Comparison of Two Methods for Isolating DNA from Human Skeletal Remains for STR Analysis

Abstract

The quality and efficiency of a standard organic DNA isolation method and a silica-based method using the QIAGEN Blood Maxi Kit were compared to obtain human DNA and short tandem repeats (STRs) profiles from 39 exhumed bone samples for paternity testing. DNA samples were quantified by real-time PCR, and STR profiles were obtained using the AmpFlSTR(®) Identifiler(®) PCR amplification kit. Overall, the silica-based method recovered less DNA ranging from 0 to 147.7 ng/g (average 7.57 ng/g, median = 1.3 ng/g) than did the organic method ranging from 0 to 605 ng/g (average 44.27 ng/g, median = 5.8 ng/g). Complete profiles (16/16 loci tested) were obtained from 37/39 samples (95%) using the organic method and from 9/39 samples (23%) with the silica-based method. Compared with a standard organic DNA isolation method, our results indicate that the published silica-based method does not improve neither the quality nor the quantity of DNA for STR profiling.

Assessing the Utility of Soil DNA Extraction Kits for Increasing DNA Yields and Eliminating PCR Inhibitors from Buried Skeletal Remains

“… and Rucinski et al. reported PCR inhibition following organic extraction of DNA from bone, the latter of which overcame it through DNA dilution. Cattaneo et al.…”

“…Ideally, skeletal DNA isolation procedures maximize DNA recovery while effectively removing PCR inhibitors. However, tremendous variety exists among DNA isolation methods and among laboratories, as is well detailed in both the forensic science (11)(12)(13)(14)(15)(16)(17)(18) and the ancient DNA literature (19)(20)(21)(22). Three commonly used techniques for isolating DNA from bone include extraction via organic solvents (12,19), binding DNA to silica beads or columns (13,15,16,22), and precipitation of non-nucleic acid material by "salting out" (11,14).…”

“…Three commonly used techniques for isolating DNA from bone include extraction via organic solvents , binding DNA to silica beads or columns , and precipitation of non‐nucleic acid material by “salting out” . Further purification steps, such as use of centrifugal filter columns or DNA precipitation , also vary widely.…”

Recent Advances in Forensic DNA Analysis

“…Once the cells are lysed, DNA can be extracted using organic extraction [20]. This organic method using phenol-chloroform and the silica solid-phase extraction have been compared to each other with results indicating that the phenol-chloroform solution was able to capture more complete DNA profiles than silica based extraction [28]. Unfortunately, the DNA preserved in bones can vary greatly from one cadaver to the next due to environmental conditions, animals, insects, and microbes, leaving the remaining DNA limited in quantityor degraded [29].…”

Ancient DNA and Forensics Mutual Benefits a Practical Sampling and Laboratory Guide Through a Virtual Ancient DNA Study

“…Further Considerations In human identification a DNA profile (composite of STR-markers) or a mitochondrial DNA sequence is compared to a reference sample -in case of a match p o s i t i v e i d e n t i fi c a t i o n a c h i e v e d w i t h m i n u t e uncertainties: Regardless whether the questionnaire comes from regular forensics of from the historians the reference sample of choice is a 'direct comparison sample': anything from a toothbrush to worn clothes may provide biological remnants from the user or owner; in 20 case of a match, it appears highly likely (approx. 1:10 ) that the person under investigation has left its biological material on the reference trace sample versus a random match.…”