Generating population data for the EMPOP database—An overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example

Brandstätter, Anita; Niederstätter, Harald; Pavlic, Marion; Grubwieser, Petra; Parson, Walther

doi:10.1016/j.forsciint.2006.05.006

Cited by 90 publications

(60 citation statements)

References 43 publications

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“…Buccal swaps were taken from volunteers and DNA was extracted using the Chelex method [Brandstätter et al, 2007]. PCR amplification was conducted in a Gene Amp PCR System 9700 (Applied Biosystems, Foster City, CA) using 20-ml reactions comprising 1 Â AmpliTaq Gold PCR Buffer II (Applied Biosystems), 1.5 mM MgCl 2 , 1 ml DNA extract, 1.0 mM of each primer, 1 unit AmpliTaq Gold Polymerase (Applied Biosystems), and 0.2 mM of each dNTP.…”

Section: Materials and Methods Polymerase Chain Reactionmentioning

confidence: 99%

Increased forensic efficiency of DNA fingerprints through simultaneous resolution of length and nucleotide variability by high-performance mass spectrometry

et al. 2008

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Short tandem repeat (STR) typing is the most powerful method for determining the origin of a sample for a number of molecular disciplines such as medical genetics, population genetics, tumor analysis, transplantation medicine, or forensic crime scene analysis. STR alleles are routinely differentiated based upon their fragment size by electrophoresis under denaturing conditions, which does not take nucleotide variability into consideration. This simplification leads to loss of biological information as the nature of the individual sequence motifs that build an STR is not described. An alternative detection platform would be mass spectrometry, which captures the underlying sequence variation by comparing the molecular masses of DNA fragments. Here, we demonstrate that the combination of ion-pair reversed-phase high-performance liquid chromatography and electrospray ionization quadrupole time-of-flight mass spectrometry (ICEMS) is able to simultaneously detect length and nucleotide variability in STRs. Overall, 21 forensically relevant STRs that are also used in other scientific fields were screened in an Austrian population sample for the occurrence of nucleotide variability within or close to the repeat region. A total of 11 of the investigated loci (SE33, D2S1338, vWA, D21S11, D3S1358, D16S539, D8S1179, D7S820, D13S317, D5S818, and D2S441) brought additional allele (sequence) variants. Forensic efficiency, as determined by typical statistical parameters, was significantly increased by 20 to 30%. The beauty of ICEMS-STR-analysis is the fact that it represents one of the few technological advancements that allows direct comparison of newly generated data with existing data such as stored in DNA databases, which have a retarding effect on new developments.

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Section: Materials and Methods Polymerase Chain Reactionmentioning

confidence: 99%

Increased forensic efficiency of DNA fingerprints through simultaneous resolution of length and nucleotide variability by high-performance mass spectrometry

et al. 2008

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“…Differences from the rCRS were transferred electronically into an in-house LIMS system and the data were verified. An additional quality control check was performed by EMPOP [26] (http://www.empop.org).…”

Section: Dna Samples and Extractionmentioning

confidence: 99%

Homogeneity in mitochondrial DNA control region sequences in Swedish subpopulations

et al. 2009

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In order to promote mitochondrial DNA (mtDNA) testing in Sweden we have typed 296 Swedish males, which will serve as a Swedish mtDNA frequency database. The tested males were taken from seven geographically different regions representing the contemporary Swedish population. The complete mtDNA control region was typed and the Swedish population was shown to have high haplotype diversity with a random match probability of 0.5%. Almost 47% of the tested samples belonged to haplogroup H and further haplogroup comparison with worldwide populations clustered the Swedish mtDNA data together with other European populations. AMOVA analysis of the seven Swedish subregions displayed no significant maternal substructure in Sweden (F (ST) = 0.002). Our conclusion from this study is that the typed Swedish individuals serve as good representatives for a Swedish forensic mtDNA database. Some caution should, however, be taken for individuals from the northernmost part of Sweden (provinces of Norrbotten and Lapland) due to specific demographic conditions. Furthermore, our analysis of a small sample set of a Swedish Saami population confirmed earlier findings that the Swedish Saami population is an outlier among European populations.

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“…These three databases are: 1/a first database [16] concerning 104 Slovenians and 144 Bosnians; 2/a second database [17] concerning 273 unrelated West-Eurasians from Austria; 3/a third database [18] concerning one hundred of samples that were collected from native German speakers in the middle of Southern Germany (in the region of Ulm city, that is located between Lake Constance and the Swabian Alps).…”

Section: Discussionmentioning

confidence: 99%

Y-Chromosomal Profile and Mitochondrial DNA of the Chevalier Bayard (1476?-1524)

Lucotte¹,

Wilkinson²

2017

OJGen

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Objective: We report the results of Y-chromosomal profile and mtDNA (mitochondrial DNA) of the Chevalier Bayard (1476Bayard ( ?-1524. Methods: His genomic DNA was extracted from a tooth of his mandible. His Y-STRs profile was obtained using the AmFirst identifier PCR amplification kit. The mtDNA genomic sequence intervals for HVR1 and HVR2 were amplified by PCR, with specific primers. Results: We obtained the complete STR (Short Tandem Repeats) profile, based on fourteen STRs (DYS19, DYS385.a, DYS389.I and .b, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, DYS448, DYS456 and DYS458 and Y-GATA-H4). The deduced Y-STRs profile corresponds to the sub-clade S21 of the major European haplogroup R1b-M269 (the "Germanic" haplotype). There are six mutations (16093C, 16211T and 16519C in the HVR1 sequence, 263G, 309.1C and 315.1C in the HVR2 sequence) in the mtDNA of Bayard. The 263G mutation determines the H mtDNA haplogroup and the 16211T suggests the H5 sub-clade of the H haplogroup (a sub-clade found at >8% frequency in France, at the periphery of the Alpine arch region). This sub-clade H5 (subsequently assimilated to the H10e haplotype) is that (with a perfect match) of a modern living male related (to 32 generations) to the Bayard maternal ascendance. The Bayard mtDNA haplotype was found once only in a database of 100 South-German mtDNA control sequences. Conclusions: The resulting R1b-M269 Y haplogroup established confirms the Germanic origin of the Bayard ancestors, suggested by genealogic studies concerning his paternal ascendance. The result concerning the mtDNA H10e haplotype found in the modern living male related to Bayard by matrilinear ascendance establishes that the DNA tooth is well of him, with a 99% of chance.

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Generating population data for the EMPOP database—An overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example

Cited by 90 publications

References 43 publications

Increased forensic efficiency of DNA fingerprints through simultaneous resolution of length and nucleotide variability by high-performance mass spectrometry

Increased forensic efficiency of DNA fingerprints through simultaneous resolution of length and nucleotide variability by high-performance mass spectrometry

Homogeneity in mitochondrial DNA control region sequences in Swedish subpopulations

Y-Chromosomal Profile and Mitochondrial DNA of the Chevalier Bayard (1476?-1524)

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