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 (ΔLOD) 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 ΔLOD as marker density increases better than the traditional entropy-based information measure.
Highlights
Linkage analysis has been mainly based on widely spaced microsatellite markers (~10 cM), but it is possible to type very dense single-nucleotide polymorphisms (SNPs) markers at low cost
Using the original data set for microsatellites (7.5-cM spacing) and SNPs (3-cM spacing), we studied all 10 chromosomes for three groups (Danacaa, Aipotu, and Karangar), but most of our results presented here are restricted to the Danacca group for chromosome 1 and 7; chromosome 1 contains a strong disease locus, while chromosome 7 contains no disease loci
We compared information contained in microsatellites to that of SNPs using the Genetic Analysis Workshop 14 (GAW14) simulated dataset
Summary
Linkage analysis has been mainly based on widely spaced microsatellite markers (~10 cM), but it is possible to type very dense single-nucleotide polymorphisms (SNPs) markers at low cost. There has been some debate about whether it is better to use microsatellite or SNP panels. Most comparisons have been made based on the information content (IC) measure proposed by Kruglyak et al [1]. According to Kruglyak [2], "Information content measures the fraction of inheritance information extracted by the map relative to that which would be extracted by an infinitely dense polymorphic map". If most of the information is extracted by the current map, it is not necessary to type additional markers. Nicolae and Kong [3] proposed new measures of relative information (RI) using the allele-sharing expo-
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