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      Genome-wide association study of multiple congenital heart disease phenotypes identifies a susceptibility locus for atrial septal defect at chromosome 4p16

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      Author(s): 1 , 2 , 1 , 3 , 4 , 3 , 5 , 1 , 2 , 6 , 7 , 7 , 8 , 9 , 1 , 1 , 1 , 1 , 10 , 11 , 12 , 11 , 13 , 13 , 14 , 15 , 16 , 17 , 13 , 18 , 19 , 8 , 6 , 2 , 9 , 7 , 20 , 21 , 11 , 3 , 4 , 2 , 1 , 1 , 22
      Publication date (Electronic):
      Journal: Nature genetics

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          Abstract

          We carried out a genome-wide association study (GWAS) of congenital heart disease (CHD). Our discovery cohort comprised 1,995 CHD cases and 5,159 controls, and included patients from each of the three major clinical CHD categories (septal, obstructive and cyanotic defects). When all CHD phenotypes were considered together, no regions achieved genome-wide significant association. However, a region on chromosome 4p16, adjacent to the MSX1 and STX18 genes, was associated (P=9.5×10 −7) with the risk of ostium secundum atrial septal defect (ASD) in the discovery cohort (N=340 cases), and this was replicated in a further 417 ASD cases and 2520 controls (replication P=5.0×10 −5; OR in replication cohort 1.40 [95% CI 1.19-1.65]; combined P=2.6×10 −10). Genotype accounted for ~9% of the population attributable risk of ASD.

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          Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.

          Jeffrey Barrett, James Lee, Charles Lees … (2009)
          Ulcerative colitis is a common form of inflammatory bowel disease with a complex etiology. As part of the Wellcome Trust Case Control Consortium 2, we performed a genome-wide association scan for ulcerative colitis in 2,361 cases and 5,417 controls. Loci showing evidence of association at P < 1 x 10(-5) were followed up by genotyping in an independent set of 2,321 cases and 4,818 controls. We find genome-wide significant evidence of association at three new loci, each containing at least one biologically relevant candidate gene, on chromosomes 20q13 (HNF4A; P = 3.2 x 10(-17)), 16q22 (CDH1 and CDH3; P = 2.8 x 10(-8)) and 7q31 (LAMB1; P = 3.0 x 10(-8)). Of note, CDH1 has recently been associated with susceptibility to colorectal cancer, an established complication of longstanding ulcerative colitis. The new associations suggest that changes in the integrity of the intestinal epithelial barrier may contribute to the pathogenesis of ulcerative colitis.
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            Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis

            George Mells, James A.B. Floyd, Katherine I. Morley … (2011)
            In addition to the HLA-locus, six genetic risk factors for primary biliary cirrhosis (PBC) have been identified in recent genome-wide association studies (GWAS). To identify additional loci, we carried out a GWAS using 1,840 cases from the UK PBC Consortium and 5,163 UK population controls as part of the Wellcome Trust Case Control Consortium 3 (WTCCC3). Twenty-eight loci were followed up in an additional UK cohort of 620 PBC cases and 2,514 population controls. We identified 12 novel risk loci (P<5×10−8) and replicated all previously associated loci. Three further novel loci were identified by meta-analysis of data from our study and previously published GWAS results. New candidate genes include STAT4, DENND1B, CD80, IL7R, CXCR5, TNFRSF1A, CLEC16A, and NFKB1. This study has considerably expanded our knowledge of the genetic architecture of PBC.
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              20-year survival of children born with congenital anomalies: a population-based study.

