DNA quality and STR success rate in different formalin-fixed tissues

Area of Science:

• Forensic Science
• Molecular Biology
• Genetics

Background:

• Formalin-fixed tissues are valuable DNA sources when fresh samples are unavailable.
• Formaldehyde fixation causes DNA cross-linking and fragmentation, complicating extraction and amplification.
• Optimizing DNA extraction from formalin-fixed paraffin-embedded (FFPE) tissues is crucial for forensic identification.

Purpose of the Study:

• To optimize DNA extraction from various formalin-fixed tissues for downstream short tandem repeat (STR) analysis.
• To evaluate the impact of pre-extraction treatments and different DNA extraction kits on DNA yield and quality.
• To determine the optimal timeframe for DNA extraction from FFPE tissues to minimize allelic dropout.

Main Methods:

• Tested two pre-extraction treatments: gradual dehydration with ethanol and pre-digestion heat treatment.
• Employed three DNA extraction methods: Chelex-100, TIANamp FFPE DNA Kit, and ML Ultra-micro DNA extraction kit.
• Analyzed DNA quality and quantity using spectrophotometry and Quantifiler® Trio DNA Quantification Kits, with STR analysis using the GSTAR™ 25 kit.

Main Results:

• Pre-extraction treatments did not significantly affect STR success rates.
• Allelic dropout was observed in heart, liver, spleen, lung, and kidney tissues by day 9.
• Allelic dropout occurred later in muscle (day 12) and brain (day 15) tissues.

Conclusions:

• Effective DNA extraction and STR analysis from formalin-fixed tissues are feasible within 9 days.
• The study provides insights into the temporal stability of DNA in FFPE tissues for forensic applications.
• Properly timed DNA extraction is critical to mitigate allelic dropout and ensure reliable identification results.