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A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies.

Publication ,  Journal Article
Neely, ML; Bondell, HD; Tzeng, J-Y
Published in: Biometrics
June 2015

Pharmacogenetics investigates the relationship between heritable genetic variation and the variation in how individuals respond to drug therapies. Often, gene-drug interactions play a primary role in this response, and identifying these effects can aid in the development of individualized treatment regimes. Haplotypes can hold key information in understanding the association between genetic variation and drug response. However, the standard approach for haplotype-based association analysis does not directly address the research questions dictated by individualized medicine. A complementary post-hoc analysis is required, and this post-hoc analysis is usually under powered after adjusting for multiple comparisons and may lead to seemingly contradictory conclusions. In this work, we propose a penalized likelihood approach that is able to overcome the drawbacks of the standard approach and yield the desired personalized output. We demonstrate the utility of our method by applying it to the Scottish Randomized Trial in Ovarian Cancer. We also conducted simulation studies and showed that the proposed penalized method has comparable or more power than the standard approach and maintains low Type I error rates for both binary and quantitative drug responses. The largest performance gains are seen when the haplotype frequency is low, the difference in effect sizes are small, or the true relationship among the drugs is more complex.

Duke Scholars

Published In

Biometrics

DOI

EISSN

1541-0420

Publication Date

June 2015

Volume

71

Issue

2

Start / End Page

529 / 537

Location

England

Related Subject Headings

  • Statistics & Probability
  • Regression Analysis
  • Pharmacogenetics
  • Ovarian Neoplasms
  • Models, Statistical
  • Likelihood Functions
  • Humans
  • Haplotypes
  • Genes, bcl-2
  • Female
 

Citation

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Neely, M. L., Bondell, H. D., & Tzeng, J.-Y. (2015). A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies. Biometrics, 71(2), 529–537. https://doi.org/10.1111/biom.12259
Neely, Megan L., Howard D. Bondell, and Jung-Ying Tzeng. “A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies.Biometrics 71, no. 2 (June 2015): 529–37. https://doi.org/10.1111/biom.12259.
Neely ML, Bondell HD, Tzeng J-Y. A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies. Biometrics. 2015 Jun;71(2):529–37.
Neely, Megan L., et al. “A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies.Biometrics, vol. 71, no. 2, June 2015, pp. 529–37. Pubmed, doi:10.1111/biom.12259.
Neely ML, Bondell HD, Tzeng J-Y. A penalized likelihood approach for investigating gene-drug interactions in pharmacogenetic studies. Biometrics. 2015 Jun;71(2):529–537.
Journal cover image

Published In

Biometrics

DOI

EISSN

1541-0420

Publication Date

June 2015

Volume

71

Issue

2

Start / End Page

529 / 537

Location

England

Related Subject Headings

  • Statistics & Probability
  • Regression Analysis
  • Pharmacogenetics
  • Ovarian Neoplasms
  • Models, Statistical
  • Likelihood Functions
  • Humans
  • Haplotypes
  • Genes, bcl-2
  • Female