dc.date.accessioned | 2017-08-04T12:38:20Z | |
dc.date.available | 2017-08-04T12:38:20Z | |
dc.date.created | 2014-10-14T15:41:44Z | |
dc.date.issued | 2014 | |
dc.identifier.citation | Star, Bastiaan Nederbragt, Alexander Johan Hansen, Marianne Helén Selander Skage, Morten Gilfillan, Gregor Duncan Bradbury, Ian R. Pampoulie, Christophe Stenseth, Nils Christian Jakobsen, Kjetill Sigurd Jentoft, Sissel . Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA. PLoS ONE. 2014, 9(3) | |
dc.identifier.uri | http://hdl.handle.net/10852/56795 | |
dc.description.abstract | Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua), which forms interrupted palindromes consisting of reverse complementary sequence at the 5′ and 3′-ends of sequencing reads. The palindromic sequences themselves have specific properties – the bases at the 5′-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3′-end. The terminal 3′ bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA), which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3′-end of DNA strands, with the 5′-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA) datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias. | en_US |
dc.language | EN | |
dc.publisher | Public Library of Science (PLoS) | |
dc.rights | Attribution 4.0 International | |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | |
dc.title | Palindromic sequence artifacts generated during next generation sequencing library preparation from historic and ancient DNA | en_US |
dc.type | Journal article | en_US |
dc.creator.author | Star, Bastiaan | |
dc.creator.author | Nederbragt, Alexander Johan | |
dc.creator.author | Hansen, Marianne Helén Selander | |
dc.creator.author | Skage, Morten | |
dc.creator.author | Gilfillan, Gregor Duncan | |
dc.creator.author | Bradbury, Ian R. | |
dc.creator.author | Pampoulie, Christophe | |
dc.creator.author | Stenseth, Nils Christian | |
dc.creator.author | Jakobsen, Kjetill Sigurd | |
dc.creator.author | Jentoft, Sissel | |
cristin.unitcode | 185,15,29,50 | |
cristin.unitname | Centre for Ecological and Evolutionary Synthesis | |
cristin.ispublished | true | |
cristin.fulltext | original | |
cristin.qualitycode | 1 | |
dc.identifier.cristin | 1164002 | |
dc.identifier.bibliographiccitation | info:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS ONE&rft.volume=9&rft.spage=&rft.date=2014 | |
dc.identifier.jtitle | PLoS ONE | |
dc.identifier.volume | 9 | |
dc.identifier.issue | 3 | |
dc.identifier.doi | http://dx.doi.org/10.1371/journal.pone.0089676 | |
dc.identifier.urn | URN:NBN:no-59538 | |
dc.type.document | Tidsskriftartikkel | en_US |
dc.type.peerreviewed | Peer reviewed | |
dc.source.issn | 1932-6203 | |
dc.identifier.fulltext | Fulltext https://www.duo.uio.no/bitstream/handle/10852/56795/2/journal.pone.0089676.PDF | |
dc.type.version | PublishedVersion | |
cristin.articleid | e89676 | |