A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Harney, Éadaoin; Cheronet, Olivia; Fernandes, Daniel; Sirak, Kendra; Mah, Matthew; Bernardos, Rebecca; Adamski, Nicole; Broomandkhoshbacht, Nasreen; Lawson, Ann Marie; Oppenheimer, Jonas; Stewardson, Kristin; Zalzala, Fatma; Anders, Alexandra; Candilio, Francesca; Constantinescu, Mihai; Coppa, Alfredo; Ciobanu, Ion; Dani, János; Gallina, Zsolt; Genchi, Francesco; Nagy, Emese Gyöngyvér; Hajdu, Tamás; Hellebrandt, Magdolna; Horváth, Antónia; Király, Ágnes; Kiss, Krisztián; Kolozsi, Barbara; Kovács, Péter; Köhler, Kitti; Lucci, Michaela; Pap, Ildikó; Popovici, Sergiu; Raczky, Pál; Simalcsik, Angela; Szeniczey, Tamás; Vasilyev, Sergey; Virag, Cristian; Rohland, Nadin; Reich, David; Pinhasi, Ron

doi:10.1101/2020.08.19.256412

Cited by 3 publications

(2 citation statements)

References 44 publications

(60 reference statements)

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“…The variant was present in five ancient individuals of Europe and West Asia; MLH1 c.589-2A > G is an American founder PV arose 340-585 years ago [42]. It was identified in two ancient individuals, one dated to 4440-4250 BP in southwest Asia (' Ain Ghazal, Jordan) [43] and the other 1400-900 BP in northeast Asia (Chukotka Autonomous Okrug, Russian) [44].…”

Section: Archeological Analysis Of Human Mmr Pvsmentioning

confidence: 99%

Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes

Lei,

Li,

Zhao

et al. 2024

Hum Genomics

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Background Mismatch repair (MMR) system is evolutionarily conserved for genome stability maintenance. Germline pathogenic variants (PVs) in MMR genes that lead to MMR functional deficiency are associated with high cancer risk. Knowing the evolutionary origin of germline PVs in human MMR genes will facilitate understanding the biological base of MMR deficiency in cancer. However, systematic knowledge is lacking to address the issue. In this study, we performed a comprehensive analysis to know the evolutionary origin of human MMR PVs. Methods We retrieved MMR gene variants from the ClinVar database. The genomes of 100 vertebrates were collected from the UCSC genome browser and ancient human sequencing data were obtained through comprehensive data mining. Cross-species conservation analysis was performed based on the phylogenetic relationship among 100 vertebrates. Rescaled ancient sequencing data were used to perform variant calling for archeological analysis. Results Using the phylogenetic approach, we traced the 3369 MMR PVs identified in modern humans in 99 non-human vertebrate genomes but found no evidence for cross-species conservation as the source for human MMR PVs. Using the archeological approach, we searched the human MMR PVs in over 5000 ancient human genomes dated from 45,045 to 100 years before present and identified a group of MMR PVs shared between modern and ancient humans mostly within 10,000 years with similar quantitative patterns. Conclusion Our study reveals that MMR PVs in modern humans were arisen within the recent human evolutionary history.

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Section: Archeological Analysis Of Human Mmr Pvsmentioning

confidence: 99%

Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes

Lei,

Li,

Zhao

et al. 2024

Hum Genomics

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“…The limited sequencing depth decreases the accuracy of TE detection and genotyping. Second, aDNA templates are highly fragmented, and shotgun WGS libraries are sometimes sequenced by the single-end mode with short read length [33,158]. For libraries sequenced by the paired-end mode, read pairs largely overlap with their mate reads.…”

Section: Technical Challenges In Te Insertion Profiling With Ancient Dnamentioning

confidence: 99%

Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans

et al. 2021

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Transposable elements (TEs) significantly contribute to shaping the diversity of the human genome, and lines of evidence suggest TEs as one of driving forces of human brain evolution. Existing computational approaches, including cross-species comparative genomics and population genetic modeling, can be adapted for the study of the role of TEs in evolution. In particular, diverse ancient and archaic human genome sequences are increasingly available, allowing reconstruction of past human migration events and holding the promise of identifying and tracking TEs among other evolutionarily important genetic variants at an unprecedented spatiotemporal resolution. However, highly degraded short DNA templates and other unique challenges presented by ancient human DNA call for major changes in current experimental and computational procedures to enable the identification of evolutionarily important TEs. Ancient human genomes are valuable resources for investigating TEs in the evolutionary context, and efforts to explore ancient human genomes will potentially provide a novel perspective on the genetic mechanism of human brain evolution and inspire a variety of technological and methodological advances. In this review, we summarize computational and experimental approaches that can be adapted to identify and validate evolutionarily important TEs, especially for human brain evolution. We also highlight strategies that leverage ancient genomic data and discuss unique challenges in ancient transposon genomics.

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Ancient DNA analysis

Orlando

Allaby

Skoglund

et al. 2021

Nat Rev Methods Primers

248

167

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While the first ancient DNA molecules were extracted more than three decades ago, the first ancient nuclear genomes could only be characterized after high-throughput sequencing was invented. Genome-scale data have now been gathered from thousands of ancient archaeological specimens, and the number of ancient biological tissues amenable to genome sequencing is growing steadily. Ancient DNA fragments are typically ultrashort molecules and carry extensive amounts of chemical damage accumulated after death. Their extraction, manipulation and authentication require specific experimental wet-lab and dry-lab procedures before patterns of genetic variation present in past individuals, populations and species can be confidently interpreted. Ancient DNA data help to address an entire array of questions in anthropology, evolutionary biology, and the environmental and archaeological sciences. The data have revealed a considerably more dynamic past than previously appreciated and have revolutionized our understanding of many major prehistoric and historic events. This article provides an overview of the concepts and state-of-the-art methods underlying ancient DNA analysis and illustrates the diversity of resulting applications. It also addresses some of the ethical challenges associated with the destructive analysis of irreplaceable material, emphasizes the need to fully involve archeologists and stakeholders as part of the research design and analytical process, and discusses future perspectives.

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A Minimally Destructive Protocol for DNA Extraction from Ancient Teeth

Cited by 3 publications

References 44 publications

Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes

Evolutionary origin of germline pathogenic variants in human DNA mismatch repair genes

Genomic approaches to trace the history of human brain evolution with an emerging opportunity for transposon profiling of ancient humans

Ancient DNA analysis

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