Original Article

Pedigree analysis package (PAP) vs. MORGAN: Model selection and hypothesis testing on a large pedigree

  1. Gregory L. Snow1,
  2. Ellen M. Wijsman1,2,*

Article first published online: 6 DEC 1998

DOI: 10.1002/(SICI)1098-2272(1998)15:4<355::AID-GEPI3>3.0.CO;2-1

Issue

Genetic Epidemiology

Genetic Epidemiology

Volume 15, Issue 4, pages 355–369, 1998

Additional Information

How to Cite

Snow, G. L. and Wijsman, E. M. (1998), Pedigree analysis package (PAP) vs. MORGAN: Model selection and hypothesis testing on a large pedigree. Genetic Epidemiology, 15: 355–369. doi: 10.1002/(SICI)1098-2272(1998)15:4<355::AID-GEPI3>3.0.CO;2-1

Author Information

  1. 1

    Department of Biostatistics, University of Washington, Seattle, Washington

  2. 2

    Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington

*Div. of Medical Genetics, Box 357720, University of Washington, Seattle WA 98195-7720. E-mail: wijsman@u.washington.edu

Publication History

  1. Issue published online: 6 DEC 1998
  2. Article first published online: 6 DEC 1998
  3. Manuscript Accepted: 30 AUG 1997
  4. Manuscript Revised: 22 AUG 1997
  5. Manuscript Received: 6 JUN 1997

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

Get PDF (92K)

Keywords:

  • complex segregation analysis;
  • likelihood ratio tests;
  • simulation methods;
  • Monte Carlo Markov chain;
  • model selection

Abstract

The MORGAN package of programs is compared to a commonly used package, PAP, with respect to model selection in segregation analysis of a quantitative trait. MORGAN uses Monte Carlo Markov chain (MCMC) methods to estimate the likelihood, whereas both versions of PAP used employ an approximation to the likelihood for the mixed model. Comparisons are done by using results obtained from simulated data. All simulations were done on the same 232-member pedigree using data generated under each of several variations of models, which included different combinations of environmental, polygenic, and major gene components. PAP, version 4.0, and MORGAN gave similar results with respect to model selection for the majority of situations, suggesting that MCMC methods provide a computationally tractable approach for analysis of more complex models that cannot be analyzed by more direct computational methods. PAP, version 3.0, gave somewhat more disparate results compared with either PAP version 4.0 or MORGAN. Both MORGAN and the two versions of PAP confirmed that the major gene component is much easier to detect in the presence of some dominance. All three packages frequently falsely accepted the polygenic model when there was high residual heritability. Genet. Epidemiol. 15:355–369,1998. © 1998 Wiley-Liss, Inc.

Get PDF (92K)