Original Paper

Practical Considerations for Dividing Data into Subsets Prior to PPL Analysis
M. Govil^a, V.J. Vieland<sup>b

a</sup>Department of Oral Biology and Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pa.,
^bBattelle Center of Mathematical Medicine, The Research Institute at Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio, USA

Address of Corresponding Author

Hum Hered 2008;66:223-237 (DOI: 10.1159/000143405)

  Key Words

• Complex traits
• Linkage analysis
• Genetic mapping
• Posterior probability of linkage
• PPL
• Sequential updating
• Heterogeneity
• Clinically defined subsets
• Bayesian linkage analysis

  Abstract

Objective: The PPL, a class of statistics for complex trait genetic mapping in humans, utilizes Bayesian sequential updating to accumulate evidence for or against linkage across potentially heterogeneous data (sub)sets. Here, we systematically explore the relative efficacy of alternative subsetting approaches for purposes of PPL calculation. Methods: We simulated genotypes for three pedigree sets (sib pairs; 2-3 generations; 4 generations) based on families from an ongoing study. For each pedigree set, 100 replicates were generated under different levels of heterogeneity (1000 under 'no linkage'). Within each replicate, updating was performed across subsets defined randomly (RAND2, RAND4), by true (TRUE) linkage status, with a realistic (REAL) classification, by individual pedigree (PED), or without any subsetting (NONE). Results: Under 'linkage', REAL yields larger PPLs compared to NONE, RAND2, RAND4, or PED. Under 'no linkage', RAND2, RAND4 and PED yield PPLs close to NONE. Conclusions: We have examined the impact of different subsetting strategies on the sampling behavior of the PPL. Our results underscore the utility of finding variables that can help delineate more homogeneous data subsets and demonstrate that, once such variables are found, sequential updating can be highly beneficial in the presence of appreciable heterogeneity at a linked locus, without inflation at an unlinked locus.

Copyright © 2008 S. Karger AG, Basel

  Author Contacts

Manika Govil
Suite 500 Cellomics/Bridgeside Point
100 Technology Drive
Pittsburgh, PA 15219 (USA)
Tel. +1 412 648 9204, Fax +1 412 648 8779, E-Mail govil@pitt.edu

  Article Information

Received: September 24, 2007
Accepted after revision: November 16, 2007
Published online: July 9, 2008
Number of Print Pages : 15
Number of Figures : 5, Number of Tables : 6, Number of References : 30