Genotyping errors are a source of concern in both linkage and association analyses. In a linkage study it is generally easier to detect genotyping errors for microsatellites than for single-nucleotide polymorphisms (SNPs) because microsatellite errors are more likely to give rise to Mendelian inheritance incompatibilities. However, because SNPs are primarily diallelic, genotyping errors often do not give rise to a Mendelian transmission inconsistency. Indeed, in some settings such as a linkage study of affected sibships, it is impossible to detect genotyping errors for individual SNP markers if parents are not genotyped.
