New software unlocks hidden genetic data from ancient DNA samples
Researchers have developed a more efficient method for extracting genetic information from degraded ancient DNA, potentially stretching the scientific value of rare archaeological finds. The breakthrough could enable cheaper, faster studies of human migration and evolution while reducing the need to destroy precious biological material.
Originaltitel: Achieving improved accuracy for imputation of ancient DNA
<p><strong>Motivation</strong></p><p>Genotype imputation has the potential to increase the amount of information that can be gained from the often limited biological material available in ancient samples. As many widely used tools have been developed with modern data in mind, their design is not necessarily reflective of the requirements in studies of ancient DNA. Here, we investigate if an imputation method based on the full probabilistic Li and Stephens model of haplotype frequencies might be beneficial for the particular challenges posed by ancient data.</p><p><strong>Results</strong></p><p>We present an implementation called prophaser and compare imputation performance to two alternative pipelines that have been used in the ancient DNA community based on the Beagle software. Considering empirical ancient data downsampled to lower coverages as well as present-day samples with artificially thinned genotypes, we show that the proposed method is advantageous at lower coverages, where it yields improved accuracy and ability to capture rare variation. The software prophaser is optimized for running in a massively parallel manner and achieved reasonable runtimes on the experiments performed when executed on a GPU.</p>