Score test for detecting linkage to quantitative traits

Genet Epidemiol. 2002 Apr;22(4):345-55. doi: 10.1002/gepi.01104.


The two most popular methods to detect linkage of a quantitative trait to a marker are the Haseman-Elston regression method and the variance components likelihood-ratio test. In the literature, these methods are frequently compared and the relative advantages and disadvantages of each method are well known. In this article, we derive a score test for the variance component attributable to a specific quantitative trait locus and show that for sib-pairs it is mathematically equivalent to a recently proposed version of the Haseman-Elston method that optimally combines the sum squared and the difference squared of the centered phenotype values of the sibs. Because score tests and likelihood-ratio tetsts are equivalent for large sample sizes, the variance components likelihood-ratio test is also asymptotically equivalent to this optimal Haseman-Elston test. This fact gives a theoretical explanation of the empirical observation from simulation studies reporting similar power of the variance components likelihood-ratio test and the optimal Haseman-Elston method. Perhaps more importantly for practical purposes, the score test can also be extended in a natural way to support the simultaneous analysis of more than two subjects and multivariate phenotypes.

MeSH terms

  • Chromosome Mapping / methods*
  • Genetic Linkage / genetics*
  • Genotype
  • Humans
  • Likelihood Functions
  • Models, Genetic
  • Nuclear Family
  • Quantitative Trait, Heritable*