STRs, mini STRs and SNPs – A comparative study for typing degraded DNA

Abstract Short tandem repeat (STR) systems are the most powerful and widely used genetic marker systems in forensic DNA typing. Optimized amplification conditions and PCR reagents in combination with laser fluorescence based detection methods have increased the sensitivity and decreased the detectio...

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Bibliographic Details
Published in:Legal medicine (Tokyo, Japan) Japan), 2011-03, Vol.13 (2), p.68-74
Main Authors: Senge, Tim, Madea, Burkhard, Junge, Anke, Rothschild, Markus A, Schneider, Peter M
Format: Article
Language:English
Subjects:
5′ Nuclease assay
Blood Chemical Analysis
DNA - chemistry
DNA - classification
DNA - genetics
DNA degradation
DNA Fingerprinting - methods
Electrophoresis - methods
Forensic genetics
Genotype
Humans
Internal Medicine
Microsatellite Repeats
Mini STR
Minisatellite Repeats
Minisequencing
Polymerase Chain Reaction - methods
Polymorphism, Single Nucleotide
Saliva - chemistry
SNP typing
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Summary:Abstract Short tandem repeat (STR) systems are the most powerful and widely used genetic marker systems in forensic DNA typing. Optimized amplification conditions and PCR reagents in combination with laser fluorescence based detection methods have increased the sensitivity and decreased the detection threshold down to approximately 100 pg. The quality of human DNA from forensic samples can be influenced by environmental factors. These may cause different degrees of degradation which have a negative impact on the amplification process especially of STR systems with large amplicons. Therefore, methods which need only small amplicon sizes to detect DNA markers are a better choice for typing degraded DNA. Here we report investigations on different types of DNA markers and typing methods which should all be applicable for analysing degraded DNA. These are two commercially available mini STR kits and five SNP markers which were analysed with two self established assays, a 5′ nuclease assay and a minisequencing (SNaPshot) assay. The investigations comprised sensitivity studies, different types of stain material, as well as intact and degraded DNA. Results indicate that mini STRs are superior to standard STR typing methods, especially for typing old stain material with small amounts of degraded DNA. SNP typing based on the minisequencing (SNaPshot) assay achieved a better success rate in typing aged blood and saliva stains compared to standard STRs and SNP typing using the 5′ nuclease assay.
ISSN:1344-6223
1873-4162
DOI:10.1016/j.legalmed.2010.12.001