Comparison of Variance Components and Sibpair-Based Approaches to
Quantitative Trait Linkage Analysis in Unselected Samples
Williams JT, Blangero J
Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio,
Texas 78245-0549, USA.
jeffw@darwin.sfbr.org
Genetic Epidemiology, 16(2):113-134 (1999)
Abstract
We compared the statistical performance of sibpair-based and variance components
approaches to multipoint linkage analysis of a quantitative trait in unselected samples.
As a benchmark dataset, we used the simulated family data from Genetic Analysis
Workshop 10 [Goldin et al., 1997], and each method was used to screen all 200
replications of the GAW10 genome for evidence of linkage to quantitative trait Q1. The
sibpair and variance components methods were each applied to datasets comprising
single-sibpairs and complete sibships, and for further comparison we also applied the
variance components method to the nuclear family and extended pedigree datasets. For
each analysis, the unbiasedness and efficiency of parameter estimation, the power to
detect linkage, and the Type I error rate were estimated empirically. Sibpair and variance
components methods exhibited comparable performance in terms of the unbiasedness
of the estimate of QTL location and the Type I error rate. Within the single-sibpair and
sibship sampling units, the variance components approach gave consistently superior
power and efficiency of parameter estimation. Within each method, the statistical
performance was improved by the use of the larger and more informative sampling
units.
Variance component linkage analysis