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Target Capture for Ancient DNA: Temperature, Time, and Tiling Density

Author(s): Jacob Enk

Year: 2016

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Summary

Bait-target hybridization (a.k.a., "target capture") is rapidly replacing PCR as the enrichment method of choice for ancient DNA sequencing projects. Though very successful in recent years, ancient DNA target capture outcomes vary substantially and could be better understood. Here we performed a series of experiments to measure how three commonly-varied parameters - temperature, time, and bait tiling density - impact enrichment of short, rare targets embedded in complex DNA backgrounds. We found that specificity (% on-target) and sensitivity (unique target reads recovered) varied with these parameters, sometimes in unexpected ways. Temperature was particularly impactful across the range typically employed in ancient DNA research (~45-65ºC), and should be carefully considered when designing or optimizing an ancient DNA enrichment project.


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Target Capture for Ancient DNA: Temperature, Time, and Tiling Density. Jacob Enk. Presented at The 81st Annual Meeting of the Society for American Archaeology, Orlando, Florida. 2016 ( tDAR id: 404604)


Keywords


Arizona State University The Andrew W. Mellon Foundation National Science Foundation National Endowment for the Humanities Society for American Archaeology Archaeological Institute of America