Giant magnetoresistive nanosensor analysis of circulating tumor DNA for therapy response monitoring and early detection of cancer

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In the era of precision medicine, molecular subtyping of non--small cell lung cancer (NSCLC) has revolutionized therapeutics tailored to individual actionable mutations, particularly the use of tyro- sine kinase inhibitors (TKIs) for Epidermal Growth Factor Receptor (EGFR) mutations. However, efficient therapy selection remains challenging for some patients, and it is estimated that 20% of lung cancer patients begin therapy prior to EGFR testing. Common reasons for lack of molecular testing include insufficient tissue biopsy or inability to biopsy certain patients, and long turnaround times to results. Clearly, new technologies that are rapid, cost--effective, and highly sensitive are needed for effective companion diagnostics. This thesis outlines the development and clinical translation of a blood--based circulating tumor (ct) DNA EGFR genotyping assay using giant magnetoresistive (GMR) nanosensors as an alternative for therapy selection and response monitoring. This GMR as- say achieved analytical sensitivities of 0.01% mutant allelic fraction for 3 common "hot spot" EGFR mutations, equivalent to detecting 1 mutant allele in a background of 10,000 wild--type alleles. In a clinical study of therapy selection and response monitoring of metastatic NSCLC patients, the assay achieved high sensitivity and specificity (AUC > 0.95) and was able to accurately predict therapy response after just 2 weeks. This represents a vast improvement compared to the current clinical standard of radiographic (CT) assessment after 2--3 months, which can be a harmful delay for patients who do not respond to targeted therapy and need immediate changes in therapeutic regimen. GMR sensors were also utilized for the early detection of colorectal cancer (CRC). While CRC diagnosis in Stage I is associated with a 90% 5--year survival rate, common screening methods such as colonoscopy or fecal testing are underutilized, resulting in a majority of CRC patients diagnosed at later stages. A non--invasive blood--based ctDNA test with GMR sensors could aid in screening efforts, with methylation biomarkers indicated for improved early cancer detection compared to mu- tations. This thesis also details the technology development of integrating methylation--specific PCR with high resolution melt (HRM) analysis on GMR sensors for quantifying methylation density. The technology was first optimized in a melanoma cell line model, and then extended to a multiplexed panel of 4 putative biomarkers of early CRC. This assay achieved analytical sensitivities of 0.01% methylated allelic fraction for 3 of 4 markers, and was validated in 2 late stage CRC patient samples.


Type of resource text
Form electronic resource; remote; computer; online resource
Extent 1 online resource.
Place California
Place [Stanford, California]
Publisher [Stanford University]
Copyright date 2020; ©2020
Publication date 2020; 2020
Issuance monographic
Language English


Author Nesvet, Jared Charles
Degree supervisor Wang, Shan X
Thesis advisor Wang, Shan X
Thesis advisor Bertozzi, Carolyn R, 1966-
Thesis advisor Karunadasa, Hemamala
Degree committee member Bertozzi, Carolyn R, 1966-
Degree committee member Karunadasa, Hemamala
Associated with Stanford University, Department of Chemistry.


Genre Theses
Genre Text

Bibliographic information

Statement of responsibility Jared C. Nesvet.
Note Submitted to the Department of Chemistry.
Thesis Thesis Ph.D. Stanford University 2020.
Location electronic resource

Access conditions

© 2020 by Jared Charles Nesvet

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