Abstract
Genome wide association studies (GWAS) for fasting glucose (FG) and insulin (FI) have identified common variant signals which explain 4.8% and 1.2% of trait variance, respectively. It is hypothesized that low-frequency and rare variants could contribute substantially to unexplained genetic variance. To test this, we analyzed exome-array data from up to 33,231 non-diabetic individuals of European ancestry. We found exome-wide significant (P<5×10-7) evidence for two loci not previously highlighted by common variant GWAS: GLP1R (p.Ala316Thr, minor allele frequency (MAF)=1.5%) influencing FG levels, and URB2 (p.Glu594Val, MAF = 0.1%) influencing FI levels. Coding variant associations can highlight potential effector genes at (non-coding) GWAS signals. At the G6PC2/ABCB11 locus, we identified multiple coding variants in G6PC2 (p.Val219Leu, p.His177Tyr, and p.Tyr207Ser) influencing FG levels, conditionally independent of each other and the non-coding GWAS signal. In vitro assays demonstrate that these associated coding alleles result in reduced protein abundance via proteasomal degradation, establishing G6PC2 as an effector gene at this locus. Reconciliation of single-variant associations and functional effects was only possible when haplotype phase was considered. In contrast to earlier reports suggesting that, paradoxically, glucose-raising alleles at this locus are protective against type 2 diabetes (T2D), the p.Val219Leu G6PC2 variant displayed a modest but directionally consistent association with T2D risk. Coding variant associations for glycemic traits in GWAS signals highlight PCSK1, RREB1, and ZHX3 as likely effector transcripts. These coding variant association signals do not have a major impact on the trait variance explained, but they do provide valuable biological insights.
| Original language | English |
|---|---|
| Article number | e1004876 |
| Journal | PLoS Genetics |
| Volume | 11 |
| Issue number | 1 |
| DOIs | |
| State | Published - Jan 27 2015 |
Bibliographical note
Publisher Copyright:© 2015, Public Library of Science, All Rights Reserved.
Funding
Funding: HJN was supported by the Agency for Science, Technology and Research in Singapore. CF was supported by the Austrian Science Fund (FWF) grant J-3401. JCF was supported by MGH Research Scholars Award. APM is a Wellcome Trust Senior Research Fellow in Basic and Biomedical Science. JBM was supported by NIDDK R01 DK078616 and K24 DK080140. MIM is a Wellcome Trust Senior Investigator (WT098381); and a National Institute of Health Research Senior Investigator. CML is a Wellcome Trust Research Career Development Fellow (086596/ Z/08/Z). ALG is a Wellcome Trust Senior Research Fellow in Basic and Biomedical Science (095010/Z/ 10/Z). Funding for the GoT2D and T2D-GENES studies was provided by grants NIH U01s DK085526, DK085501, DK085524, DK085545, and DK085584 (Multiethnic Study of Type 2 Diabetes Genes) and DK088389 (Low-Pass Sequencing and High-Density SNP Genotyping for Type 2 Diabetes). Analysis and genotyping of the British UK cohorts was supported by Wellcome Trust funding 090367, 098381, 090532, 083948, 085475, MRC (G0601261), EU (Framework 7) HEALTH-F4-2007-201413, and NIDDK DK098032. The Oxford Biobank is supported by the Oxford Biomedical Research Centre and part of the National NIHR Bioresource. The PIVUS/ ULSAM cohort was supported by Wellcome Trust Grants WT098017, WT064890, WT090532, Uppsala University, Uppsala University Hospital, the Swedish Research Council and the Swedish Heart-Lung Foundation. GoDARTS study was funded by The Wellcome Trust Study Cohort Wellcome Trust Functional Genomics Grant (2004-2008) (Grant No: 072960/2/ 03/2) and The Wellcome Trust Scottish Health Informatics Programme (SHIP) (2009-2012) (Grant No: 086113/Z/08/Z). TwinsUK study was funded by the Wellcome Trust; European Community’s Seventh Framework Programme (FP7/2007–2013). The study also receives support from the National Institute for Health Research (NIHR) BioResource Clinical Research Facility and Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust and King's College London. TDS is holder of an ERC Advanced Principal Investigator award. The Danish studies were supported by the Lundbeck Foundation (Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention and Care (LuCamp); http://www. Research. The Novo Nordisk Foundation Center for Basic Metabolic Research is an independent Research Center at the University of Copenhagen, partially funded by an unrestricted donation from the Novo Nordisk Foundation (http://www.metabol.ku.dk/). HJN was supported by the Agency for Science, Technology and Research in Singapore. CF was supported by the Austrian Science Fund (FWF) grant J-3401. JCF was supported by MGH Research Scholars Award. APM is a Wellcome Trust Senior Research Fellow in Basic and Biomedical Science. JBM was supported by NIDDK R01 DK078616 and K24 DK080140. MIM is a Wellcome Trust Senior Investigator (WT098381); and a National Institute of Health Research Senior Investigator. CML is a Wellcome Trust Research Career Development Fellow (086596/ Z/08/Z). ALG is a Wellcome Trust Senior Research Fellow in Basic and Biomedical Science (095010/Z/ 10/Z). Funding for the GoT2D and T2D-GENES studies was provided by grants NIH U01s DK085526, DK085501, DK085524, DK085545, and DK085584 (Multiethnic Study of Type 2 Diabetes Genes) and DK088389 (Low-Pass Sequencing and High-Density SNP Genotyping for Type 2 Diabetes). Analysis and genotyping of the British UK cohorts was supported by Wellcome Trust funding 090367, 098381, 090532, 083948, 085475, MRC (G0601261), EU (Framework 7) HEALTH-F4-2007-201413, and NIDDK DK098032. The Oxford Biobank is supported by the Oxford Biomedical Research Centre and part of the National NIHR Bioresource. The PIVUS/ ULSAM cohort was supported by Wellcome Trust Grants WT098017, WT064890, WT090532, Uppsala University, Uppsala University Hospital, the Swedish Research Council and the Swedish Heart-Lung Foundation. GoDARTS study was funded by The Wellcome Trust Study Cohort Wellcome Trust Functional Genomics Grant (2004-2008) (Grant No: 072960/2/ 03/2) and The Wellcome Trust Scottish Health Informatics Programme (SHIP) (2009-2012) (Grant No: 086113/Z/08/Z). TwinsUK study was funded by the Wellcome Trust; European Community?s Seventh Framework Programme (FP7/2007-2013). The study also receives support from the National Institute for Health Research (NIHR) BioResource Clinical Research Facility and Biomedical Research Centre based at Guy''s and St Thomas'' NHS Foundation Trust and King''s College London. TDS is holder of an ERC Advanced Principal Investigator award. The Danish studies were supported by the Lundbeck Foundation (Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction, Prevention and Care (LuCamp); http://www. lucamp.org/) and the Danish Council for Independent Research. The Novo Nordisk Foundation Center for Basic Metabolic Research is an independent Research Center at the University of Copenhagen, partially funded by an unrestricted donation from the Novo Nordisk Foundation (http://www.metabol.ku.dk/). The METSIM study was supported by the Academy of Finland (contract 124243), the Finnish Heart Foundation, the Finnish Diabetes Foundation, Tekes (contract 1510/31/06), and the Commission of the European Community (HEALTH-F2-2007-201681), and the US National Institutes of Health grants DK093757, DK072193, DK062370, and 1Z01 HG000024. The FUSION study was supported by DK093757, DK072193, DK062370, and 1Z01 HG000024. Genotyping of the METSIM and DPS studies was conducted at the Genetic Resources Core Facility (GRCF) at the Johns Hopkins Institute of Genetic Medicine. VS is funded by the Finnish Foundation for Cardiovascular Research and the Academy of Finland (grant # 139635). The FIN-D2D 2007 study has been financially supported by the hospital districts of Pirkanmaa, South Ostrobothnia, and Central Finland, the Finnish National Public Health Institute (current National Institute for Health and Welfare), the Finnish Diabetes Association, the Ministry of Social Affairs and Health in Finland, the Academy of Finland (grant number 129293), Commission of the European Communities, Directorate C-Public Health (grant agreement no. 2004310) and Finland?s Slottery Machine Association. The DPS has been financially supported by grants from the Academy of Finland (117844 and 40758, 211497, and 118590 (MU); The EVO funding of the Kuopio University Hospital from Ministry of Health and Social Affairs (5254), Finnish Funding Agency for Technology and Innovation (40058/07), Nordic Centre of Excellence on ?Systems biology in controlled dietary interventions and cohort studies, SYSDIET (070014), The Finnish Diabetes Research Foundation, Yrj? Jahnsson Foundation (56358), Sigrid Juselius Foundation and TEKES grants 70103/06 and 40058/07. The DR''s EXTRA Study was supported by grants to RR by the Ministry of Education and Culture of Finland (627;2004-2011), Academy of Finland (102318; 123885), Kuopio University Hospital, Finnish Diabetes Association, Finnish Heart Association, P?ivikki and Sakari Sohlberg Foundation and by grants from European Commission FP6 Integrated Project (EXGENESIS); LSHM-CT-2004-005272, City of Kuopio and Social Insurance Institution of Finland (4/26/ 2010). The Broad Genomics Platform for genotyping of the FIN-D2D 2007, FINRISK 2007, DR''sEXTRA, FUSION, and PPP studies. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The METSIM study was supported by the Academy
