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Department of Information Technology

Computational methods for human ancient DNA

Sub-project of: Computational Genomics

Participants

  • Carl Nettelblad Assistant Professor in Scientific Computing)
  • Kristiina Ausmees (PhD student in Scientific Computing, Princial advisor: C. Nettelblad. Co-advisor: M. Jakobsson, Department of Organism Biology, UU)

Summary

The analysis of ancient DNA, i.e. DNA samples from specimens that have been deceased for long, poses special challenges. Compared to sampling a living individual, the amount of DNA that can extracted is often limited, especially for precious archeological samples. The DNA can be contaminated (by human DNA from excavators and lab staff, as well as from e.g. microbes). It is also frequently severely degraded.

We look at different computational advances needed for this specific class of genomic analyses. Our initial goal is to provide methods adapted for imputing and phasing genotypes in the case where the amount of sampled DNA is limited. This means that the absence of a certain genetic variant in the data does not mean that it is truly absent, only that its presence has not been confirmed. This is in stark opposition to most phasing methods, which either treat a position as fully known, or as fully unknown.

Our work is done in close collaboration with the lab of Mattias Jakobsson. The methods developed should be of direct use to the research in that lab, but also be general enough to be used by other groups. The PhD project of ((Kristiina Ausmees) is co-funded by 50% by the Centre for Interdisciplinary Mathematics and by 25% by the Jakobsson lab.

Updated  2017-02-05 11:39:16 by Kurt Otto.