Evaluating the effect of genotype imputation of ancient whole genome Sus scrofa DNA

Activity: Talk and presentationAcademic presentationAcademic


Poster presentation on international conference. Abstract:

Advances in sequencing techniques of the last decades have increased the amount of sequenced ancient DNA. However, sequencing ancient DNA to high coverage is often limited by sample quality or cost. Imputing missing genotypes has the potential to increase information content, cost-effectiveness, and quality of downstream analyses in ancient data. Ancient DNA has certain methodological and computational challenges compared to modern DNA, and requires a different imputation approach than imputation of modern samples. Recent studies on imputation of ancient human data have shown promising results but it is still unclear to what extent the human approach can be applied to other species with different genetic architecture, demography history and less available genetic resources (e.g. whole genome sequencing data). Sus scrofa is an important farm animal that played a key role in understanding the emergence of animal husbandry in Europe and is therefore an interesting case study. In this study we present a systematic evaluation of imputation on whole genome ancient Sus scrofa DNA from Early to Late Neolithic (~7,100-4,500 BP). We investigate how issues like genetic architecture, sample quality, low coverage, and reference divergence and size affect imputation accuracy. We will present results from different imputation strategies and provide guidelines on best imputation practices from ancient pig samples.
Event title9th International Symposium on Biomolecular Archaeology
Event typeConference
LocationToulouse, FranceShow on map
Degree of RecognitionInternational