Excap: maximization of haplotypic diversity of linked markers.

Kahles A, Sarqume F, Savolainen P, Arvestad L

PLoS ONE 8 (11) e79012 [2013-11-07; online 2013-11-07]

Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choosing the right set of markers for forensic applications can be difficult and requires careful consideration. In particular, one wants to maximize the utility of the markers. Until now, this has mainly been done by hand. We propose an algorithm that finds the most informative subset of a set of markers. The algorithm uses a depth first search combined with a branch-and-bound approach. Since the worst case complexity is exponential, we also propose some data-reduction techniques and a heuristic. We implemented the algorithm and applied it to two forensic caseworks using mitochondrial DNA, which resulted in marker sets with significantly improved haplotypic diversity compared to previous suggestions. Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy.

Affiliated researcher

PubMed 24244403

DOI 10.1371/journal.pone.0079012

Crossref 10.1371/journal.pone.0079012

pii: PONE-D-12-38929
pmc: PMC3820696

Publications 9.5.0