Analysis of mtDNA HVRII in several human populations using an immobilised SSO probe hybridisation assay

Abstract

Several populations were typed for the hypervariable region II (HVRII) of the mitochondrial DNA (mtDNA) control region using immobilised sequence-specific oligonucleotide (SSO) probes. A total of 16 SSO probes was used to type 1081 individuals from eight different ethnic groups (African Americans, Somali, US Europeans, US Hispanics, Bosnians, Finns, Saami and Japanese). Data was compared with already published sequence data by analysis of principal components, genetic distances and analysis of the molecular variance (AMOVA). The analyses performed group the samples in several clusters according to their geographical origins. Most of the variability detected is assigned to differences between individuals and only 7% is assigned to differences among groups of populations within and between geographical regions. Several features are patent in the samples studied: Somali, as a representative East African population, seem to have experienced a detectable amount of Caucasoid maternal influence; different degrees of admixture in the US samples studied are detected; Finns and Saami belong to the European genetic landscape, although Saami present an outlier position attributable to a strong maternal founder effect. The technique used is a rapid and simple method to detect human variation in the mtDNA HVRII in a large number of samples, which might be useful in forensic and population genetic studies.

Forensic and phylogeographic characterisation of mtDNA lineages from Somalia

“…Despite a few individual sequences, little is known so far about the mtDNA variation in Somalis [18,19]. In this study for the first time whole mtDNA control region sequences of 190 unrelated Somali individuals are presented serving as basis for forensic applications.…”

A multiplex allele-specific primer extension assay for forensically informative SNPs distributed throughout the mitochondrial genome

“…Currently, a variety of assays and technologies exist for the detection of SNPs. Specific to mtDNA, a linear hybridization array is currently available for a series of informative SNPs within HV1/HV2 [5]. Among the many other potential options available are: flow cytometry with bead-based hybridization arrays (Luminex), 5' nuclease (Taq Man), primer extension with MS detection (Mass Array Sequenom), and short fragment sequencing with pyrophosphate monitoring (Pyrosequencing) [6,7,8,9,10,11,12,13,14,15,16].…”

Mitochondrial DNA Variability in Bosnians and Slovenians

“…Genetic studies of the Southern Slavs by the use of molecular markers of mitochondrial DNA (mtDNA) and the Y chromosome have attracted the interest of population geneticists (Calafell et al 1996;Comas et al 1999;Rosser et al 2000;Tolk et al 2000;Zaharova et al 2000;Sterlinko et al 2001;Torroni et al 2001). However, mtDNA population data are so far available only for Bulgarians (Calafell et al 1996; and a Croatian sample from the Adriatic islands (Tolk et al 2000).…”