Rapid identification of fluorescently labelled DNA by image analysis

Brazier, Jack A. D. (2021). Rapid identification of fluorescently labelled DNA by image analysis. University of Birmingham. M.Sc.

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Abstract

A masters thesis on the current DNA identification techniques and potential image analysis methods.

There are currently many DNA identification methods such as nanopore sequencing (identifying DNA sequences base by base) and restriction mapping (creating maps of DNA fragmented at certain sites). DNA identification is a tool that can be used for identifying diseases and species. The more frequently these methods are used, the quicker and cheaper they need to be. For example, in a disease outbreak many people may need to be tested. The current issue is that methods may cost over £100 per sample or produce results which do not contain enough data to be matched to a species. There is no method that can quickly (in one day or less) and cheaply (< £100) identify viruses and bacteria in a sample of DNA.

Optical Mapping of fluorescently labelled DNA is a technique which costs no more than £1 per sample. It has the potential to produce enough data to match a variety of DNA in a sample (a swab from someones mouth) to a range of species (bacteria). This is a candidate for the solution to rapid diagnosis in hospitals.

Optical mapping is currently being developed and DNA can be analysed and matched to a species. However, this method only works for short DNA molecules (λ DNA is 48.5k base pairs long) and matches have only been made to 5 different species. My approach is working towards labelling and combing longer DNA, extracting the molecule’s Fluorescent Intensity Profiles (FIPs) from the images, and matching a variety of DNA molecules from a species to its reference FIP sequence. The challenge of the current method is that long DNA molecules do not comb in a perfectly straight line and will cover multiple images. The new method aims to identify molecules which may be curved by using a different method of identification and extraction.

Type of Work:

Thesis (Masters by Research > M.Sc.)

Award Type:

Masters by Research > M.Sc.

Supervisor(s):