SNP+ to predict dropout rates in SNP arrays

Abstract

Genotyping individuals using forensic or non-invasive samples such as hair or fecal samples increases the risk of allelic amplification failure (dropout) due to the low quality and quantity of DNA. One way to decrease genotyping errors is to increase the number of replicates per sample. Here, we have developed the software SNP+ to estimate the dropout probability and the subsequent required number of replicates to obtain the reliable genotype with probability 95%. Moreover, the software predicts the minor allele frequency and compares two competing models assuming equal or allele-specific dropout probabilities by Bayes factor. The software handles data from one SNP to high density arrays (e.g., 100,000 SNPs).