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

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. Y., Rooks, M., Bhattacharjee, A., Brizuela, L., Albert, F. W., De La Rasilla, M., Fortea, J., Rosas, A., Lachmann, M., Hannon, G. J., Paabo, S. (2010) Targeted investigation of the neandertal genome by array-based sequence capture. Science, 328 (5979). pp. 723-725.

URL: http://www.ncbi.nlm.nih.gov/pubmed/20448179
DOI: 10.1126/science.1188046

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.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > analysis and processing > microarray gene expression processing
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
organism description > animal > mammal > primates > hominids > human
organism description > animal > mammal > primates
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL Cancer Center Shared Resources > Bioinformatics Service
CSHL Cancer Center Shared Resources > DNA Sequencing Service
CSHL Cancer Center Shared Resources > Microarray Service
Depositing User: CSHL Librarian
Date Deposited: 27 Sep 2011 14:46
Last Modified: 30 Dec 2014 16:07
PMCID: PMC3140021
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15369

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