ArticlePloS one2013
Ligation bias in illumina next-generation DNA libraries: implications for sequencing ancient genomes.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
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- Identifying a living great-grandson of the Lakota Sioux leader Tatanka Iyotake (Sitting Bull).Science advances · 2021Article
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- Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis.PloS one · 2021Article
- Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes.PloS one · 2021Article
- Genome-wide piggyBac transposon-based mutagenesis and quantitative insertion-site analysis in haploid Candida species.Nature protocols · 2020Article
- ChIP-Seq from Limited Starting Material of K562 Cells andBio-protocol · 2020Article
- Accurate Adapter Information Is Crucial for Reproducibility and Reusability in Small RNA Seq Studies.Non-coding RNA · 2019Article
- High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach.The Journal of infectious diseases · 2019Article
- TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay.Life science alliance · 2019Article
- Paleogenomics: reconstruction of plant evolutionary trajectories from modern and ancient DNA.Genome biology · 2019Article
- 3' Branch ligation: a novel method to ligate non-complementary DNA to recessed or internal 3'OH ends in DNA or RNA.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- A Guide to Carrying Out a Phylogenomic Target Sequence Capture Project.Frontiers in genetics · 2019Review
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- A massively parallel strategy for STR marker development, capture, and genotyping.Nucleic acids research · 2017Article
- A Robust Framework for Microbial Archaeology.Annual review of genomics and human genetics · 2017Review
- Less effective selection leads to larger genomes.Genome research · 2017Article
- gargammel: a sequence simulator for ancient DNA.Bioinformatics (Oxford, England) · 2017Article
- Human evolution: a tale from ancient genomes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
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9 authors.
Funding
No grant is acknowledged in the PubMed record.
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 bias on fresh DNA extracts sheared on Bioruptor, Covaris and nebulizers. This contradicts previous reports suggesting that this bias could originate from the methods used for shearing DNA. This also suggests that AT-overhang adapter ligation efficiency is affected in a sequence-dependent manner and results in an uneven representation of different genomic contexts. We then show how this bias could affect the base composition of ancient DNA libraries prepared following AT-overhang ligation, mainly by limiting the ability to ligate DNA templates starting with thymines and therefore deaminated cytosines. This results in particular nucleotide misincorporation damage patterns, deviating from the signature generally expected for authenticating ancient sequence data. Consequently, we show that models adequate for estimating post-mortem DNA damage levels must be robust to the molecular tools used for building ancient DNA libraries.
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