| Funders | Funder number |
|---|---|
| Agency for Science, Technology and Research, Singapore | |
| Central Finland Biobank | |
| City of Kuopio and Social Insurance Institution of Finland | |
| Commission of the European Communities | |
| Commission of the European Community | HEALTH-F2-2007-201681 |
| Danish Council for Independent Research Sapere Aude programme | |
| Public Health Directorate | |
| EXGENESIS | |
| European Commission FP6 STRP | LSHM-CT-2004-005272 |
| European Commission FP6 Integrated Project | |
| FP7/2007 | |
| Finland?s Slottery Machine Association | MU |
| Finnish Diabetes Foundation, Tekes | 1510/31/06 |
| Finnish Foundation for Cardiovascular Research and the Academy of Finland | |
| Finnish Funding Agency for Technology and Innovation | 40058/07 |
| Finnish Heart Association, Päivikki and Sakari Sohlberg Foundation | |
| Finnish Heart Foundation | |
| Finnish National Public Health Institute | |
| Jahnsson Foundation | |
| Johns Hopkins Institute of Genetic Medicine | |
| Kuo-pio and Social Insurance Institution of Finland | 4/26/ 2010 |
| Lundbeck Foundation Centre for Applied Medical Genomics in Personalised Disease Prediction | |
| MGH Research Scholars Award | |
| Ministry of Education and Culture of Finland | 123885, 2004-2011, 102318 |
| Ministry of Social Affairs and Health in Finland | |
| NIDDK DK098032 | |
| NIH U01s DK085526 | Diabetes |
| National Institute for Health and Welfare | |
| National NIHR Bioresource | WT098017, WT064890, WT090532 |
| Nordic Centre of Excellence on | |
| David W. Taylor Naval Ship | |
| SYSDIET | 070014 |
| Sigrid Juselius Foundation | |
| Finland?s Slottery Machine Association | 117844, 211497, 40758, 118590 |
| US National Institutes for Health | DK093757, DK062370, DK072193, 1Z01 HG000024 |
| Wellcome Trust Scottish Health Informatics Programme | 2009-2012, 086113/Z/08/Z |
| Yrjö Jahns-son Foundation | 56358 |
| National Institutes of Health (NIH) | DK088389, DK085584, DK085524, DK085501, DK085545, U01s DK085526 |
| National Institutes of Health (NIH) | |
| Foundation for the National Institutes of Health | |
| National Institute of Diabetes and Digestive and Kidney Diseases | R01DK078616, K24 DK080140, WT098381 |
| National Institute of Diabetes and Digestive and Kidney Diseases | |
| Massachusetts General Hospital | |
| Center for Outcomes Research and Evaluation, Yale School of Medicine | |
| Wellcome Trust | 085475, 083948, 072960/2/ 03/2, 098381, 090367, 090532 |
| Wellcome Trust | |
| Heart of England NHS Foundation Trust | |
| Manchester Biomedical Research Centre | |
| Medical Research Council | G0601261 |
| Medical Research Council | |
| National Institute for Health Research | |
| Novo Nordisk Foundation Center for Protein Research | |
| Imperial College London | |
| University of London, King's College London, UK | |
| European Commission | Framework 7, DK098032, HEALTH-F4-2007-201413 |
| European Commission | |
| H2020 European Research Council | |
| Agency for Science Technology and Research | |
| Københavns Universitet | |
| Academy of Finland | 139635, 124243 |
| Academy of Finland | |
| Austrian Science Fund/FWF | J-3401 |
| Austrian Science Fund/FWF | |
| Tekes | 70103/06 |
| Tekes | |
| Lundbeckfonden | |
| Hjärt-Lungfonden | |
| Kuopion Yliopistollinen Sairaala | |
| Päivikki ja Sakari Sohlbergin Säätiö | |
| Vetenskapsrådet | |
| Guy's and St Thomas' NHS Foundation Trust | |
| Seventh Framework Programme | |
| Socialdepartementet | 5254 |
| Socialdepartementet | |
| Akademiska Sjukhuset | |
| Sydäntutkimussäätiö | |
| Uppsala Universitet | |
| Diabetesliitto | |
| Sosiaali- ja Terveysministeriö | 129293, 2004310 |
| Sosiaali- ja Terveysministeriö | |
| Novo Nordisk Fonden | |
| Jeffrey Cheah Foundation | |
| Wellcome Trust Centre for Mitochondrial Research | 086596/ Z/08/Z, 095010/Z/ 10/Z |
| Wellcome Trust Centre for Mitochondrial Research | |
| NIHR Oxford Biomedical Research Centre | |
| Diabetestutkimussäätiö |
ASJC Scopus subject areas
- Ecology, Evolution, Behavior and Systematics
- Molecular Biology
- Genetics
- Genetics(clinical)
- Cancer Research
