Ancient DNA is notoriously easy to contaminate, requiring special protocols in all steps of its purification and identification process. Even when taking proper contamination precautions, sequencing of aDNA is hard due to poor preservation. However, a new protocol has shown some promise for increasing endogenous DNA extraction. By 'pre-digesting' bone and tooth fragments, endogenous DNA yields can be increased by nearly 300%, which will allow us to make new discoveries.
Source:
http://www.nature.com/articles/srep11184
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