Multiplex genotyping system for efficient inference of matrilineal genetic ancestry with continental resolution

Mannis Van Oven,Manfred Kayser,Mark Vermeulen

doi:10.1186/2041-2223-2-6

Abstract

BackgroundIn recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. However, a multiplex genotyping system for the detection of the mtDNA haplogroups of major continental distribution that would be desirable for efficient DNA-based bio-geographic ancestry testing in various applications is still missing.ResultsThree multiplex genotyping assays, based on single-base primer extension technology, were developed targeting a total of 36 coding-region mtDNA variants that together differentiate 43 matrilineal haplo-/paragroups. These include the major diagnostic haplogroups for Africa, Western Eurasia, Eastern Eurasia and Native America. The assays show high sensitivity with respect to the amount of template DNA: successful amplification could still be obtained when using as little as 4 pg of genomic DNA and the technology is suitable for medium-throughput analyses.ConclusionsWe introduce an efficient and sensitive multiplex genotyping system for bio-geographic ancestry inference from mtDNA that provides resolution on the continental level. The method can be applied in forensics, to aid tracing unknown suspects, as well as in population studies, genealogy and personal ancestry testing. For more complete inferences of overall bio-geographic ancestry from DNA, the mtDNA system provided here can be combined with multiplex systems for suitable autosomal and, in the case of males, Y-chromosomal ancestry-sensitive DNA markers.

Highlights

In recent years, phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA variants, linking specific clades of the mtDNA phylogeny with certain geographic areas
MtDNA only reveals information about matrilineal ancestry, it can be seen as a first step toward a more comprehensive picture of personal ancestry when combined with suitable non-recombining portion of the Y-chromosome (NRY) and autosomal DNA evidence [10,11]
We describe a sensitive genotyping system based on single-base primer extension technology, consisting of three independent multiplex assays that together include 36 simple nucleotide polymorphism (SNP) determining 43 mtDNA haplo-/paragroups that allow the inference of matrilineal bio-geographic ancestry at the level of continental resolution

Summary

Introduction

Phylogeographic studies have produced detailed knowledge on the worldwide distribution of mitochondrial DNA (mtDNA) variants, linking specific clades of the mtDNA phylogeny with certain geographic areas. Establishing the geographic region of a person’s genetic origin - called bio-geographic ancestry - is of forensic relevance when the short tandem repeat (STR) profile of trace DNA found at a crime scene does not match that of a suspect or does not yield any matches in a criminal DNA database because it may provide investigative leads to finding unknown persons [1]. Such information can be useful for locating antemortem samples or putative relatives of unidentified body remains, including disaster victim identification [2]. Investigating the geographic origin of mtDNA in comparison to that van Oven et al Investigative Genetics 2011, 2:6 http://www.investigativegenetics.com/content/2/1/6 of the Y-chromosome in a population can reveal insights into sex-biased aspects of human population history such as those caused by patri- or matrilocal residence patterns [12]

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