Patterns of damage in genomic DNA sequences from a Neandertal

By Adrian W. Briggs, U. Stenzel, Philip L. F. Johnson, R. Green, J. Kelso, Kay Prüfer, M. Meyer, J. Krause, Michael T. Ronan, M. Lachmann and 1 more. Proceedings of the National Academy of Sciences of the United States of America, 2007

928 citations recorded by the source corpus.

Subfields: Anthropology, Archeology, Genetics

View Paper: https://www.semanticscholar.org/paper/93fb336cac19c95a104a602c7d22d3121bece0a7

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Anthropology

In Genetics

Citations in the corpus

From the field to the laboratory: Controlling DNA contamination in human ancient DNA research in the high-throughput sequencing era (2017, neutral): “The observation that post-mortem DNA fragmentation occurs preferentially at depurinated sites is a second criterion to characterise aDNA (Briggs et al. 2007), although it does not seem to correlate with ancient samples age (Sawyer et al. 2012).”
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments (2013, background): “DNA fragmentation is at least partly driven by depurination (1, 2), a continually occurring process.”
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes (2013, background): “454-based pyrosequencing is known to generate artificial duplicates (Briggs et al., 2007).”
Accurate sex identification of ancient human remains using DNA shotgun sequencing (2013, background): “…and may thus increase the rate of contamination (Krause et al., 2010), and the patterns of post-mortem damage that can be used to authenticate putatively ancient DNA are strongest at the ends of molecules (Briggs et al., 2007) which are preferentially lost in such primer-based approaches.”
A Draft Sequence of the Neandertal Genome (2010, neutral): “At the 3′-ends, complementary G to A transitions are seen as a result of the enzymatic fill-in procedure in which blunt DNA ends are created before adaptor ligation (23).”
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (2014, background): “However, aDNA sequences often show an excess of nucleotide misincorporations at read termini, owing to the presence of DNA overhangs in which post-mortem cytosine deamination rates are inflated 53 .”
Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA (2015, background): “Deaminated cytosines are misread as thymines during sequencing and lead to the characteristic increase in frequency of cytosine to thymine transitions near the ends of ancient molecules [2].”
Single‐tube library preparation for degraded DNA (2017, background): “This pattern has been shown to be a result of cytosine deamination of single-stranded overhangs in combination with the 3’-5’ exonuclease activity and 5’-3’ polymerase activity of the T4 DNA Polymerase during end repair (Briggs et al. 2007; Brotherton et al. 2007).”
The complete genome sequence of a Neandertal from the Altai Mountains (2013, positive): “These libraries, together with one library prepared using a previous protocol 8 , were treated with uracil-DNA-glycosylase to remove uracil residues, a common miscoding lesion in ancient DNA that results from the deamination of cytosine 9–11 (SI 5a).”