Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

Abstract

Most ancient specimens contain very low levels of endogenous DNA, precluding the shotgun sequencing of many interesting samples because of cost. Ancient DNA (aDNA) libraries often contain <1% endogenous DNA, with the majority of sequencing capacity taken up by environmental DNA. Here we present a capture-based method for enriching the endogenous component of aDNA sequencing libraries. By using biotinylated RNA baits transcribed from genomic DNA libraries, we are able to capture DNA fragments from across the human genome. We demonstrate this method on libraries created from four Iron Age and Bronze Age human teeth from Bulgaria, as well as bone samples from seven Peruvian mummies and a Bronze Age hair sample from Denmark. Prior to capture, shotgun sequencing of these libraries yielded an average of 1.2% of reads mapping to the human genome (including duplicates). After capture, this fraction increased substantially, with up to 59% of reads mapped to human and enrichment ranging from 6- to 159-fold. Furthermore, we maintained coverage of the majority of regions sequenced in the precapture library. Intersection with the 1000 Genomes Project reference panel yielded an average of 50,723 SNPs (range 3,062-147,243) for the postcapture libraries sequenced with 1 million reads, compared with 13,280 SNPs (range 217-73,266) for the precapture libraries, increasing resolution in population genetic analyses. Our whole-genome capture approach makes it less costly to sequence aDNA from specimens containing very low levels of endogenous DNA, enabling the analysis of larger numbers of samples.

Tracing the origin of our species through palaeogenomics

“…The estimation of the time of admixture between the ancestors of the Ust'-Ishim individual and Neanderthals, based on the simplifying assumption that the gene flow occurred as a single event and assuming a generation time of 29 years, yielded approximately 60,000 to 50,000 years BP, which 00005-p. 9 BIO Web of Conferences is in agreement with the estimated time of the major expansion of modern humans out of Africa and the Middle East. Thus, the bulk of the Neanderthal contribution of present-day people outside Africa does not go back to mixture between Neanderthals and the anatomically modern humans who lived in the Middle East at earlier times, such as those whose remains have been found at Skhul and Qafzeh [39].…”

“…Enrichment also reduces sequencing costs since it reduces the proportion of the sequences that have to be discarded. This research is underway and some promising solutions have been proposed [7][8][9][10]. The first enrichment method was based on the hybridization of small synthetic DNA molecules that "capture" the complementary DNA strands from the fossil extracts from the Neanderthal bones of the caves of Vindija and El Sidron [7].…”

Genome-wide ancestry of 17th-century enslaved Africans from the Caribbean

“…DNA libraries using two recently developed whole-genome capture methods (8,9). Following enrichment, we generated between 0.1-and 0.5-fold genome-wide coverage for the three individuals, which proved to be sufficient to infer their likely origins within Africa.…”

Almost 20 years of Neanderthal palaeogenetics: adaptation, admixture, diversity, demography and extinction

“…B 370: 20130374 been retrieved with high-coverage using this approach [32,55,67]. Recently, a whole genome capture method that uses home-made biotinylated RNA probes as bait (which significantly reduces the cost of probe design) has been developed [68]. While this approach sounds attractive, it seems to introduce a bias against shorter DNA molecules, which is something that will have to be addressed before it can be fruitfully applied to samples of very degraded (and therefore short) Neanderthal DNA [69].…”