publication . Article . 2014

Pathway-based analysis of rare and common variants to test for association with blood pressure.

Alsulami, Huda; Liu, Xiaofeng; Beyene, Joseph;
Open Access
  • Published: 01 Jun 2014 Journal: BMC Proceedings, volume 8, page S101 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
Abstract
Our goal is to test the effect of both rare and common variants in a blood pressure study. We use a pathway-based approach, gene-set enrichment analysis, to search for related genes affecting 4 phenotypes: systolic blood pressure, diastolic blood pressure, the difference between each of them and mean arterial pressure, which is a weighted linear combination of systolic and diastolic blood pressure. Using the real Genetic Analysis Workshop 18 data, we consider both rare and common variants in our analysis and incorporate other covariates by using a recently proposed test statistic. Our study identified a commonly enriched gene set/pathway for the two derived phen...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Text mining, business.industry, business, Medicine, Covariate, Blood pressure, Mean arterial pressure, Test statistic, Bioinformatics, Proceedings
Related Organizations
Funded by
NIH| Identifying T2D Variants by DNA Sequencing in Multiethnic Samples
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01DK085584-01
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Identification and Replication of Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085501-02
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Discovery of Functional Variants in Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085524-05
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
CIHR
Project
  • Funder: Canadian Institutes of Health Research (CIHR)
,
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

Levy, D, Ehret, GB, Rice, K, Verwoert, GC, Launer, LJ, Dehghan, A, Glazer, NL, Morrison, AC, Johnson, AD, Aspelund, T. Genome-wide association study of blood pressure and hypertension. Nat Genet. 2009; 41: 677-687 [OpenAIRE] [PubMed] [DOI]

Lin, Y, Lai, X, Chen, B, Xu, Y, Huang, B, Chen, Z, Zhu, S, Yao, J, Jiang, Q, Huang, H, Wen, J, Chen, G. Genetic variations in CYP17A1, CACNB2 and PLEKHA7 are associated with blood pressure and/or hypertension in She ethnic minority of China. Atherosclerosis. 2011; 219: 709-714 [OpenAIRE] [PubMed] [DOI]

Adeyemo, A, Gerry, N, Chen, G, Herbert, A, Doumatey, A, Huang, H, Zhou, J, Lashley, K, Chen, Y, Christman, M, Rotimi, C. A genome-wide association study of hypertension and blood pressure in African Americans. PLoS Genet. 2009; 5: e1000564 [OpenAIRE] [PubMed] [DOI]

Wang, K, Li, M, Bucan, M. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet. 2007; 81: 1278-1283 [OpenAIRE] [PubMed] [DOI]

Beyene, J, Hu, P, Hamid, J, Parkhomenko, E, Paterson, A, Tritchler, D. Pathway-based analysis of a genome-wide case-control association study of rheumatoid arthritis. BMC Proc. 2009; 3 (Suppl 7): S128 [OpenAIRE] [PubMed] [DOI]

Subramanian, A, Tamayo, P, Mootha, VK, Mukherjee, S, Ebert, BL, Gillette, MA, Paulovich, A, Pomeroy, SL, Golub, TR, Lander, ES, Mesirov, JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102: 15545-15550 [OpenAIRE] [PubMed] [DOI]

Mootha, VK, Lindgren, CM, Eriksson, KF, Subramanian, A, Sihag, S, Lehar, J, Puigserver, P, Carlsson, E, Ridderstråle, M, Laurila, E. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003; 34: 267-273 [OpenAIRE] [PubMed] [DOI]

Sha, Q, Wang, X, Wang, X, Zhang, S. Detecting association of rare and common variants by testing an optimally weighted combination of variants. Genet Epidemiol. 2012; 36: 561-571 [OpenAIRE] [PubMed] [DOI]

GSEA:Gene Set Enrichment Analysis. MSigDB.

Marsit, CJ, Wiencke, JK, Liu, M, Kelsey, KT. The race associated allele of Semaphorin 3B (SEMA3B) T415I and its role in lung cancer in African-Americans and Latino-Americans. Carcinogenesis. 2005; 26: 1446-1449 [OpenAIRE] [PubMed] [DOI]

Joseph, D, Ho, SM, Syed, V. Hormonal regulation and distinct functions of semaphorin-3B and semaphorin-3F in ovarian cancer. Mol Cancer Ther. 2010; 9: 499-509 [OpenAIRE] [PubMed] [DOI]

Isenberg, JS, Qin, Y, Maxhimer, JB, Sipes, JM, Despres, D, Schnermann, J, Frazier, WA, Roberts, DD. Thrombospondin-1 and CD47 regulate blood pressure and cardiac responses to vasoactive stress. Matrix Biol. 2009; 28: 110-119 [OpenAIRE] [PubMed] [DOI]

Bauer, EM, Qin, Y, Miller, TW, Bandle, RW, Csanyi, G, Pagano, PJ, Bauer, PM, Schnermann, J, Roberts, DD, Isenberg, JS. Thrombospondin-1 supports blood pressure by limiting eNOS activation and endothelial-dependent vasorelaxation. Cardiovasc Res. 2010; 88: 471-781 [OpenAIRE] [PubMed] [DOI]

