Next generation sequencing as a suitable analysis for authentication of degraded and ancient DNA

Abstract

Ancient DNA studies require the authentication of the results since it is essential to verify the absence of contaminating sequences. Cloning the amplified products obtained from these samples has been one of the principal methods traditionally used to assure the absence of contamination. However, this is an arduous analysis, not routinely applied in forensic laboratories. Recently, the development of next generation sequencing (NGS) technologies opens new ways to authenticate ancient DNA results. NGS data allow the discrimination between endogenous and contaminating sequences. Here we present the results obtained by both traditional cloning and next generation sequencing based on ion semiconductor sequencing on Ion Torrent™ PGM®. The comparison of both methods shows that ion semiconductor sequencing provides a better estimation of the proportion of contaminating sequences present in the sample and more information about the preservation state of the analyzed DNA than traditional cloning. Thus, NGS technology, and in particular, ion semiconductor sequencing, is revealed as a suitable method to authenticate the results obtained from degraded and ancient DNA samples since it provides more information, it is less time and money consuming and it would be unaffordable to obtain the same quantity of data by traditional cloning.