title: Selective enrichment of damaged DNA molecules for ancient genome sequencing.
abstract: Contamination by present-day human and microbial DNA is one of the major hindrances for large-scale genomic studies using ancient biological material. We describe a new molecular method, U selection, which exploits one of the most distinctive features of ancient DNA--the presence of deoxyuracils--for selective enrichment of endogenous DNA against a complex background of contamination during DNA library preparation. By applying the method to Neanderthal DNA extracts that are heavily contaminated with present-day human DNA, we show that the fraction of useful sequence information increases ∼ 10-fold and that the resulting sequences are more efficiently depleted of human contamination than when using purely computational approaches. Furthermore, we show that U selection can lead to a four- to fivefold increase in the proportion of endogenous DNA sequences relative to those of microbial contaminants in some samples. U selection may thus help to lower the costs for ancient genome sequencing of nonhuman samples also.
authors: Max Planck Institute for Evolutionary Anthropology, Evolutionary Genetics Department, Deutscher Platz 6, D-04103 Leipzig, Germany marie_gansauge@eva.mpg.de mmeyer@eva.mpg.de.
authors: Marie-Theres
authors: MT
authors: Gansauge
authors: Max Planck Institute for Evolutionary Anthropology, Evolutionary Genetics Department, Deutscher Platz 6, D-04103 Leipzig, Germany marie_gansauge@eva.mpg.de mmeyer@eva.mpg.de.
authors: Matthias
authors: M
authors: Meyer
mesh_terms: D000818:Animals; D001483:Base Sequence; D059018:DNA Contamination; D003856:Deoxyuracil Nucleotides / Q000737:chemistry* / Q000235:genetics; D016678:Genome; D006801:Humans; D008969:Molecular Sequence Data; D059125:Neanderthals / Q000235:genetics*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D003856:Deoxyuracil Nucleotides