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Excap: maximization of haplotypic diversity of linked markers.
Kungliga Tekniska Högskolan.
Kungliga Tekniska Högskolan.
Kungliga Tekniska Högskolan.
Stockholm University, Faculty of Science, Numerical Analysis and Computer Science (NADA).ORCID iD: 0000-0001-5341-1733
2013 (English)In: PLoS One, ISSN 1932-6203, Vol. 8, no 11, e79012- p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2013. Vol. 8, no 11, e79012- p.
National Category
Bioinformatics (Computational Biology)
URN: urn:nbn:se:su:diva-97256DOI: 10.1371/journal.pone.0079012ISI: 000327162900030PubMedID: 24244403OAI: diva2:676298
Swedish e‐Science Research Center

AuthorCount: 4;

Funding Agencies:

Foundation of German Business (Stiftung der Deutschen Wirtschaft, SDW);

Knuth and Alice Wallenberg Foundation 

Available from: 2013-12-05 Created: 2013-12-05 Last updated: 2014-01-13Bibliographically approved

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