DNA Degradation and Linear Amplification

DNA degradation is a major concern for forensic evidence and human identification. Analysis of DNA in the forensic community utilizes short tandem repeats (STRs) that range from 100 to 500 base pairs (bp) in size. The more extensive the degradation, the smaller the fragments of DNA, and the less likelihood to obtain a full profile for identification due to drop-out of the larger loci. I've been wanting to try this pre-PCR enhancement method that increases DNA typing success for low template DNA and I'm curious about its application for degraded samples. If degradation is observed via drop-out of larger loci or a ski-slope effect, the sample usually gets re-amplified with additional PCR cycles. However, this can lead to stochastic effects.

The method I'd like to try, linear amplification, increases starting template DNA by producing a single copy of the template for every cycle number as opposed to exponential amplification. This occurs in separate forward and reverse primer reactions that are then pooled together for downstream analysis. The thinking behind this was that the linear (and non-exponential) fashion of amplification would be more representative of the DNA in a sample without the stochastic effects of low template DNA. However, if a degraded samples can be amplified with specifically the larger loci in mind then perhaps we could see more balanced peaks and additional true alleles getting called. The drawback to this is that you would have to get permission to use commercial kit's proprietary primers and it would be difficult to customize a linear amplification multiplex specific to a sample's observed locus drop-out. In addition, most scientists prefer first pass success for increased productivity and lower costs.

References:

Grisedale, K., et al. Linear amplification of target prior to PCR for improved low template DNA results. Biotechniques 56(3) (2014) 145-7.