Targeted investigation of the neandertal genome by array-based sequence capture

Hernán A. Burbano; Emily Hodges; Richard E. Green; Adrian W. Briggs; Johannes Krause; Matthias Meyer; Jeffrey M. Good; Tomislav Maricic; Philip L.F. Johnson; Zhenyu Xuan; Michelle Rooks; Arindam Bhattacharjee; Leonardo Brizuela; Frank W. Albert; Marco De La Rasilla; Javier Fortea; Antonio Rosas; Michael Lachmann; Gregory J. Hannon; Svante Pääbo

doi:10.1126/science.1188046

Targeted investigation of the neandertal genome by array-based sequence capture

Hernán A. Burbano, Emily Hodges, Richard E. Green, Adrian W. Briggs, Johannes Krause, Matthias Meyer, Jeffrey M. Good, Tomislav Maricic, Philip L.F. Johnson, Zhenyu Xuan, Michelle Rooks, Arindam Bhattacharjee, Leonardo Brizuela, Frank W. Albert, Marco De La Rasilla, Javier Fortea, Antonio Rosas, Michael Lachmann, Gregory J. Hannon, Svante Pääbo

Genetics, Cell Biology and Development (CBS)

Research output: Contribution to journal › Article › peer-review

227 Scopus citations

Abstract

It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of ∼99.8% microbial DNA. Using this approach, we have sequenced -14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.

Original language	English (US)
Pages (from-to)	723-725
Number of pages	3
Journal	Science
Volume	328
Issue number	5979
DOIs	https://doi.org/10.1126/science.1188046
State	Published - May 7 2010

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Burbano, H. A., Hodges, E., Green, R. E., Briggs, A. W., Krause, J., Meyer, M., Good, J. M., Maricic, T., Johnson, P. L. F., Xuan, Z., Rooks, M., Bhattacharjee, A., Brizuela, L., Albert, F. W., De La Rasilla, M., Fortea, J., Rosas, A., Lachmann, M., Hannon, G. J., & Pääbo, S. (2010). Targeted investigation of the neandertal genome by array-based sequence capture. Science, 328(5979), 723-725. https://doi.org/10.1126/science.1188046

Burbano, HA, Hodges, E, Green, RE, Briggs, AW, Krause, J, Meyer, M, Good, JM, Maricic, T, Johnson, PLF, Xuan, Z, Rooks, M, Bhattacharjee, A, Brizuela, L, Albert, FW, De La Rasilla, M, Fortea, J, Rosas, A, Lachmann, M, Hannon, GJ & Pääbo, S 2010, 'Targeted investigation of the neandertal genome by array-based sequence capture', Science, vol. 328, no. 5979, pp. 723-725. https://doi.org/10.1126/science.1188046

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abstract = "It is now possible to perform whole-genome shotgun sequencing as well as capture of specific genomic regions for extinct organisms. However, targeted resequencing of large parts of nuclear genomes has yet to be demonstrated for ancient DNA. Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of ∼99.8% microbial DNA. Using this approach, we have sequenced -14,000 protein-coding positions inferred to have changed on the human lineage since the last common ancestor shared with chimpanzees. By generating the sequence of one Neandertal and 50 present-day humans at these positions, we have identified 88 amino acid substitutions that have become fixed in humans since our divergence from the Neandertals.",

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AU - Bhattacharjee, Arindam

AU - Brizuela, Leonardo

AU - Albert, Frank W.

AU - De La Rasilla, Marco

AU - Fortea, Javier

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Targeted investigation of the neandertal genome by array-based sequence capture

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