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

Détails

Ressource 1Télécharger: s12864-018-4945-x.pdf (2923.67 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_2A08928BDEB8
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
In-solution Y-chromosome capture-enrichment on ancient DNA libraries.
Périodique
BMC genomics
Auteur⸱e⸱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-dernier), Ávila-Arcos M.C. (co-dernier)
ISSN
1471-2164 (Electronic)
ISSN-L
1471-2164
Statut éditorial
Publié
Date de publication
14/08/2018
Peer-reviewed
Oui
Volume
19
Numéro
1
Pages
608
Langue
anglais
Notes
Publication types: Historical Article ; Journal Article
Publication Status: epublish
Résumé
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.
Mots-clé
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
Oui
Création de la notice
02/09/2018 18:59
Dernière modification de la notice
21/11/2022 8:25
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