Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.

ABSTRACT: Ancient DNA extracts consist of a mixture of endogenous molecules and contaminant DNA templates, often originating from environmental microbes. These two populations of templates exhibit different chemical characteristics, with the former showing depurination and cytosine deamination by-products, resulting from post-mortem DNA damage. Such chemical modifications can interfere with the molecular tools used for building second-generation DNA libraries, and limit our ability to fully characterize the true complexity of ancient DNA extracts. In this study, we first use fresh DNA extracts to demonstrate that library preparation based on adapter ligation at AT-overhangs are biased against DNA templates starting with thymine residues, contrarily to blunt-end adapter ligation. We observe the same

SUBMITTER: Seguin-Orlando A 

PROVIDER: S-EPMC3812280 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature