Comparison of empirical strategies to maximize GENEHUNTER lod scores

Chien H. Chen, Stephen J. Finch, Nancy R. Mendell, Derek Gordon

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


We compare four strategies for finding the settings of genetic parameters that maximize the lod scores reported in GENEHUNTER 1.2. The four strategies are iterated complete factorial designs, iterated orthogonal Latin hypercubes, evolutionary operation, and numerical optimization. The genetic parameters that are set are the phenocopy rate, penetrance, and disease allele frequency; both recessive and dominant models are considered. We selected the Optimization of a recessive model on the Collaborative Study on the Genetics of Alcoholism (COGA) data of chromosome I for complete analysis. Convergence to a setting producing a local maximum required the evaluation of over 100 settings (for a time budget of 800 minutes on a Pentium II 300 MHz PC). Two notable local maxima were detected, suggesting the need for a more extensive search before claiming that a global maximum had been found. The orthogonal Latin hypercube design was the best strategy for finding areas that produced high lod scores with small numbers of evaluations. Numerical optimization starting from a region producing high lod scores was the strategy that found the highest maximum observed.

Original languageEnglish (US)
Pages (from-to)S103-S108
JournalGenetic Epidemiology
Issue numberSUPPL. 1
StatePublished - 1999

All Science Journal Classification (ASJC) codes

  • Epidemiology
  • Genetics(clinical)


  • Global maximum
  • Latin hypercube
  • Local maximum
  • Methodology
  • Numerical optimization
  • Statistical genetics

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