Incorporating epistasis interaction of genetic susceptibility single nucleotide polymorphisms in a lung cancer risk prediction model

  • Authors:
    • Michael W. Marcus
    • Olaide Y. Raji
    • Stephen W. Duffy
    • Robert P. Young
    • Raewyn J. Hopkins
    • John K. Field
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  • Published online on: April 25, 2016     https://doi.org/10.3892/ijo.2016.3499
  • Pages: 361-370
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Abstract

Incorporation of genetic variants such as single nucleotide polymorphisms (SNPs) into risk prediction models may account for a substantial fraction of attributable disease risk. Genetic data, from 2385 subjects recruited into the Liverpool Lung Project (LLP) between 2000 and 2008, consisting of 20 SNPs independently validated in a candidate-gene discovery study was used. Multifactor dimensionality reduction (MDR) and random forest (RF) were used to explore evidence of epistasis among 20 replicated SNPs. Multivariable logistic regression was used to identify similar risk predictors for lung cancer in the LLP risk model for the epidemiological model and extended model with SNPs. Both models were internally validated using the bootstrap method and model performance was assessed using area under the curve (AUC) and net reclassification improvement (NRI). Using MDR and RF, the overall best classifier of lung cancer status were SNPs rs1799732 (DRD2), rs5744256 (IL-18), rs2306022 (ITGA11) with training accuracy of 0.6592 and a testing accuracy of 0.6572 and a cross-validation consistency of 10/10 with permutation testing P<0.0001. The apparent AUC of the epidemiological model was 0.75 (95% CI 0.73-0.77). When epistatic data were incorporated in the extended model, the AUC increased to 0.81 (95% CI 0.79-0.83) which corresponds to 8% increase in AUC (DeLong's test P=2.2e-16); 17.5% by NRI. After correction for optimism, the AUC was 0.73 for the epidemiological model and 0.79 for the extended model. Our results showed modest improvement in lung cancer risk prediction when the SNP epistasis factor was added.
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July-2016
Volume 49 Issue 1

Print ISSN: 1019-6439
Online ISSN:1791-2423

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Spandidos Publications style
Marcus MW, Raji OY, Duffy SW, Young RP, Hopkins RJ and Field JK: Incorporating epistasis interaction of genetic susceptibility single nucleotide polymorphisms in a lung cancer risk prediction model. Int J Oncol 49: 361-370, 2016
APA
Marcus, M.W., Raji, O.Y., Duffy, S.W., Young, R.P., Hopkins, R.J., & Field, J.K. (2016). Incorporating epistasis interaction of genetic susceptibility single nucleotide polymorphisms in a lung cancer risk prediction model. International Journal of Oncology, 49, 361-370. https://doi.org/10.3892/ijo.2016.3499
MLA
Marcus, M. W., Raji, O. Y., Duffy, S. W., Young, R. P., Hopkins, R. J., Field, J. K."Incorporating epistasis interaction of genetic susceptibility single nucleotide polymorphisms in a lung cancer risk prediction model". International Journal of Oncology 49.1 (2016): 361-370.
Chicago
Marcus, M. W., Raji, O. Y., Duffy, S. W., Young, R. P., Hopkins, R. J., Field, J. K."Incorporating epistasis interaction of genetic susceptibility single nucleotide polymorphisms in a lung cancer risk prediction model". International Journal of Oncology 49, no. 1 (2016): 361-370. https://doi.org/10.3892/ijo.2016.3499