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The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies. [ABSTRACT FROM AUTHOR]

• Mitochondrial DNA analyses were performed on Viking Age bone material. • The majority of individuals in a mass grave were maternally unrelated. • Individuals were assigned to West Eurasian mtDNA haplogroups. • Precision ID mtDNA Whole Genome Panel was efficient for processing challenging DNA samples. In 1998, a Viking Age mass grave was discovered and excavated at St. Laurence´s churchyard in Sigtuna, Sweden. The excavated bones underwent osteoarchaeological analysis and were assigned to at least 19 individuals. Eleven skeletons showed sharp force trauma from bladed weapons. Mass graves are an unusual finding from this time period, making the burial context extraordinary. To investigate a possible maternal kinship among the individuals, bones and teeth from the skeletal remains were selected for mitochondrial DNA (mtDNA) analysis. Sanger sequencing of short stretches of the hypervariable segments I and II (HVS-I and HVS-II) was performed. A subset of the samples was also analysed by massively parallel sequencing analysis (MPS) of the entire mtDNA genome using the Precision ID mtDNA Whole Genome Panel. A total of 15 unique and three shared mtDNA profiles were obtained. Based on a combination of genetic and archaeological data, we conclude that a minimum of 20 individuals was buried in the mass grave. The majority of the individuals were not maternally related. However, two possible pairs of siblings or mother-child relationships were identified. All individuals were assigned to West Eurasian haplogroups, with a predominance of haplogroup H. Although the remains showed an advanced level of DNA degradation, the combined use of Sanger sequencing and MPS with the Precision ID mtDNA Whole Genome Panel revealed at least partial mtDNA data for all samples. [ABSTRACT FROM AUTHOR]

Saint Birgitta (Saint Bridget of Sweden) lived between 1303 and 1373 and was designated one of Europe's six patron saints by the Pope in 1999. According to legend, the skulls of St. Birgitta and her daughter Katarina are maintained in a relic shrine in Vadstena abbey, mid Sweden. The origin of the two skulls was assessed first by analysis of mitochondrial DNA (mtDNA) to confirm a maternal relationship. The results of this analysis displayed several differences between the two individuals, thus supporting an interpretation of the two skulls not being individuals that are maternally related. Because the efficiency of PCR amplification and quantity of DNA suggested a different amount of degradation and possibly a very different age for each of the skulls, an orthogonal procedure, radiocarbon dating, was performed. The radiocarbon dating results suggest an age difference of at least 200 years and neither of the dating results coincides with the period St. Birgitta or her daughter Katarina lived. The relic, thought to originate from St. Birgitta, has an age corresponding to the 13th century (1215-1270 cal AD, 2σ confidence), which is older than expected. Thus, the two different analyses are consistent in questioning the authenticity of either of the human skulls maintained in the Vadstena relic shrine being that of St. Birgitta. Of course there are limitations when interpreting the data of any ancient biological materials and these must be considered for a final decision on the authenticity of the remains. [ABSTRACT FROM AUTHOR]

As a contribution to the geographic coverage of EMPOP, currently the best available forensic mitochondrial DNA (mtDNA) database, a total of 299 Swedish individuals were analysed by sequencing of the first and second hypervariable regions of the mtDNA genome. In this sample set, a total of 179 different haplotypes were detected. The genetic diversity was estimated to be 0.9895 (±0.0023), and the random match probability was 1.39 %. The most abundant haplogroups were HV (including its subhaplogroups H and V) with a frequency of 46.5 %, followed by haplogroup U (including its subhaplogroup K) at 27.8 %, haplogroup T at 10.0 % and haplogroup J at 7.0 %, a distribution that is consistent with previous observations in other European populations. [ABSTRACT FROM AUTHOR]

Short tandem repeats (STRs) are highly variable, and therefore routinely used in forensic investigations for a DNA-based individual identification. The routine assay is commonly performed by size separation using capillary electrophoresis, but alternative technologies can also be used. In this study, a Pyrosequencing assay was developed for analysis of STR markers useful in forensic DNA analysis. The assay was evaluated for 10 different STR loci (CSF1PO, TH01, TPOX, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539 and Penta E) and a total of 114 Swedish individuals were genotyped. This genotyping strategy reveal the actual sequence and variant alleles were seen at several loci, providing additional information compared to fragment size analysis. At the D13S317 locus a T/A SNP located in the last repeat unit was observed in 92% of the genotypes. Moreover, an upstream flanking SNP at locus D7S820, a SNP within the repeats at D3S1358 and D8S1179 and a deletion in the flanking region at locus D5S818 were observed. The Pyrosequencing method was first developed for SNP typing and sequencing of shorter DNA fragments but the method also provides an alternative method for STR analysis of less complex repeats. This assay is suitable for investigation of new markers, a rapid compilation of population data and for confirmation of variant and new alleles.

Analysis of Y chromosome STR markers has proven to be useful in forensic cases where the samples contain a mixture of DNA from several individuals. STR markers are commonly genotyped based on length separation of PCR products. In this study we evaluated if Pyrosequencing can be used as an alternative method for determining Y-STR variants. In total 70 unrelated Swedish males were typed for the Y chromosomal markers (DYS19, DYS389 I-II, DYS390, DYS391, DYS392, DYS393 and DYS438) using Pyrosequencing. Using the 8 markers, 57 unique haplotypes were observed with a discrimination capacity of 0.81. At four loci, the Pyrosequencing analysis revealed sequence variants. The sequence variants were found in the DYS389 II, DYS390, DYS391, and DYS393 loci in frequencies between 1.43% and 14.3%. Pyrosequencing has here been shown to be a useful tool for typing Y chromosomal STRs and the method can provide a complement to conventional forensic Y STR analyses. Moreover, the Pyrosequencing method can be used to rapidly evaluate novel markers.

There is an increasing trend to use mitochondrial DNA (mtDNA) analysis in criminal investigations where only limited amounts of DNA are available. However, analysis of the mtDNA control region has the drawback of low discrimination power, due to the lack of recombination that results from uniparental (maternal) inheritance. As a strategy to increase discrimination, a number of typing assays detecting variation in the mitochondrial coding region have been developed. In this study, several of these assays are evaluated for their discriminatory capacity using data obtained from 495 complete Caucasian mtDNA sequences. In order to add a local geographic perspective to this evaluation, we have also sequenced and analysed the entire mtDNA from 20 individuals of Swedish origin. We find that the coding region assays are very useful for resolving sequences with identical HVI/HVII regions. The best-performing coding region assay was able to discriminate 46% of the resolvable sequences, compared to 20-30% for the other coding region assays we evaluated.