In-solution Y-chromosome capture-enrichment on ancient DNA libraries.

Details

Ressource 1Download: s12864-018-4945-x.pdf (2923.67 [Ko])
State: Public
Version: Final published version
Serval ID
serval:BIB_2A08928BDEB8
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
In-solution Y-chromosome capture-enrichment on ancient DNA libraries.
Journal
BMC genomics
Author(s)
Cruz-Dávalos D.I., Nieves-Colón M.A., Sockell A., Poznik G.D., Schroeder H., Stone A.C., Bustamante C.D., Malaspinas A.S. (co-last), Ávila-Arcos M.C. (co-last)
ISSN
1471-2164 (Electronic)
ISSN-L
1471-2164
Publication state
Published
Issued date
14/08/2018
Peer-reviewed
Oui
Volume
19
Number
1
Pages
608
Language
english
Notes
Publication types: Historical Article ; Journal Article
Publication Status: epublish
Abstract
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.
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.
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.
Keywords
Chromosomes, Human, Y, DNA, Ancient/analysis, DNA, Ancient/isolation & purification, Gene Library, Genomics, History, Ancient, Humans, Sequence Analysis, DNA/methods, Whole Genome Sequencing/methods, Ancient DNA, Capture-enrichment, Y chromosome
Pubmed
Web of science
Open Access
Yes
Create date
02/09/2018 18:59
Last modification date
20/08/2019 13:09
Usage data