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Wan YI, Shrine NRG, Soler Artigas M, Wain LV, Blakey JD, Moffatt MF, Bush A, Chung KF, Cookson WOCM, Strachan DP, Heaney L, Al-Momani BAH, Mansur AH, Manney S, Thomson NC, Chaudhuri R, Brightling CE, Bafadhel M, Singapuri A, Niven R, Simpson A, Holloway JW, Howarth PH, Hui J, Musk AW, James AL, Brown MA, Baltic S, Ferreira MAR, Thompson PJ, Tobin MD, Sayers I, Hall IP. Genome-wide association study to identify genetic determinants of severe asthma. Thorax 2012; 67:762-8. [PMID: 22561531 DOI: 10.1136/thoraxjnl-2011-201262] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND The genetic basis for developing asthma has been extensively studied. However, association studies to date have mostly focused on mild to moderate disease and genetic risk factors for severe asthma remain unclear. OBJECTIVE To identify common genetic variants affecting susceptibility to severe asthma. METHODS A genome-wide association study was undertaken in 933 European ancestry individuals with severe asthma based on Global Initiative for Asthma (GINA) criteria 3 or above and 3346 clean controls. After standard quality control measures, the association of 480 889 genotyped single nucleotide polymorphisms (SNPs) was tested. To improve the resolution of the association signals identified, non-genotyped SNPs were imputed in these regions using a dense reference panel of SNP genotypes from the 1000 Genomes Project. Then replication of SNPs of interest was undertaken in a further 231 cases and 1345 controls and a meta-analysis was performed to combine the results across studies. RESULTS An association was confirmed in subjects with severe asthma of loci previously identified for association with mild to moderate asthma. The strongest evidence was seen for the ORMDL3/GSDMB locus on chromosome 17q12-21 (rs4794820, p=1.03×10((-8)) following meta-analysis) meeting genome-wide significance. Strong evidence was also found for the IL1RL1/IL18R1 locus on 2q12 (rs9807989, p=5.59×10((-8)) following meta-analysis) just below this threshold. No novel loci for susceptibility to severe asthma met strict criteria for genome-wide significance. CONCLUSIONS The largest genome-wide association study of severe asthma to date was carried out and strong evidence found for the association of two previously identified asthma susceptibility loci in patients with severe disease. A number of novel regions with suggestive evidence were also identified warranting further study.
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Affiliation(s)
- Y I Wan
- Therapeutics and Molecular Medicine, University of Nottingham, Nottingham, UK.
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Sklar P, Smoller JW, Fan J, Ferreira MAR, Perlis RH, Chambert K, Nimgaonkar VL, McQueen MB, Faraone SV, Kirby A, de Bakker PIW, Ogdie MN, Thase ME, Sachs GS, Todd-Brown K, Gabriel SB, Sougnez C, Gates C, Blumenstiel B, Defelice M, Ardlie KG, Franklin J, Muir WJ, McGhee KA, MacIntyre DM, McLean A, VanBeck M, McQuillin A, Bass NJ, Robinson M, Lawrence J, Anjorin A, Curtis D, Scolnick EM, Daly MJ, Blackwood DH, Gurling HM, Purcell SM. Whole-genome association study of bipolar disorder. Mol Psychiatry 2008; 13:558-69. [PMID: 18317468 PMCID: PMC3777816 DOI: 10.1038/sj.mp.4002151] [Citation(s) in RCA: 560] [Impact Index Per Article: 35.0] [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] [Indexed: 01/17/2023]
Abstract
We performed a genome-wide association scan in 1461 patients with bipolar (BP) 1 disorder, 2008 controls drawn from the Systematic Treatment Enhancement Program for Bipolar Disorder and the University College London sample collections with successful genotyping for 372,193 single nucleotide polymorphisms (SNPs). Our strongest single SNP results are found in myosin5B (MYO5B; P=1.66 x 10(-7)) and tetraspanin-8 (TSPAN8; P=6.11 x 10(-7)). Haplotype analysis further supported single SNP results highlighting MYO5B, TSPAN8 and the epidermal growth factor receptor (MYO5B; P=2.04 x 10(-8), TSPAN8; P=7.57 x 10(-7) and EGFR; P=8.36 x 10(-8)). For replication, we genotyped 304 SNPs in family-based NIMH samples (n=409 trios) and University of Edinburgh case-control samples (n=365 cases, 351 controls) that did not provide independent replication after correction for multiple testing. A comparison of our strongest associations with the genome-wide scan of 1868 patients with BP disorder and 2938 controls who completed the scan as part of the Wellcome Trust Case-Control Consortium indicates concordant signals for SNPs within the voltage-dependent calcium channel, L-type, alpha 1C subunit (CACNA1C) gene. Given the heritability of BP disorder, the lack of agreement between studies emphasizes that susceptibility alleles are likely to be modest in effect size and require even larger samples for detection.
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Affiliation(s)
- P Sklar
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA.
| | - JW Smoller
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Departments of Genetics, Psychiatry and Medicine, Harvard Medical School, Boston, MA, USA
| | - J Fan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - MAR Ferreira
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
,Queensland Institute of Medical Research, Australia
| | - RH Perlis
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Departments of Genetics, Psychiatry and Medicine, Harvard Medical School, Boston, MA, USA
| | - K Chambert
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - MB McQueen
- University of Colorado, Boulder, CO, USA
| | - SV Faraone
- Upstate Medical University, State University of New York, Syracuse, NY, USA
| | - A Kirby
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - PIW de Bakker
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - MN Ogdie
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - ME Thase
- University of Pittsburgh, Pittsburgh, PA, USA
| | - GS Sachs
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Departments of Genetics, Psychiatry and Medicine, Harvard Medical School, Boston, MA, USA
| | - K Todd-Brown
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - SB Gabriel
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - C Sougnez
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - C Gates
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - B Blumenstiel
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - M Defelice
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - KG Ardlie
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - J Franklin
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - WJ Muir
- University of Edinburgh, Scotland
| | | | | | - A McLean
- University of Edinburgh, Scotland
| | | | | | - NJ Bass
- University College London, United Kingdom
| | - M Robinson
- University College London, United Kingdom
| | - J Lawrence
- University College London, United Kingdom
| | - A Anjorin
- University College London, United Kingdom
| | - D Curtis
- University College London, United Kingdom
| | | | - MJ Daly
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
,Departments of Genetics, Psychiatry and Medicine, Harvard Medical School, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - HM Gurling
- University College London, United Kingdom
| | - SM Purcell
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
,Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
,Departments of Genetics, Psychiatry and Medicine, Harvard Medical School, Boston, MA, USA
,Broad Institute of Harvard and MIT, Cambridge, MA, USA
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