RT Journal Article
SR Electronic
T1 Comparative Performance of Two Whole Genome Capture Methodologies on Ancient DNA Illumina Libraries
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 007419
DO 10.1101/007419
A1 María C. Ávila-Arcos
A1 Marcela Sandoval-Velasco
A1 Hannes Schroeder
A1 Meredith L. Carpenter
A1 Anna-Sapfo Malaspinas
A1 Nathan Wales
A1 Fernando Peñaloza
A1 Carlos D. Bustamante
A1 M. Thomas P. Gilbert
YR 2014
UL http://biorxiv.org/content/early/2014/07/24/007419.abstract
AB The application of whole genome capture (WGC) methods to ancient DNA (aDNA) promises to increase the efficiency of ancient genome sequencing.We compared the performance of two recently developed WGC methods in enriching human aDNA within Illumina libraries built using both double-stranded (DSL) and single-stranded (SSL) build protocols. Although both methods effectively enriched aDNA, one consistently produced marginally better results, giving us the opportunity to further explore the parameters influencing WGC experiments.Our results suggest that bait length has an important influence on library enrichment. Moreover, we show that WGC biases against the shorter molecules that are enriched in SSL preparation protocols. Therefore application of WGC to such samples is not recommended without future optimization. Lastly, we document the effect of WGC on other features including clonality, GC composition and repetitive DNA content of captured libraries.Our findings provide insights for researchers planning to perform WGC on aDNA, and suggest future tests and optimization to improve WGC efficiency.