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Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

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dc.contributor.author Mak, Sarah Siu Tze
dc.contributor.author Gopalakrishnan, Shyam
dc.contributor.author Carøe, Christian
dc.contributor.author Geng, Chunyu
dc.contributor.author Liu, Shanlin
dc.contributor.author Sinding, Mikkel Holger S.
dc.contributor.author Kuderna, Lukas, 1989-
dc.contributor.author Zhang, Wenwei
dc.contributor.author Fu, Shujin
dc.contributor.author Vieira, Filipe Garrett
dc.contributor.author Germonpré, Mietje
dc.contributor.author Bocherens, Hervé
dc.contributor.author Fedorov, Sergey E.
dc.contributor.author Petersen, Bent
dc.contributor.author Sicheritz-Ponten, Thomas
dc.contributor.author Marquès i Bonet, Tomàs, 1975-
dc.contributor.author Zhang, Guojie
dc.contributor.author Jiang, Hui
dc.contributor.author Gilbert, M Thomas
dc.date.accessioned 2018-04-05T17:37:03Z
dc.date.available 2018-04-05T17:37:03Z
dc.date.issued 2017
dc.identifier.citation Mak SST, Gopalakrishnan S, Carøe C, Geng C, Liu S, Sinding MS et al. Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing. Gigascience. 2017 Aug 1;6(8):1-13. DOI: 10.1093/gigascience/gix049
dc.identifier.issn 2047-217X
dc.identifier.uri http://hdl.handle.net/10230/34298
dc.description.abstract Ancient DNA research has been revolutionized following development of next-generation sequencing platforms. Although a number of such platforms have been applied to ancient DNA samples, the Illumina series are the dominant choice today, mainly because of high production capacities and short read production. Recently a potentially attractive alternative platform for palaeogenomic data generation has been developed, the BGISEQ-500, whose sequence output are comparable with the Illumina series. In this study, we modified the standard BGISEQ-500 library preparation specifically for use on degraded DNA, then directly compared the sequencing performance and data quality of the BGISEQ-500 to the Illumina HiSeq2500 platform on DNA extracted from 8 historic and ancient dog and wolf samples. The data generated were largely comparable between sequencing platforms, with no statistically significant difference observed for parameters including level (P = 0.371) and average sequence length (P = 0718) of endogenous nuclear DNA, sequence GC content (P = 0.311), double-stranded DNA damage rate (v. 0.309), and sequence clonality (P = 0.093). Small significant differences were found in single-strand DNA damage rate (δS; slightly lower for the BGISEQ-500, P = 0.011) and the background rate of difference from the reference genome (θ; slightly higher for BGISEQ-500, P = 0.012). This may result from the differences in amplification cycles used to polymerase chain reaction-amplify the libraries. A significant difference was also observed in the mitochondrial DNA percentages recovered (P = 0.018), although we believe this is likely a stochastic effect relating to the extremely low levels of mitochondria that were sequenced from 3 of the samples with overall very low levels of endogenous DNA. Although we acknowledge that our analyses were limited to animal material, our observations suggest that the BGISEQ-500 holds the potential to represent a valid and potentially valuable alternative platform for palaeogenomic data generation that is worthy of future exploration by those interested in the sequencing and analysis of degraded DNA.
dc.description.sponsorship The authors would like to acknowledge the ERC Consolidator Grant (681396 - Extinction Genomics), the Marie Skłodowska-Curie Actions (H2020-MSCA-ETN-643063 “Microwine”), Danish Council for Independent Research (4005-00107 Wine-ometrics), the Qimmeq project, funded by The Velux Foundations and Aage og Johanne Louis-Hansens Fond, China National GeneBank, and BGI-Shenzhen China for funding. L.F.K.K is supported by an FPI fellowship associated with BFU2014-55090-P (FEDER), T.M.B. is supported by MINECO BFU2014-55090-P (FEDER) and BFU2015-6215-ERC, a U01 MH106874 grant, and the Secretaria d'Universitats i Recerca del Departament d'Economia i Coneixement de la Generalitat de Catalunya.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Gigascience. 2017 Aug 1;6(8):1-13
dc.rights © The Author 2017. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.title Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/gigascience/gix049
dc.subject.keyword BGISEQ-500
dc.subject.keyword Illumina HiSeq 2500
dc.subject.keyword Ancient DNA
dc.subject.keyword Comparative performance
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/681396
dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/643063
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion

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