Inferring ethnicity from mitochondrial DNA sequence

Abstract

BackgroundThe assignment of DNA samples to coarse population groups can be a useful but difficult task. One such example is the inference of coarse ethnic groupings for forensic applications. Ethnicity plays an important role in forensic investigation and can be inferred with the help of genetic markers. Being maternally inherited, of high copy number, and robust persistence in degraded samples, mitochondrial DNA may be useful for inferring coarse ethnicity. In this study, we compare the performance of methods for inferring ethnicity from the sequence of the hypervariable region of the mitochondrial genome.ResultsWe present the results of comprehensive experiments conducted on datasets extracted from the mtDNA population database, showing that ethnicity inference based on support vector machines (SVM) achieves an overall accuracy of 80-90%, consistently outperforming nearest neighbor and discriminant analysis methods previously proposed in the literature. We also evaluate methods of handling missing data and characterize the most informative segments of the hypervariable region of the mitochondrial genome.ConclusionsSupport vector machines can be used to infer coarse ethnicity from a small region of mitochondrial DNA sequence with surprisingly high accuracy. In the presence of missing data, utilizing only the regions common to the training sequences and a test sequence proves to be the best strategy. Given these results, SVM algorithms are likely to also be useful in other DNA sequence classification applications.

Assessment of the Relationship between Self-Declared Ethnicity, Mitochondrial Haplogroups and Genomic Ancestry in Brazilian Individuals

“…Several studies have indicated the feasibility of inferring the probable geographic origin of an individual from the sequence of hypervariable regions (HV) of the mitochondrial genome. These studies clearly demonstrate that the mitochondrial sequence alone does not determine one's ethnicity because it relates exclusively to maternal inheritance [2], [12], [13].…”

“…The analysis of both types of information, AIMs and mtDNA, could be strongly associated and, thereby, used to infer more accurately the ethnic origin of an individual [2], [12], [13].…”

Mitochondrial diversity in Amerindian Kichwa and Mestizo populations from Ecuador

“…MtDNA studies have been used to reconstruct the human demographic history as well as to infer the ancestry of individuals [5]. In this sense, the study of American human groups has awakened a growing interest because of their complexity and diversity [6].…”

Relação entre a etnia auto-declarada, haplogrupo mitocondrial e ancestralidade genômica em indivíduos do sudeste brasileiro.

“…Several studies have indicated the feasibility of inferring the probable geographic origin of an individual from the sequence of the hypervariable regions (HV) of mitochondrial genome. These studies clearly demonstrate that the mitochondrial sequence alone does not determine one's ethnicity, by presenting exclusively maternal inheritance 1,10 .…”

“…However, in highly admixed populations, such as in Brazil, this personal information cannot provide the same robust estimative as in less diverse populations 1,2 .…”