Sequencing Ancient DNA

Next Generation sequencing continues to address previously unanswered questions. In a recent publication in Science, Meyer et al. describes the sequencing of DNA isolated from a fragment of bone more than 50,000 years old, found in a Siberia’s Denisova Cave. Ancient DNA is highly degraded and generally breaks down to single strands during purification, thus it was necessary to start with single-stranded DNA (ssDNA). Researchers used a novel enzyme, Circligase™ II ssDNA Ligase, to attach a single-stranded oligomer tag to the ssDNA fragments isolated from the bone.  The tagged DNA was immobilized, and enzymatically copied. An Illumina® Genome Analyzer IIx platform was used with 76-bp, double-index reads. The result was that more than 99% of the nucleotides were sequenced at least 10 times and 92% were sequenced at least 20 times. The quality of the genome information allowed for the determination that the Denisovan female had brown eyes, hair and skin, had 23 pairs of chromosomes consistent with modern humans, and sets the stage for dating fossils by their genomes.

Meyer M et al. (2012). A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science (New York, N.Y.) PMID: 22936568