Haplogrouping mitochondrial DNA sequences in Legal Medicine/Forensic Genetics

Abstract

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.

Cuba: Exploring the History of Admixture and the Genetic Basis of Pigmentation Using Autosomal and Uniparental Markers

“…MtSNPs were selected from a wider mtSNP panel published by Álvarez-Iglesias et al [46], [47], with minor changes on primer designs (details are provided in Table S4). Haplogrouping ( sensu [48]) was carried out using as reference the worldwide mtDNA phylogeny provided by PhyloTree Build 15 [49]. The revised Cambridge Reference Sequence (rCRS) [50] was taken as reference instead of the Reconstructed Sapiens Reference Sequence or RSRS [51].…”

PhyloTree Build 17: Growing the human mitochondrial DNA tree

“…1). PhyloTree has been widely adopted as the reference phylogeny for human mtDNA and serves as the underlying haplogroup classification system for EMPOP [2], HaploGrep [3] and Phy-Mer [4], among others [5]. Here I introduce the newest version of PhyloTree, Build 17.…”

Genetic portrait of Lisboa immigrant population from Angola with mitochondrial DNA

“…These haplogroups can be related with a specific geographic region or, in some cases, with an ethnic group. Thus, the study of mtDNA and its haplogroups of different populations have been used to determine the time and routs of human migration and to investigate pre historical and historical times of humanity [21,22].…”