MALDI-TOF MS analysis of Y-SNPs in ancient samples

Petkovski, Elizabet; Keyser-Tracqui, Christine; Crubézy, Éric; Hienne, Rémi; Ludes, Bertrand

doi:10.1016/j.ics.2005.12.008

Cited by 3 publications

(2 citation statements)

References 3 publications

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“…Contamination of OC in archaeological bone is considered less of a problem than in the case of aDNA because: (i) OC is only found in bone and allochthanous OC cannot therefore be ''introduced'' by microbial contamination or sample handling; (ii) OC has a unique identifiable mass (bovine OC M þ H þ has m/z 5721), and thus species identification depends on m/z measurement, in a similar manner to the authentication of expected DNA fragment masses in forensic testing (Petkovski et al, 2005) and aDNA research (Petkovski et al, 2006); and (iii) the OC is not being amplified before analysis, whereas small amounts of contaminating DNA can potentially become much more abundant than the target DNA after amplification. In addition to this, even with the sensitive instrumentation used here, OC is no longer detectable if its concentration falls by approximately four orders of magnitude from that in modern bone.…”

Section: Lesser Hedgehog Ucscmentioning

confidence: 99%

Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites

Buckley

Anderung

Penkman

et al. 2008

Journal of Archaeological Science

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Section: Lesser Hedgehog Ucscmentioning

confidence: 99%

Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites

Buckley

Anderung

Penkman

et al. 2008

Journal of Archaeological Science

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“…Particularly, the SBE technique proved to be extremely sensitive, robust, and reliable (Sobrino, Brión, & Carracedo, ). By using the different SNP‐genotyping techniques, it was for example possible to successfully investigate Y‐chromosomal SNPs from degraded and ancient DNA material (Bouakaze, Keyser, Amory, Crubézy, & Ludes, ; Lessig et al, ; Petkovski, Keyser‐Tracqui, Crubézy, Hienne, & Ludes, ). SNP arrays are particularly known for being a high‐throughput method which requires only small amounts of DNA.…”

Section: Introductionmentioning

confidence: 99%

Genome‐wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains

Schmidt

Schücker

Krause

et al. 2020

American J Phys Anthropol

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Objective: A genome-wide high-throughput single nucleotide polymorphism (SNP) typing method was tested with respect of the applicability to ancient and degraded DNA. The results were compared to mini-sequencing data achieved through single base extension (SBE) typing. The SNPs chosen for the study allow to determine the hair colors and eye colors of humans. Material and methods: The DNA samples were extracted from the skeletal remains of 59 human individuals dating back to the Late Bronze Age. The 3,000 years old bones had been discovered in the Lichtenstein Cave in Lower Saxony, Germany. The simultaneous typing of 24 SNPs for each of the ancient DNA samples was carried out using the 192.24 Dynamic Array™ by Fluidigm ® . Results: Thirty-eight of the ancient samples (=64%) revealed full and reproducible SNP genotypes allowing hair and eye color phenotyping. In 10 samples (=17%) at least half of the SNPs were unambiguously determined, in 11 samples (=19%) the SNP typing failed. For 23 of the 59 individuals, a comparison of the SNP typing results with genotypes from an earlier performed SBE typing approach was possible.The comparison confirmed the full concordance of the results for 90% of the SNP typings. In the remaining 10% allelic dropouts were identified.Discussion: The high genotyping success rate could be achieved by introducing modifications to the preamplification protocol mainly by increasing the DNA input and the amplification cycle number. The occurrence of allelic dropouts indicates that a further increase of DNA input to the preamplification step is desirable. K E Y W O R D S ancient and degraded DNA, eye color, genome wide, hair color, high-throughput SNP typing, phenotype

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Diversity of Mitochondrial DNA Variants within Okunevo Culture Carriers from the Syda V Burial Ground (Minusinsk Basin)

Pilipenko

Pristyazhnyuk

Trapezov

et al. 2022

VNSUIP

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Purpose. Despite a long study, the problem of the Okunevo population origin remains unresolved, including the level of participation of autochthonous and possible migrant groups in the formation of its genetic composition. The purpose of this article is to obtain new data on the mitochondrial DNA diversity in the Okunevo population, in particular in a series of samples from the Syda V burial ground, and also to interpret these new paleogenetic results in the light of possible mechanisms for the formation of specific features of the Okunevo gene pool.Results. We successfully analyzed structure, phylogeny and phylogeography of 25 new mitochondrial DNA samples from the burial grounds of the Okunevo culture of the Minusinsk basin. The study made it possible to almost double the total number of successfully studied Okunevo mtDNA samples. The series of samples we studied from the Syda V burial ground (N = 23) is the first high representative local-territorial series of mtDNA samples for the Okunev population of the region. The new results and literature data are discussed in the context of the problem of the formation of the Okunevo population`s genetic composition and its role in the further genetic history of the southern regions of Siberia.Conclusion. The main role in the formation of the Okunev population were played by genetic elements of autochthonous origin associated with the aboriginal pre-Afanasievo groups. Possible role of migrants remains unclear and requires further research using paleogenetic methods.

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MALDI-TOF MS analysis of Y-SNPs in ancient samples

Cited by 3 publications

References 3 publications

Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites

Comparing the survival of osteocalcin and mtDNA in archaeological bone from four European sites

Genome‐wide SNP typing of ancient DNA: Determination of hair and eye color of Bronze Age humans from their skeletal remains

Diversity of Mitochondrial DNA Variants within Okunevo Culture Carriers from the Syda V Burial Ground (Minusinsk Basin)

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