Association of structural variation with cardiometabolic traits in Finns
The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive meth...
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| Published in | American journal of human genetics Vol. 108; no. 4; pp. 583 - 596 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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United States
Elsevier Inc
01.04.2021
Elsevier |
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| Abstract | The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10−54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10−28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10−21) and alanine (p = 6.14 × 10−12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10−10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10−35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk. |
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| AbstractList | The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10-54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10-21) and alanine (p = 6.14 × 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk.The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10-54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10-28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10-21) and alanine (p = 6.14 × 10-12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10-10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10-35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk. The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10−54) and is also associated with increased levels of total cholesterol (p = 1.22 × 10−28) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10−21) and alanine (p = 6.14 × 10−12) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10−10), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10−35). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk. The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10 ) and is also associated with increased levels of total cholesterol (p = 1.22 × 10 ) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10 ) and alanine (p = 6.14 × 10 ) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10 ), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10 ). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk. The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present the results of a study examining genetic association between SVs and cardiometabolic traits in the Finnish population. We used sensitive methods to identify and genotype 129,166 high-confidence SVs from deep whole-genome sequencing (WGS) data of 4,848 individuals. We tested the 64,572 common and low-frequency SVs for association with 116 quantitative traits and tested candidate associations using exome sequencing and array genotype data from an additional 15,205 individuals. We discovered 31 genome-wide significant associations at 15 loci, including 2 loci at which SVs have strong phenotypic effects: (1) a deletion of the ALB promoter that is greatly enriched in the Finnish population and causes decreased serum albumin level in carriers (p = 1.47 × 10 −54 ) and is also associated with increased levels of total cholesterol (p = 1.22 × 10 −28 ) and 14 additional cholesterol-related traits, and (2) a multi-allelic copy number variant (CNV) at PDPR that is strongly associated with pyruvate (p = 4.81 × 10 −21 ) and alanine (p = 6.14 × 10 −12 ) levels and resides within a structurally complex genomic region that has accumulated many rearrangements over evolutionary time. We also confirmed six previously reported associations, including five led by stronger signals in single nucleotide variants (SNVs) and one linking recurrent HP gene deletion and cholesterol levels (p = 6.24 × 10 −10 ), which was also found to be strongly associated with increased glycoprotein level (p = 3.53 × 10 −35 ). Our study confirms that integrating SVs in trait-mapping studies will expand our knowledge of genetic factors underlying disease risk. |
| Author | Kuusisto, Johanna Abel, Haley J. Christ, Ryan Boehnke, Michael Chiang, Colby Das, Indraniel Kanchi, Krishna L. Kang, Chul Joo Young, Erica P. Hall, Ira M. Havulinna, Aki S. Larson, David E. Regier, Allison A. Locke, Adam E. Freimer, Nelson B. Laakso, Markku Scott, Alexandra J. Ganel, Liron Chen, Lei Service, Susan K. Wang, Xinxin Chiang, Charleston W.K. Ripatti, Samuli Palotie, Aarno Lu, Shuangjia Stitziel, Nathan O. |
| Author_xml | – sequence: 1 givenname: Lei orcidid: 0000-0003-4346-713X surname: Chen fullname: Chen, Lei organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 2 givenname: Haley J. surname: Abel fullname: Abel, Haley J. organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 3 givenname: Indraniel surname: Das fullname: Das, Indraniel organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 4 givenname: David E. surname: Larson fullname: Larson, David E. organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 5 givenname: Liron surname: Ganel fullname: Ganel, Liron organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 6 givenname: Krishna L. surname: Kanchi fullname: Kanchi, Krishna L. organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 7 givenname: Allison A. surname: Regier fullname: Regier, Allison A. organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 8 givenname: Erica P. surname: Young fullname: Young, Erica P. organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 9 givenname: Chul Joo surname: Kang fullname: Kang, Chul Joo organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 10 givenname: Alexandra J. surname: Scott fullname: Scott, Alexandra J. organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 11 givenname: Colby surname: Chiang fullname: Chiang, Colby organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 12 givenname: Xinxin surname: Wang fullname: Wang, Xinxin organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 13 givenname: Shuangjia surname: Lu fullname: Lu, Shuangjia organization: Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA – sequence: 14 givenname: Ryan surname: Christ fullname: Christ, Ryan organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 15 givenname: Susan K. surname: Service fullname: Service, Susan K. organization: Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA – sequence: 16 givenname: Charleston W.K. surname: Chiang fullname: Chiang, Charleston W.K. organization: Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA – sequence: 17 givenname: Aki S. surname: Havulinna fullname: Havulinna, Aki S. organization: Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland – sequence: 18 givenname: Johanna surname: Kuusisto fullname: Kuusisto, Johanna organization: Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland – sequence: 19 givenname: Michael surname: Boehnke fullname: Boehnke, Michael organization: Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA – sequence: 20 givenname: Markku surname: Laakso fullname: Laakso, Markku organization: Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio 70210, Finland – sequence: 21 givenname: Aarno surname: Palotie fullname: Palotie, Aarno organization: Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland – sequence: 22 givenname: Samuli surname: Ripatti fullname: Ripatti, Samuli organization: Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00014, Finland – sequence: 23 givenname: Nelson B. surname: Freimer fullname: Freimer, Nelson B. organization: Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA – sequence: 24 givenname: Adam E. surname: Locke fullname: Locke, Adam E. organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 25 givenname: Nathan O. surname: Stitziel fullname: Stitziel, Nathan O. email: nstitziel@wustl.edu organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA – sequence: 26 givenname: Ira M. surname: Hall fullname: Hall, Ira M. email: ira.hall@yale.edu organization: McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33798444$$D View this record in MEDLINE/PubMed |
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| Keywords | structural variation cardiometabolic traits Finnish population genome-wide association study |
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| Snippet | The contribution of genome structural variation (SV) to quantitative traits associated with cardiometabolic diseases remains largely unknown. Here, we present... |
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| SubjectTerms | Alleles cardiometabolic traits Cardiovascular Diseases - genetics Cholesterol - blood DNA Copy Number Variations - genetics Female Finland Finnish population Genome, Human - genetics genome-wide association study Genomic Structural Variation - genetics Genotype High-Throughput Nucleotide Sequencing Humans Male Mitochondrial Proteins - genetics Promoter Regions, Genetic - genetics Pyruvate Dehydrogenase (Lipoamide)-Phosphatase - genetics Pyruvic Acid - metabolism Serum Albumin, Human - genetics structural variation |
| Title | Association of structural variation with cardiometabolic traits in Finns |
| URI | https://dx.doi.org/10.1016/j.ajhg.2021.03.008 https://www.ncbi.nlm.nih.gov/pubmed/33798444 https://www.proquest.com/docview/2508578992 https://pubmed.ncbi.nlm.nih.gov/PMC8059371 |
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