Related research
Abstract
Our goal is to test the effect of both rare and common variants in a blood pressure study. We use a pathway-based approach, gene-set enrichment analysis, to search for related genes affecting 4 phenotypes: systolic blood pressure, diastolic blood pressure, the difference between each of them and mean arterial pressure, which is a weighted linear combination of systolic and diastolic blood pressure. Using the real Genetic Analysis Workshop 18 data, we consider both rare and common variants in our analysis and incorporate other covariates by using a recently proposed test statistic. Our study identified a commonly enriched gene set/pathway for the two derived phen...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Text mining, business.industry, business, Medicine, Covariate, Blood pressure, Mean arterial pressure, Test statistic, Bioinformatics, Proceedings
Related Organizations
Funded by
NIH| Identifying T2D Variants by DNA Sequencing in Multiethnic Samples
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1U01DK085584-01
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Identification and Replication of Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085501-02
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Discovery of Functional Variants in Type 2 Diabetes Genes in Mexican Americans
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5U01DK085524-05
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
CIHR
Project
  • Funder: Canadian Institutes of Health Research (CIHR)
,
NIH| Genetic Analysis of Common Diseases: An Evaluation
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM031575-22
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

Levy, D, Ehret, GB, Rice, K, Verwoert, GC, Launer, LJ, Dehghan, A, Glazer, NL, Morrison, AC, Johnson, AD, Aspelund, T. Genome-wide association study of blood pressure and hypertension. Nat Genet. 2009; 41: 677-687 [OpenAIRE] [PubMed] [DOI]

Lin, Y, Lai, X, Chen, B, Xu, Y, Huang, B, Chen, Z, Zhu, S, Yao, J, Jiang, Q, Huang, H, Wen, J, Chen, G. Genetic variations in CYP17A1, CACNB2 and PLEKHA7 are associated with blood pressure and/or hypertension in She ethnic minority of China. Atherosclerosis. 2011; 219: 709-714 [OpenAIRE] [PubMed] [DOI]

Adeyemo, A, Gerry, N, Chen, G, Herbert, A, Doumatey, A, Huang, H, Zhou, J, Lashley, K, Chen, Y, Christman, M, Rotimi, C. A genome-wide association study of hypertension and blood pressure in African Americans. PLoS Genet. 2009; 5: e1000564 [OpenAIRE] [PubMed] [DOI]

Wang, K, Li, M, Bucan, M. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet. 2007; 81: 1278-1283 [OpenAIRE] [PubMed] [DOI]

Beyene, J, Hu, P, Hamid, J, Parkhomenko, E, Paterson, A, Tritchler, D. Pathway-based analysis of a genome-wide case-control association study of rheumatoid arthritis. BMC Proc. 2009; 3 (Suppl 7): S128 [OpenAIRE] [PubMed] [DOI]

Subramanian, A, Tamayo, P, Mootha, VK, Mukherjee, S, Ebert, BL, Gillette, MA, Paulovich, A, Pomeroy, SL, Golub, TR, Lander, ES, Mesirov, JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005; 102: 15545-15550 [OpenAIRE] [PubMed] [DOI]

Mootha, VK, Lindgren, CM, Eriksson, KF, Subramanian, A, Sihag, S, Lehar, J, Puigserver, P, Carlsson, E, Ridderstråle, M, Laurila, E. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet. 2003; 34: 267-273 [OpenAIRE] [PubMed] [DOI]

Sha, Q, Wang, X, Wang, X, Zhang, S. Detecting association of rare and common variants by testing an optimally weighted combination of variants. Genet Epidemiol. 2012; 36: 561-571 [OpenAIRE] [PubMed] [DOI]

GSEA:Gene Set Enrichment Analysis. MSigDB.

Marsit, CJ, Wiencke, JK, Liu, M, Kelsey, KT. The race associated allele of Semaphorin 3B (SEMA3B) T415I and its role in lung cancer in African-Americans and Latino-Americans. Carcinogenesis. 2005; 26: 1446-1449 [OpenAIRE] [PubMed] [DOI]

Joseph, D, Ho, SM, Syed, V. Hormonal regulation and distinct functions of semaphorin-3B and semaphorin-3F in ovarian cancer. Mol Cancer Ther. 2010; 9: 499-509 [OpenAIRE] [PubMed] [DOI]

Isenberg, JS, Qin, Y, Maxhimer, JB, Sipes, JM, Despres, D, Schnermann, J, Frazier, WA, Roberts, DD. Thrombospondin-1 and CD47 regulate blood pressure and cardiac responses to vasoactive stress. Matrix Biol. 2009; 28: 110-119 [OpenAIRE] [PubMed] [DOI]

Bauer, EM, Qin, Y, Miller, TW, Bandle, RW, Csanyi, G, Pagano, PJ, Bauer, PM, Schnermann, J, Roberts, DD, Isenberg, JS. Thrombospondin-1 supports blood pressure by limiting eNOS activation and endothelial-dependent vasorelaxation. Cardiovasc Res. 2010; 88: 471-781 [OpenAIRE] [PubMed] [DOI]

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