Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera, Italy

Gilbert, M. Thomas P.; Rudbeck, Lars; Willerslev, Eske; Hansen, Anders J.; Smith, Colin; Penkman, Kirsty; Prangenberg, Kurt; Nielsen-Marsh, Christina M.; Jans, Miranda E.; Arthur, Paul; Lynnerup, Niels; Turner‐Walker, Gordon; Biddle, Martin; Kjølbye-Biddle, Birthe; Collins, Matthew J.

doi:10.1016/j.jas.2004.12.008

Cited by 92 publications

(12 citation statements)

References 37 publications

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“…Several papers have reported that, despite the use of rigorous protocols [10,88], modern human DNA contamination is prevalent in amplification products from DNA extracts of ancient specimens [13,88-91]. In fact, it has been shown that even with extensive UV and bleach treatments, it is impossible to completely remove modern human DNA from ancient bones and teeth [92]. This is probably due to the porosity of bone and tooth dentine, which are the main entry routes for DNA coming from sweat, skin fragments and exhaled cells.…”

Section: Reviewmentioning

confidence: 99%

Ancient DNA studies: new perspectives on old samples

et al. 2012

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In spite of past controversies, the field of ancient DNA is now a reliable research area due to recent methodological improvements. A series of recent large-scale studies have revealed the true potential of ancient DNA samples to study the processes of evolution and to test models and assumptions commonly used to reconstruct patterns of evolution and to analyze population genetics and palaeoecological changes. Recent advances in DNA technologies, such as next-generation sequencing make it possible to recover DNA information from archaeological and paleontological remains allowing us to go back in time and study the genetic relationships between extinct organisms and their contemporary relatives. With the next-generation sequencing methodologies, DNA sequences can be retrieved even from samples (for example human remains) for which the technical pitfalls of classical methodologies required stringent criteria to guaranty the reliability of the results. In this paper, we review the methodologies applied to ancient DNA analysis and the perspectives that next-generation sequencing applications provide in this field.

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Section: Reviewmentioning

confidence: 99%

Ancient DNA studies: new perspectives on old samples

et al. 2012

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“…If teeth are extracted from the jaw under ideal conditions, the value of external decontamination via physical removal or treatment with harsh chemicals needs to be balanced against the negative impact on endogenous DNA recovery. The resistance of teeth to contamination even when post recovery handling is not performed in an ideal manner has been demonstrated [28,29] suggesting that severe decontamination measures may not always be warranted.…”

Section: Discussionmentioning

confidence: 99%

Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures

et al. 2013

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BackgroundTeeth are a valuable source of DNA for identification of fragmented and degraded human remains. While the value of dental pulp as a source of DNA is well established, the quantity and presentation of DNA in the hard dental tissues has not been extensively studied. Without this knowledge common decontamination, sampling and DNA extraction techniques may be suboptimal. Targeted sampling of specific dental tissues could maximise DNA profiling success, while minimising the need for laborious sampling protocols and DNA extraction techniques, thus improving workflows and efficiencies. We aimed to determine the location of cellular DNA in non-degraded human teeth to quantify the yield of nuclear DNA from cementum, the most accessible and easily sampled dental tissue, and to investigate the effect of a common decontamination method, treatment with sodium hypochlorite (bleach).We examined teeth histologically and subsequently quantified the yield of nuclear DNA from the cementum of 66 human third molar teeth. We also explored the effects of bleach (at varying concentrations and exposure times) on nuclear DNA within teeth, using histological and quantitative PCR methods.ResultsHistology confirmed the presence of nucleated cells within pulp and cementum, but not in dentine. Nuclear DNA yields from cementum varied substantially between individuals but all samples gave sufficient DNA (from as little as 20 mg of tissue) to produce full short tandem repeat (STR) profiles. Variation in yield between individuals was not influenced by chronological age or sex of the donor. Bleach treatment with solutions as dilute as 2.5% for as little as 1 min damaged the visible nuclear material and reduced DNA yields from cementum by an order of magnitude.ConclusionsCementum is a valuable, and easily accessible, source of nuclear DNA from teeth, and may be a preferred source where large numbers of individuals need to be sampled quickly (for example, mass disaster victim identification) without the need for specialist equipment or from diseased and degraded teeth, where pulp is absent. Indiscriminant sampling and decontamination protocols applied to the outer surface of teeth can destroy this DNA, reducing the likelihood of successful STR typing results.

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“…(Neparáczki et al, 2016) aimed at characterizing an entire cemetery which limited the ability of sample selection, so in spite of the more reliable method their haplotype determination proved error prone. The lesson from this study is that PCR based haplotypes need to be handled cautiously, which has been well known in the aDNA field (Handt et al, 1994), (Richards et al, 1995), (Gilbert et al, 2005), (Sampietro et al, 2006). It also follows that incorrect haplotypes particularly distort sequence based statistical analysis, like Fst statistics or shared haplotype analysis applied in (Tömöry et al, 2007) and (Csősz et al, 2016).…”

Section: Contrasting Ngs and Pcr Based Sequence Datamentioning

confidence: 90%

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

Neparáczki

Kocsy

Tóth

et al. 2016

Preprint

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As part of the effort to create a high resolution representative sequence database of the medieval Hungarian conquerors we have resequenced the entire mtDNA genome of 24 published ancient samples with Next Generation Sequencing, whose haplotypes had been previously determined with traditional PCR based methods. We show that PCR based methods are prone to erroneous haplotype or haplogroup determination due to ambiguous sequence reads, and many of the resequenced samples had been classified inaccurately. The SNaPshot method applied with published ancient DNA authenticity criteria is the most straightforward and cheapest PCR based approach for testing a large number of coding region SNP-s, which greatly facilitates correct haplogroup determination.

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Biochemical and physical correlates of DNA contamination in archaeological human bones and teeth excavated at Matera, Italy

Cited by 92 publications

References 37 publications

Ancient DNA studies: new perspectives on old samples

Ancient DNA studies: new perspectives on old samples

Targeted sampling of cementum for recovery of nuclear DNA from human teeth and the impact of common decontamination measures

Revising mtDNA haplotypes of the ancient Hungarian conquerors with next generation sequencing

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