Integrated genetic analysis systems

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dc.contributor.advisor Galvin, Paul en
dc.contributor.advisor McCarthy, Tommie V. en
dc.contributor.author Brennan, Desmond
dc.date.accessioned 2014-03-20T10:35:37Z
dc.date.issued 2014
dc.date.submitted 2014
dc.identifier.citation Brennan, D. 2014. Integrated genetic analysis systems. PhD Thesis, University College Cork. en
dc.identifier.uri http://hdl.handle.net/10468/1480
dc.description.abstract The overall objective of this thesis is to integrate a number of micro/nanotechnologies into integrated cartridge type systems to implement such biochemical protocols. Instrumentation and systems were developed to interface such cartridge systems: (i) implementing microfluidic handling, (ii) executing thermal control during biochemical protocols and (iii) detection of biomolecules associated with inherited or infectious disease. This system implements biochemical protocols for DNA extraction, amplification and detection. A digital microfluidic chip (ElectroWetting on Dielectric) manipulated droplets of sample and reagent implementing sample preparation protocols. The cartridge system also integrated a planar magnetic microcoil device to generate local magnetic field gradients, manipulating magnetic beads. For hybridisation detection a fluorescence microarray, screening for mutations associated with CFTR gene is printed on a waveguide surface and integrated within the cartridge. A second cartridge system was developed to implement amplification and detection screening for DNA associated with disease-causing pathogens e.g. Escherichia coli. This system incorporates (i) elastomeric pinch valves isolating liquids during biochemical protocols and (ii) a silver nanoparticle microarray for fluorescent signal enhancement, using localized surface plasmon resonance. The microfluidic structures facilitated the sample and reagent to be loaded and moved between chambers with external heaters implementing thermal steps for nucleic acid amplification and detection. In a technique allowing probe DNA to be immobilised within a microfluidic system using (3D) hydrogel structures a prepolymer solution containing probe DNA was formulated and introduced into the microfluidic channel. Photo-polymerisation was undertaken forming 3D hydrogel structures attached to the microfluidic channel surface. The prepolymer material, poly-ethyleneglycol (PEG), was used to form hydrogel structures containing probe DNA. This hydrogel formulation process was fast compared to conventional biomolecule immobilization techniques and was also biocompatible with the immobilised biomolecules, as verified by on-chip hybridisation assays. This process allowed control over hydrogel height growth at the micron scale. en
dc.description.sponsorship European Commission (NMP4-CT-2005-016833); Enterprise Ireland (Collaborative Centre for Applied Nanotechnology (CCAN)) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher University College Cork en
dc.rights © 2014, Desmond Brennan en
dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/3.0/ en
dc.subject Molecular diagnostics en
dc.subject Microfluidics en
dc.subject PCR en
dc.subject Hydrogel en
dc.subject.lcsh Genetic screening en
dc.subject.lcsh Molecular diagnosis en
dc.title Integrated genetic analysis systems en
dc.type Doctoral thesis en
dc.type.qualificationlevel Doctoral en
dc.type.qualificationname PhD (Science) en
dc.internal.availability Full text not available en
dc.check.info Indefinite en
dc.check.date 10000-01-01
dc.description.version Accepted Version
dc.contributor.funder European Commission en
dc.contributor.funder Enterprise Ireland en
dc.description.status Not peer reviewed en
dc.internal.school Biochemistry en
dc.check.reason Releasing this thesis would cause substantial prejudice to the commercial interests of University College Cork en
dc.check.opt-out Yes en
dc.thesis.opt-out true
dc.check.entireThesis Entire Thesis Restricted
dc.check.embargoformat Both hard copy thesis and e-thesis en
dc.internal.conferring Spring Conferring 2014 en


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© 2014, Desmond Brennan Except where otherwise noted, this item's license is described as © 2014, Desmond Brennan
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