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

Abstract

BackgroundAs 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.ResultsThe 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.ConclusionsWe 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 materialThe online version of this article (10.1186/s12864-018-4945-x) contains supplementary material, which is available to authorized users.

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“…It is possible that the correlation of capture success with precapture subject DNA proportions may become nonlinear at lower values due to, for example, increased rates of misbinding between baits and library DNA, leading to deviation from our predictions. Although a number of studies focused on ancient DNA provide some evidence that the correlation of capture success with precapture subject DNA proportions holds for lower quality samples (Ávila‐Arcos et al., ; Carpenter et al., ; Cruz‐Dávalos et al., , ), these studies lack the sample sizes needed for statistical tests of this hypothesis. Thus, further experimental work on samples with low proportions of subject DNA are necessary.…”

“…Along with the two tissue extracts which serve as high‐quality DNA controls, we chose 110 faecal extracts, each representing a unique individual, for exome sequencing based on their estimated percentage of subject DNA relative to total DNA concentration. Because studies of ancient DNA found that hybridization capture of samples with <1% subject DNA yielded only small amounts of useable data (Ávila‐Arcos et al., ; Cruz‐Dávalos et al., ), we conservatively chose extracts with more than 2% subject DNA. In addition, we only used samples with total DNA concentrations >6 ng/μl so that we could remove 200 ng for library preparation without needing to concentrate the extract.…”

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Hybrid Capture-Based Next Generation Sequencing and Its Application to Human Infectious Diseases

“…Another uniparental marker, the Y-chromosome DNA (Y-DNA), was also used to study aDNA. As each cell possesses only one copy of the Y chromosome, the hybridization capture was carried out to enrich specific genomic regions of the Y chromosome both on solid support ( Fu et al, 2013 ) and in solution ( Cruz Dávalos et al, 2017 ). However, targeting mitochondrial DNA or Y chromosome involves discarding a large proportion of potentially informative sequences present in autosomal DNA.…”