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Parametric versus nonparametric and two-point versus multipoint: controversies in gene mapping

Part 1. Genetics

1.4. Gene Mapping

Introductory Review

  1. Joan E. Bailey-Wilson

Published Online: 15 JUL 2005

DOI: 10.1002/047001153X.g104104

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Bailey-Wilson, J. E. 2005. Parametric versus nonparametric and two-point versus multipoint: controversies in gene mapping. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 1:1.4:48.

Author Information

  1. National Human Genome Research Institute, Baltimore, MD, USA

Publication History

  1. Published Online: 15 JUL 2005

Abstract

In parametric or model-based linkage analysis (often called LOD score linkage analysis), one assumes that models describing both the trait and marker loci are known without error. This means that one assumes that the allele frequencies, dominance relationships among the alleles, and relationships between genotypes and phenotypes are known without error at both the trait and marker loci. Nonparametric (or model-free or weakly parametric) linkage methods make fewer assumptions about the trait model, although the assumption that the marker locus model(s) is known without error is still in force. These methods of analysis have different strengths and weaknesses that should be taken into account by the analyst when choosing how to analyze linkage data. Parametric linkage analysis is more powerful than nonparametric linkage methods if the genetic model for both trait and marker loci are correctly specified but for complex traits where such correct model specification is difficult, nonparametric methods may be more powerful. Both parametric and nonparametric analyses may be performed between a trait locus and a single marker locus (two-point linkage) or between a trait locus and a map of multiple markers (multipoint linkage). Again, these methods have different strengths and weaknesses that should be understood before embarking upon their use. Multipoint methods give more power to detect linkage than two-point methods as long as the marker order and intermarker distances are correctly specified and assumptions about the trait and marker models are correct, but failures of these assumptions may strongly decrease the power of multipoint methods.

Keywords:

  • linkage;
  • LOD score;
  • parametric;
  • nonparametric;
  • multipoint;
  • two-point;
  • single-point;
  • gene mapping