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Cruz-Dávalos DI, Nieves-Colón MA, Sockell A, Poznik GD, Schroeder H, Stone AC, Bustamante CD, Malaspinas AS, Ávila-Arcos MC. In-solution Y-chromosome capture-enrichment on ancient DNA libraries. BMC Genomics 2018; 19:608. [PMID: 30107783 PMCID: PMC6092841 DOI: 10.1186/s12864-018-4945-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/16/2018] [Indexed: 12/04/2022] Open
Abstract
Background As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach—in-solution capture-enrichment—retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. Results The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1–1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12–9549 times more targeted unique Y-chromosome sequences after capture, where 0.0–6.2% (WGC + YCC) and 0.0–23.5% (YCC) of the sequence reads were on-target, compared to 0.0–0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries’ initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. Conclusions We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round. Electronic supplementary material The online version of this article (10.1186/s12864-018-4945-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Diana I Cruz-Dávalos
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - María A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA
| | | | | | - Hannes Schroeder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, USA.,Institute of Human Origins, Arizona State University, Tempe, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, Stanford, USA.,Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Anna-Sapfo Malaspinas
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Computational Biology, University of Lausanne, Lausanne, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico, Mexico, Mexico.
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