A comparison between microsatellite and single-nucleotide polymorphism markers with respect to two measures of information content

Abstract

Using the Genetic Analysis Workshop 14 (GAW14) simulated dataset, we compare microsatellite and single-nucleotide polymorphism (SNP) markers in terms of two measures of information content, the traditional entropy-based information content measure, and a new "relative information" measure. Both attempt to measure the amount of information contained in the markers about the identity-by-descent (IBD) sharing among relatives. The performance of the two information measures are compared based on their variability and ability to predict change in the LOD score (Delta LOD) as map density increases for SNP markers. Although in a linked region, LOD scores are correlated with measures of information, we observe that none of the measures predict the LOD score itself very well. In an unlinked region, the LOD score is not related to either measures of information. The information content of microsatellite markers with 7.5-cM spacing is slightly higher than that of SNP markers with 3-cM spacing. At these map densities, microsatellites are found to be uniformly more informative than SNPs irrespective of their level of heterozygosity. For SNPs, we found that as the level of heterozygosity increases, the information content increases. As reported in all other previous studies, we also found that high-density SNPs have higher information content compared to low-density microsatellites. Performance of both the two information measures considered here are similar, but the relative information measure predicts Delta LOD as marker density increases better than the traditional entropy-based information measure.

Figure 1

LOD scores, IC and RI for microsatellites and SNPs. A, Mean LOD score for microsatellites (dashed red) and SNPs with 3-cM spacing (solid blue) for chromosome 1. B, Mean IC and RI for microsatellites (IC: upper solid red, RI: long dashed green) and SNPs with 3-cM spacing (IC: lower solid black, RI: dot dashed blue) for chromosome 1. C, Mean IC and RI for microsatellites (IC: upper solid red, RI: long dashed green) and SNPs with 3-cM spacing (IC: lower solid black, RI: dot dashed blue) for chromosome 7. D, Standard deviation of IC and RI for microsatellites (IC: lower solid red, RI: long dashed green) and SNPs with 3-cM spacing (IC: upper solid black, RI: dot dashed blue) for chromosome 1. E, Mean IC for microsatellites (solid Red with squares) and SNPs (0.3 cM: solid Brown, 1 cM: black with dots, 2 cM: green with triangles, 3 cM: blue with stars) for chromosome 7. F, LOD against IC at the disease locus in chromosome 1. Regression line of the scatter plot and average IC at 4 map densities are also shown here. All these figures use marker data for Danacaa group only.