Maximum-likelihood estimation of allelic dropout and false allele error rates from microsatellite genotypes in the absence of reference data

The importance of quantifying and accounting for stochastic genotyping errors when analyzing microsatellite data is increasingly being recognized. This awareness is motivating the development of data analysis methods that not only take errors into consideration but also recognize the difference between two distinct classes of error, allelic dropout and false alleles. Currently methods to estimate rates of allelic dropout and false alleles depend upon the availability of error-free reference genotypes or reliable pedigree data, which are often not available. We have developed a maximum-likelihood-based method for estimating these error rates from a single replication of a sample of genotypes. Simulations show it to be both accurate and robust to modest violations of its underlying assumptions. We have applied the method to estimating error rates in two microsatellite data sets. It is implemented in a computer program, Pedant, which estimates allelic dropout and false allele error rates with 95% confidence regions from microsatellite genotype data and performs power analysis. Pedant is freely available at http://www.stats.gla.ac.uk/ approximately paulj/pedant.html.