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Improved Tools for Point-of-Care Nucleic Acid Amplification Testing

Citation

Jue, Erik Bradley (2020) Improved Tools for Point-of-Care Nucleic Acid Amplification Testing. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/d6mf-5081. https://resolver.caltech.edu/CaltechTHESIS:05292020-131840076

Abstract

There is a critical need for improved diagnostic tools to detect infectious diseases, especially in low-resource regions. A sample-to-answer point-of-care nucleic acid amplification test (NAAT) would be incredibly valuable for many different applications (e.g. COVID-19, Chlamydia/Gonorrhoeae, Influenza, Ebola, Zika/Chikungunya/Dengue, etc.). However, sample preparation (purification of pure nucleic acids) is a challenging bottleneck. In Chapter 2, commercial NA extraction methods were studied and improved. In Chapter 3, commercial stocks of SARS-CoV-2 RNA used in FDA emergency-use authorizations were found to be inaccurate and were independently quantified using reverse transcription digital PCR. In Chapter 4, a 3D printed meter-mix device was developed for initial processing prior to the sample preparation device. In Chapter 5, a 3D printed sample-to-device interface was prototyped to facilitate loading multi-volume SlipChip devices with purified template mixed with LAMP reactants. In Chapters 6-7, advancements were made for image processing of commercial chips to study digital LAMP reactions. In Chapter 8, additional tools were developed towards sample-to-answer point-of-care NAAT including a sample preparation module, amplification module, cell-phone readout, and automated base station.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:sample-to-answer, integrated, point-of-care, nucleic acid amplification test, infectious disease diagnostics, nucleic acid extraction, PCR, LAMP
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Bioengineering
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Ismagilov, Rustem F.
Thesis Committee:
  • Murray, Richard M. (chair)
  • Ismagilov, Rustem F.
  • Shapiro, Mikhail G.
  • Yang, Changhuei
Defense Date:18 May 2020
Non-Caltech Author Email:jue.erik (AT) gmail.com
Funders:
Funding AgencyGrant Number
Rose Hills FoundationUNSPECIFIED
NSF Graduate Research FellowshipUNSPECIFIED
NIH Training GrantUNSPECIFIED
Caltech Innovation Initiative (CI2) Research Grant.UNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)HR0011-11-2-0006
Defense Threat Reduction AgencyMCDC-18-01-01-007
Burroughs Wellcome Fund Innovation in Regulatory Science1014981
Record Number:CaltechTHESIS:05292020-131840076
Persistent URL:https://resolver.caltech.edu/CaltechTHESIS:05292020-131840076
DOI:10.7907/d6mf-5081
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41598-020-58586-3DOIChapter 2
https://doi.org/10.1101/2020.04.28.20077602DOIChapter 3
https://doi.org/10.1039/C6LC00292GDOIChapter 4
https://doi.org/10.1021/acsnano.5b07338DOIChapter 5
https://doi.org/10.1021/acs.analchem.8b04324DOIChapter 6
https://doi.org/10.1093/nar/gkaa099DOIChapter 7
ORCID:
AuthorORCID
Jue, Erik Bradley0000-0001-7585-3794
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:13735
Collection:CaltechTHESIS
Deposited By: Erik Jue
Deposited On:01 Jun 2020 22:28
Last Modified:09 Jun 2020 18:30

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