region. Our approach does not require any assumption about the directions of the genetic effects. Results: In simulation studies, we assess the power of the clustering approach and compare it with existing methodology. Our simulation results suggest that the clustering approach for rare variants is well powered, even in situations that are ideal for standard methods. The efficiency of our spatial clustering approach is not affected by the presence of rare variants that have opposite effect size directions. An application to a sequencing study for non-syndromic cleft lip with or without cleft palate (NSCL/P) demonstrates its practical relevance. The proposed testing strategy is applied to a genomic region on chromosome 15q13.3 that was implicated in NSCL/P etiology in a previous genome-wide association study, and its results are compared with standard approaches. Availability: Source code and documentation for the implementation in R will be provided online. Currently, the R-implementation only supports genotype data. We currently are working on an extension for VCF files. Contact:heide.fier@googlemail.com
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Affiliation(s)
- Heide Fier
- Department of Genomic Mathematics, University of Bonn, 53127, Germany.
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