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Excap: maximization of haplotypic diversity of linked markers
KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. (Stockholm Bioinformatics Center)
KTH, School of Biotechnology (BIO).
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-1495-8338
KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholms universitet.ORCID iD: 0000-0001-5341-1733
2013 (English)In: PLoS ONE, ISSN 1932-6203, E-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
PLOS , 2013. Vol. 8, no 11, e79012- p.
Keyword [en]
Mitochondrial-Dna, Coding Region, Mtdna, Identification, Sequence, Genome
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:kth:diva-136427DOI: 10.1371/journal.pone.0079012ISI: 000327162900030PubMedID: 24244403Scopus ID: 2-s2.0-84892418349OAI: oai:DiVA.org:kth-136427DiVA: diva2:676079
Funder
Swedish e‐Science Research CenterKnut and Alice Wallenberg FoundationScience for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20140403

Available from: 2013-12-05 Created: 2013-12-05 Last updated: 2017-12-06Bibliographically approved

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Kahles, AndréSarqume, FahadSavolainen, PeterArvestad, Lars
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