Getting the Most Out of Electropherograms

Microsatellite markers, including short tandem repeats, are widely used for genetic analysis in biomedical research and forensics (Carey and Mitnik, 2002). The length of the DNA fragments corresponding to the microsatellite alleles can be determined using electrophoresis. The result of electrophoresis is a spectrum of intensity (concentration of the chemically labelled substances) as a function of time. This spectrum is also called a trace or an electropherogram. The peaks in an electropherogram are identified by size and on the basis of this identification, genotypes are determined. In forensics, this information is used in order to determine the profile of a sample.

For any locus of interest, the underlying information of interest is very simple (a pair of numbers corresponding to genotype, represented by clear peaks in an ideal electropherogram). However, the observed signal is complex due to the experimental procedures involved. The compound effect of plusA, polymerase slippage and electrophoretic diffusion is a characteristic pattern of peaks surrounding the allelic peak (Gill et al 2015). This noisy observed signal can be represented by high-resolution time series data and must undergo a series of signal-processing steps before genotypes can be determined with high confidence (e.g. Woldegebriel et al 2017).

This project will consider the analysis of degraded DNA samples that might be the result of DNA transfer, and the ability of the resultant electropherograms to determine the sample
profiles. It will investigate the performance of common processing methods, in terms of their ability to identify alleles based on the height of the largest peaks, on extremely poor quality and low-quantity DNA samples. Additionally, we will consider if it is worthwhile capturing more information from electropherograms than just peak height when determining the profile of the sample.

Louise Branch-Smith

Murdoch University

Louise is currently in her final semester studying a Bachelor of Science, majoring in Forensic Biology and Toxicology, and minoring in Applied Statistics and Pharmacology at Murdoch University. She has a current grade point average of 3.35 out of 4. She has also completed some IT units and can now further understand databases and how they work. She is currently employed by Murdoch University as a Senior Peer Assisted Study Sessions (PASS) Leader for the Statistics and Data Analysis unit MAS183. Louise is a highly motivated person, eager to learn and to have new experiences. For example, she was recently selected to travel to Malaysia on a New Colombo Plan scholarship, with Murdoch University, to study forensic science with Murdoch’s Internationally recognised forensic entomologist Dr Paola Magni-Partridge.

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