Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing
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 pro...
| Autores: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Estado: | Versión publicada |
| Fecha de publicación: | 2017 |
| País: | España |
| Institución: | Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya) |
| Repositorio: | Recercat. Dipósit de la Recerca de Catalunya |
| OAI Identifier: | oai:recercat.cat:10230/34298 |
| Acceso en línea: | http://hdl.handle.net/10230/34298 http://dx.doi.org/10.1093/gigascience/gix049 |
| Access Level: | acceso abierto |
| Palabra clave: | BGISEQ-500 Illumina HiSeq 2500 Ancient DNA Comparative performance |
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Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing |
| title |
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing |
| spellingShingle |
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing Mak, Sarah Siu Tze BGISEQ-500 Illumina HiSeq 2500 Ancient DNA Comparative performance |
| title_short |
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing |
| title_full |
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing |
| title_fullStr |
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing |
| title_full_unstemmed |
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing |
| title_sort |
Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing |
| dc.creator.none.fl_str_mv |
Mak, Sarah Siu Tze Gopalakrishnan, Shyam Carøe, Christian Geng, Chunyu Liu, Shanlin Sinding, Mikkel Holger S. Kuderna, Lukas, 1989- Zhang, Wenwei Fu, Shujin Vieira, Filipe Garrett Germonpré, Mietje Bocherens, Hervé Fedorov, Sergey E. Petersen, Bent Sicheritz-Ponten, Thomas Marquès i Bonet, Tomàs, 1975- Zhang, Guojie Jiang, Hui Gilbert, M Thomas |
| author |
Mak, Sarah Siu Tze |
| author_facet |
Mak, Sarah Siu Tze Gopalakrishnan, Shyam Carøe, Christian Geng, Chunyu Liu, Shanlin Sinding, Mikkel Holger S. Kuderna, Lukas, 1989- Zhang, Wenwei Fu, Shujin Vieira, Filipe Garrett Germonpré, Mietje Bocherens, Hervé Fedorov, Sergey E. Petersen, Bent Sicheritz-Ponten, Thomas Marquès i Bonet, Tomàs, 1975- Zhang, Guojie Jiang, Hui Gilbert, M Thomas |
| author_role |
author |
| author2 |
Gopalakrishnan, Shyam Carøe, Christian Geng, Chunyu Liu, Shanlin Sinding, Mikkel Holger S. Kuderna, Lukas, 1989- Zhang, Wenwei Fu, Shujin Vieira, Filipe Garrett Germonpré, Mietje Bocherens, Hervé Fedorov, Sergey E. Petersen, Bent Sicheritz-Ponten, Thomas Marquès i Bonet, Tomàs, 1975- Zhang, Guojie Jiang, Hui Gilbert, M Thomas |
| author2_role |
author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
BGISEQ-500 Illumina HiSeq 2500 Ancient DNA Comparative performance |
| topic |
BGISEQ-500 Illumina HiSeq 2500 Ancient DNA Comparative performance |
| description |
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. |
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2017 |
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2017 2018 2018 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
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article |
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http://hdl.handle.net/10230/34298 http://dx.doi.org/10.1093/gigascience/gix049 |
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http://hdl.handle.net/10230/34298 http://dx.doi.org/10.1093/gigascience/gix049 |
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Inglés |
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Inglés |
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Gigascience. 2017 Aug 1;6(8):1-13 info:eu-repo/grantAgreement/EC/H2020/681396 info:eu-repo/grantAgreement/EC/H2020/643063 info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P |
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http://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess |
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http://creativecommons.org/licenses/by/4.0/ |
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openAccess |
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application/pdf application/pdf |
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Oxford University Press |
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Oxford University Press |
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Recercat. Dipósit de la Recerca de Catalunya |
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Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencingMak, Sarah Siu TzeGopalakrishnan, ShyamCarøe, ChristianGeng, ChunyuLiu, ShanlinSinding, Mikkel Holger S.Kuderna, Lukas, 1989-Zhang, WenweiFu, ShujinVieira, Filipe GarrettGermonpré, MietjeBocherens, HervéFedorov, Sergey E.Petersen, BentSicheritz-Ponten, ThomasMarquès i Bonet, Tomàs, 1975-Zhang, GuojieJiang, HuiGilbert, M ThomasBGISEQ-500Illumina HiSeq 2500Ancient DNAComparative performanceAncient 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.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.Oxford University Press201820182017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/34298http://dx.doi.org/10.1093/gigascience/gix049reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésGigascience. 2017 Aug 1;6(8):1-13info:eu-repo/grantAgreement/EC/H2020/681396info:eu-repo/grantAgreement/EC/H2020/643063info:eu-repo/grantAgreement/ES/1PE/BFU2014-55090-P© 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.http://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/342982026-05-29T05:05:01Z |
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