On the use of dense sets of SNP markers and their potential in relationship inference

With the advent of high density SNP arrays and the progress of next generation sequencing, demands for new methods to handle the subsequent data analysis have exploded. Forensic laboratories are generally hesitant to implement new methods in casework unless they are thoroughly tested and validated. This is particularly true when a third party contractor is involved in the analysis. In this paper we explore data from dense sets of SNP markers and study how different errors could potentially affect the results. Particularly, we study the effects of genotyping errors, linkage disequilibrium as well as the use of inappropriate population frequencies. We demonstrate that ignoring these concepts may lead to false conclusions for some different relationship cases and outline solutions to mitigate these problems.