              Peter WG Tennant, Mark S. Pearce, Mary Bythell … (2010)
              Congenital anomalies are a leading cause of perinatal and infant mortality. Advances in care have improved the prognosis for some congenital anomaly groups and subtypes, but there remains a paucity of knowledge about survival for many others, especially beyond the first year of life. We estimated survival up to 20 years of age for a range of congenital anomaly groups and subtypes. Information about children with at least one congenital anomaly, delivered between 1985 and 2003, was obtained from the UK Northern Congenital Abnormality Survey (NorCAS). Anomalies were categorised by group (the system affected), subtype (the individual disorder), and syndrome according to European Surveillance of Congenital Anomalies (EUROCAT) guidelines. Local hospital and national mortality records were used to identify the survival status of liveborn children. Survival up to 20 years of age was estimated by use of Kaplan-Meier methods. Cox proportional hazards regression was used to examine factors that affected survival. 13,758 cases of congenital anomaly were notified to NorCAS between 1985 and 2003. Survival status was available for 10 850 (99.0%) of 10 964 livebirths. 20-year survival was 85.5% (95% CI 84.8-86.3) in individuals born with at least one congenital anomaly, 89.5% (88.4-90.6) for cardiovascular system anomalies, 79.1% (76.7-81.3) for chromosomal anomalies, 93.2% (91.6-94.5) for urinary system anomalies, 83.2% (79.8-86.0) for digestive system anomalies, 97.6% (95.9-98.6) for orofacial clefts, and 66.2% (61.5-70.5) for nervous system anomalies. Survival varied between subtypes within the same congenital anomaly group. The proportion of terminations for fetal anomaly increased throughout the study period (from 12.4%, 9.8-15.5, in 1985 to 18.3%, 15.6-21.2, in 2003; p<0.0001) and, together with year of birth, was an independent predictor of survival (adjusted hazard ratio [HR] for proportion of terminations 0.95, 95% CI 0.91-0.99, p=0.023; adjusted HR for year of birth 0.94, 0.92-0.96, p<0.0001). Estimates of survival for congenital anomaly groups and subtypes will be valuable for families and health professionals when a congenital anomaly is detected, and will assist in planning for the future care needs of affected individuals. BDF Newlife. Copyright 2010 Elsevier Ltd. All rights reserved.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 9216904
                Journal ID (pubmed-jr-id): 2419
                Journal ID (nlm-ta): Nat Genet
                Journal ID (iso-abbrev): Nat. Genet.
                Title: Nature genetics
                ISSN (Print): 1061-4036
                ISSN (Electronic): 1546-1718
                Publication date Nihms-submitted: 8 May 2013
                Publication date (Electronic): 26 May 2013
                Publication date (Print): July 2013
                Publication date PMC-release: 01 January 2014
                Volume: 45
                Issue: 7
                Pages: 822-824
                Affiliations
                [1 ]Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, UK
                [2 ]Department of Cardiovascular Medicine, University of Oxford, Oxford, UK
                [3 ]Commisariat a l’energie Atomique (CEA), Institut Genomique, Centre National de Genotypage, Evry, France
                [4 ]Fondation Jean Dausset, Centre d’Etude du Polymorphisme Humain, Paris, France
                [5 ]Centro Nacional de Analisis Genomico, Barcelona, Spain
                [6 ]The Children’s Hospital at Westmead, Westmead, Australia
                [7 ]Institute of Genetics, Nottingham University, Nottingham, UK
                [8 ]East Midlands Congenital Heart Centre, University Hospitals of Leicester NHS Trust, Leicester, UK
                [9 ]Center for Human Genetics, University of Leuven, Leuven, Belgium
                [10 ]Department of Clinical Genetics, Academic Medical Centre, Amsterdam, The Netherlands
                [11 ]Heart Failure Research Center, Academic Medical Center, Amsterdam, The Netherlands
                [12 ]Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Centre, Amsterdam, The Netherlands
                [13 ]Heart Failure Research Center, Department of Clinical and Experimental Cardiology, Academic Medical Center, Amsterdam, The Netherlands
                [14 ]Department of Pharmacology and Pharmacotherapy, Faculty of Medicine, University of Szeged, Szeged, Hungary
                [15 ]Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
                [16 ]Muscle Research Unit, Department of Anatomy, Bosch Institute, The University of Sydney, Sydney, Australia
                [17 ]Department of Medicine, Molecular and Cellular Pharmacology, University of Miami School of Medicine, Miami, USA
                [18 ]Newcastle Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, UK
                [19 ]Pediatric Cardiology, University of Leuven, Leuven, Belgium
                [20 ]Heart Centre, Academic Medical Centre, Amsterdam, The Netherlands
                [21 ]Hospital for Sick Children, Toronto, Canada
                [22 ]Institute of Cardiovascular Sciences, The University of Manchester, Manchester, UK
                Author notes
                Correspondence: Bernard Keavney Institute of Cardiovascular Sciences The University of Manchester Core Technology Facility 46 Grafton Street Manchester M13 9NT bernard.keavney@ 123456manchester.ac.uk Or: Judith Goodship Institute of Genetic Medicine Newcastle University Central Parkway Newcastle NE1 3BZ UK judith.goodship@ 123456ncl.ac.uk
                [*]

                Contributed equally

                [§]

                Current address: Department of Genetics, Genomics and Bioinformatics, Hospital Infantil de Mexico “Federico Gomez”, Mexico City, Mexico.

                Article
                Manuscript ID: EMS53128
                DOI: 10.1038/ng.2637
                PMC ID: 3793630
                PubMed ID: 23708191
                SO-VID: 5fb3655c-aa54-4098-b4ab-bc0981df7a41
                License:

                Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

                History
                Funding
                Funded by: Wellcome Trust :
                Award ID: 087436 || WT
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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