Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics

Int J Legal Med. 2012 Nov;126(6):901-16. doi: 10.1007/s00414-012-0762-y. Epub 2012 Sep 1.


Haplogrouping refers to the classification of (partial) mitochondrial DNA (mtDNA) sequences into haplogroups using the current knowledge of the worldwide mtDNA phylogeny. Haplogroup assignment of mtDNA control-region sequences assists in the focused comparison with closely related complete mtDNA sequences and thus serves two main goals in forensic genetics: first is the a posteriori quality analysis of sequencing results and second is the prediction of relevant coding-region sites for confirmation or further refinement of haplogroup status. The latter may be important in forensic casework where discrimination power needs to be as high as possible. However, most articles published in forensic genetics perform haplogrouping only in a rudimentary or incorrect way. The present study features PhyloTree as the key tool for assigning control-region sequences to haplogroups and elaborates on additional Web-based searches for finding near-matches with complete mtDNA genomes in the databases. In contrast, none of the automated haplogrouping tools available can yet compete with manual haplogrouping using PhyloTree plus additional Web-based searches, especially when confronted with artificial recombinants still present in forensic mtDNA datasets. We review and classify the various attempts at haplogrouping by using a multiplex approach or relying on automated haplogrouping. Furthermore, we re-examine a few articles in forensic journals providing mtDNA population data where appropriate haplogrouping following PhyloTree immediately highlights several kinds of sequence errors.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Mutational Analysis / methods
  • DNA, Mitochondrial / classification*
  • DNA, Mitochondrial / genetics*
  • Forensic Genetics / methods*
  • Forensic Medicine / methods*
  • Genetic Variation / genetics
  • Genetics, Population
  • Genotype
  • HapMap Project*
  • Haplotypes / genetics*
  • Humans
  • Multiplex Polymerase Chain Reaction / methods
  • Phylogeny
  • Reference Values
  • Sequence Analysis, DNA / methods*


  • DNA, Mitochondrial