Thesis

Degradation, quantification and the theory of nucleosome protection

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Awarding institution
  • University of Strathclyde
Date of award
  • 2011
Thesis identifier
  • T12784
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Abstract
  • Partial DNA profiles are often obtained from degraded samples due to allelic and locus dropout, particularly at the high molecular weight loci. Increasing the chance of genotyping success via shortening of amplicon size has been previously demonstrated with mini-STRs. A viable alternative based on nucleosome protection influenced by base sequences was explored in this study. Different systems for accurate quantification of degraded samples were looked at, including both single- and multi-copy targets. Optimisation was successful for GAPDH and it was compared to Plexor® HY using casework samples. Although GAPDH was more accurate, Plexor® HY was chosen and used to quantify degraded saliva samples due to its higher sensitivity and informativeness. The saliva samples had been degraded via the incubation method, which was assumed to preserve the chromatin structure. Next-generation and mini-STR kits were assessed in terms of sensitivity and casework genotyping. All kits performed exceptionally well and were comparable in all categories. 60 sequences (58 STRs and amelogenin X and Y) were evaluated for their nucleosome-forming potential (NFP) using two computer programs. The markers were divided into three groups based on their NFPs and the findings were verified empirically by amplifying degraded saliva samples and casework samples using 14 randomly chosen primer sets from the three groups. The effect of nucleosome protection was not observed for degraded saliva and casework samples. This is the first study that looks at an inherent property of STRs as a determinant of survivability from degradation processes. The work can be expanded to include more sample types. Other computer programs can be used, as predicting nucleosome positions is a rapidly advancing field.
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DOI
Date Created
  • 2011
Former identifier
  • 823900

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