title: Surveying the repair of ancient DNA from bones via high-throughput sequencing.
abstract: DNA damage in the form of abasic sites, chemically altered nucleotides, and strand fragmentation is the foremost limitation in obtaining genetic information from many ancient samples. Upon cell death, DNA continues to endure various chemical attacks such as hydrolysis and oxidation, but repair pathways found in vivo no longer operate. By incubating degraded DNA with specific enzyme combinations adopted from these pathways, it is possible to reverse some of the post-mortem nucleic acid damage prior to downstream analyses such as library preparation, targeted enrichment, and high-throughput sequencing. Here, we evaluate the performance of two available repair protocols on previously characterized DNA extracts from four mammoths. Both methods use endonucleases and glycosylases along with a DNA polymerase-ligase combination. PreCR Repair Mix increases the number of molecules converted to sequencing libraries, leading to an increase in endogenous content and a decrease in cytosine-to-thymine transitions due to cytosine deamination. However, the effects of Nelson Repair Mix on repair of DNA damage remain inconclusive.
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.|Department of Biology, McMaster University, Hamilton, ON, Canada.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Mouttham
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.|Department of Biology, McMaster University, Hamilton, ON, Canada.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Klunk
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.
authors.forename: Melanie
authors.initials: M
authors.lastname: Kuch
authors.affiliation: Science and Strategic Partnerships, Forensic Science and Identification Services, Royal Canadian Mounted Police, Ottawa, ON, Canada.
authors.forename: Ron
authors.initials: R
authors.lastname: Fourney
authors.affiliation: McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada.|Department of Biology, McMaster University, Hamilton, ON, Canada.|Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Poinar
mesh_terms: D000818:Animals; D001842:Bone and Bones / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D045643:DNA Repair Enzymes / Q000737:chemistry*; D005580:Fossils; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D056665:Mammoths / Q000235:genetics*
chemical_list: D004247:DNA; D045643:DNA Repair Enzymes
keywords: DNA damage; DNA repair; ancient DNA; high-throughput sequencing