Further evaluation of the efficacy of contamination removal from bone surfaces

Abstract

Studies of low copy number (LCN) and degraded DNA are prone to contamination from exogenous DNA sources that in some cases out-compete endogenous DNA in PCR amplification, thus leading to false positives and/or aberrant results. Particularly problematic is contamination that is inadvertently deposited on the surfaces of bones through direct handling. Whereas some previous studies have shown that contamination removal is possible by subjecting samples to sodium hypochlorite prior to DNA extraction, others caution that such treatment can destroy a majority of the molecules endogenous to the sample. To further explore this topic, we experimentally contaminated ancient northern fur seal (Callorhinus ursinus) ribs with human DNA and treated them with sodium hypochlorite to remove that contamination. Our findings are consistent with previous studies that found sodium hypochlorite to be highly efficient (~81-99%) at contamination removal; however, there emerged no treatment capable of removing 100% of the contamination across all of the experiments. Moreover, the ability to estimate the degree of damage to endogenous northern fur seal molecules was compromised due to the inherent variability of preserved mtDNA across the bones, and the presence of co-extracted PCR inhibitors.