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Non-STR DNA Markers: SNPs, Y-STRs, LCN and mtDNA

Sample Preparation

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Mitochondrial DNA (mtDNA) methods are useful in analyzing degraded samples and those containing very low quantity of nuclear DNA. mtDNA is present in cells at a much higher copy number than nuclear DNA (as noted in the table/animation above). The increased copy number of mitochondrial DNA per cell increases the concern for contamination introduced in the laboratory. The procedures used in mtDNA laboratories are designed to limit the possibility of contamination.

These procedures include:

  • Wearing of special clothing (e.g., face masks, sleeves, hair nets)
  • Use of dedicated laboratory equipment and other supplies
  • Frequent cleaning and decontamination of laboratory and equipment
  • Organization of work flow
  • Monitoring of extraneous DNA through controls

Several forensic-and-ancient-remains research laboratories have published cleaning and extraction procedures for recovery of DNA from bones and teeth. The specific cleaning procedures are extremely important. If these specimens are not properly cleaned, external contaminants and potential inhibitors may be extracted with the DNA.20,21 As described in course DNA Extraction & Quantitation, inhibitors may be detrimental to the amplification process.

Published procedures include:22-27

  • Rinsing the specimen with double distilled deionized water
  • Rinsing with a dilute hypochlorite solution
  • Polishing the specimen with a grinding stone followed by water and bleach rinses
  • Exposing the specimen to ultraviolet irradiation
  • Vertical sectioning of the tooth's crown for removal of the dental pulp

Specialized tools are needed for many of these extraction procedures, e.g., a Dremel tool, a MicroMill grinder, a freezer mill, an aluminum oxide wheel, a grinding stone, a mortar, a pestle, a chisel, a hammer, and/or a saw with diamond blade, just to name a few.  The extraction of DNA from bones and teeth is a challenging process; many of the challenges can be overcome with the appropriate procedures and equipment.

Photo of specialized tools for extraction procedures, including a hammer and Dremel tool
National Institute of Justice (NIJ) (see reuse policy).

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