publication . Article . 2009

Detecting gene-by-smoking interactions in a genome-wide association study of early-onset coronary heart disease using random forests

Maenner, Matthew J; Denlinger, Loren C; Langton, Asher; Meyers, Kristin J; Engelman, Corinne D; Skinner, Halcyon G;
Open Access
  • Published: 01 Dec 2009 Journal: BMC Proceedings, volume 3, page S88 (issn: 1753-6561, Copyright policy)
  • Publisher: Springer Nature
Abstract
<p>Abstract</p> <p>Background</p> <p>Genome-wide association studies are often limited in their ability to attain their full potential due to the sheer volume of information created. We sought to use the random forest algorithm to identify single-nucleotide polymorphisms (SNPs) that may be involved in gene-by-smoking interactions related to the early-onset of coronary heart disease.</p> <p>Methods</p> <p>Using data from the Framingham Heart Study, our analysis used a case-only design in which the outcome of interest was age of onset of early coronary heart disease.</p> <p>Results</p> <p>Smoking status was dichotomized as ever versus never. The single SNP with th...
Subjects
free text keywords: General Biochemistry, Genetics and Molecular Biology, General Medicine, Genome-wide association study, Genetic association, Random forest, Single-nucleotide polymorphism, Gene, Bioinformatics, Heart disease, medicine.disease, medicine, Framingham Heart Study, business.industry, business, R, Science, Q, Proceedings
Funded by
NIH| Variant Nucleotide Receptor Function in Airway Disorders
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 1K23HL081492-01A2
  • Funding stream: NATIONAL HEART, LUNG, AND BLOOD INSTITUTE
,
NIH| Prospective Studies of Pancreatic Cancer Epidemiology
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5K07CA109361-06
  • Funding stream: NATIONAL CANCER INSTITUTE
,
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

Humphries, SE, Talmud, PJ, Hawe, E, Bolla, M, Day, IN, Miller, GJ. Apolipoprotein E4 and coronary heart disease in middle-aged men who smoke: a prospective study. Lancet. 2001; 358: 115-119 [OpenAIRE] [PubMed] [DOI]

Talmud, PJ, Stephens, JW, Hawe, E, Demisse, S, Cupples, LA, Hurel, SJ, Humphries, SE, Ordovas, JM. The significant increase in cardiovascular disease risk in APOε4 carriers is evident only in men who smoke: potential relationship between reduced antioxidant status and ApoE4. Ann Hum Genet. 2005; 69: 613-622 [OpenAIRE] [PubMed] [DOI]

Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MAR, Bender, D, Maller, J, Sklar, P, de Bakker, PIW, Daly, MJ, Sham, PC. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet. 2007; 81: 559-75 [OpenAIRE] [PubMed] [DOI]

PLINK...Whole-genome Association Toolset.

Breiman, L. Random forests. Mach Learn. 2001; 45: 5-32 [OpenAIRE] [DOI]

Random Forests.

Random Forests for Gene-Environment Interaction.

Chang, YPC, Liu, X, Kim, JDO, Ikeda, MA, Layton, MR, Weder, AB, Cooper, RS, Kardia, SLR, Rao, DC, Hunt, SC, Luke, A, Boerwinkle, E, Chakravarti, A. Multiple genes for essential-hypertension susceptibility on chromosome 1q. Am J Hum Genet. 2007; 80: 253-264 [OpenAIRE] [PubMed] [DOI]

Powered by OpenAIRE Research Graph
Any information missing or wrong?Report an Issue