Comparative Analysis of DNA Extraction Techniques on DNA yield from Ancient Teeth

Latifa Jackson, Ph.D.1,2

Christopher Cross, M.A.,2,3

Muneer Abbas1,4

Fatimah Jackson, Ph.D.2,5

  1. National Human Genome Center, Howard University Hospital
  2. W. Montague Cobb Research Laboratory, Howard University
  3. Department of Anatomy, College of Medicine, Howard University
  4. Department of Microbiology, College of Medicine, Howard University
  5. Department of Biology, Howard University
While much reporting has been done to understand ancient DNA techniques for archaic human populations, little work has been done to characterize the feasibility of extracting DNA from historical populations of humans who lived less than 200 years ago. Here we examine three methods for DNA extraction from skeletal remains using CC672, an individual from the W. Montague Cobb Skeletal Collection, who died 85 years ago. Dentine-cement powder was obtained from molar teeth. Molars were scraped free of cementum (CC), calculus (CL), and periodontal ligament (PDL). Each was isolated separately and then the remaining CC, CL, and PDL debris was combined in a mixed sample (MX). Extraction was conducted using Oragene (saliva based), Qiagen (blood and tissue), and phenol-chloroform. These techniques were implemented in parallel. Extractions were then measured for DNA concentration, confirmed for DNA quality and finally amplified to further assess DNA viability. We were able to recover DNA from all three methods in all samples. The phenol chloroform extraction yielded the largest DNA amounts (138.2-1865.6 ng/µL), next the Qiagen yielded between (12.7-13.9 ng/µL for S samples, 6.5-9.7 ng/µL for CC672 samples) and Oragene yielded intermediate DNA amounts (S5:75.5 ng/µL and MX:21.2 ng/ µL). DNA was amplified using the FOXP3 gene with 90% success. This molecular analysis suggests that conventional extraction methods for ancient DNA are robust to analysis of Cobb Collection samples. Amplification of the DNA extracted shows that human DNA was present in sufficient quality. This exciting result will be followed up with further analysis.

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