Developmental validation of mitochondrial DNA genotyping assays for adept matrilineal inference of biogeographic ancestry at a continental level

Lakshmi Chaitanya; Mannis van Oven; Natalie Weiler; Joyce Harteveld; Laura Wirken; Titia Sijen; Peter de Knijff; Manfred Kayser

doi:10.1016/j.fsigen.2014.02.010

Developmental validation of mitochondrial DNA genotyping assays for adept matrilineal inference of biogeographic ancestry at a continental level

Forensic Sci Int Genet. 2014 Jul:11:39-51. doi: 10.1016/j.fsigen.2014.02.010. Epub 2014 Feb 23.

Authors

Lakshmi Chaitanya¹, Mannis van Oven¹, Natalie Weiler², Joyce Harteveld², Laura Wirken³, Titia Sijen², Peter de Knijff³, Manfred Kayser⁴

Affiliations

¹ Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, Zuid-Holland, The Netherlands.
² Department of Human Biological Traces, Netherlands Forensic Institute, P.O. Box 24044, 2490 AA The Hague, The Netherlands.
³ Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden, University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
⁴ Department of Forensic Molecular Biology, Erasmus MC University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, Zuid-Holland, The Netherlands. Electronic address: m.kayser@erasmusmc.nl.

PMID: 24631695
DOI: 10.1016/j.fsigen.2014.02.010

Abstract

Mitochondrial DNA (mtDNA) can be used for matrilineal biogeographic ancestry prediction and can thus provide investigative leads towards identifying unknown suspects, when conventional autosomal short tandem repeat (STR) profiling fails to provide a match. Recently, six multiplex genotyping assays targeting 62 ancestry-informative mitochondrial single nucleotide polymorphisms (mt-SNPs) were developed. This hierarchical system of assays allows detection of the major haplogroups present in Africa, America, Western Eurasia, Eastern Eurasia, Australia and Oceania, thus revealing the broad geographic region of matrilineal origin of a DNA donor. Here, we provide a forensic developmental validation study of five multiplex assays targeting all the 62 ancestry-informative mt-SNPs following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. We demonstrate that the assays are highly sensitive; being able to produce full profiles at input DNA amounts of as little as 1pg. The assays were shown to be highly robust and efficient in providing information from degraded samples and from simulated casework samples of different substrates such as blood, semen, hair, saliva and trace DNA samples. Reproducible results were successfully achieved from concordance testing across three independent laboratories depicting the ease and reliability of these assays. Overall, our results demonstrate the suitability of these five mt-SNP assays for application to forensic casework and other purposes aiming to establish an individual's matrilineal genetic ancestry. With this validated tool, it is now possible to determine the matrilineal biogeographic origin of unknown individuals on the level of continental resolution from forensic DNA samples to provide investigative leads in criminal and missing person cases where autosomal STR profiling is uninformative.

Keywords: Biogeographic origin; Developmental validation; Genetic ancestry; Haplogroups; Matrilineal ancestry; mtDNA.

Publication types

Research Support, Non-U.S. Gov't
Validation Study

MeSH terms

Base Sequence
DNA Primers
DNA, Mitochondrial / genetics*
Genealogy and Heraldry*
Genotype*
Geography*
Humans
Phylogeny
Reproducibility of Results

Substances

DNA Primers
DNA, Mitochondrial