Developing High-Accuracy Sequencing Methods for Use in Early Cancer Detection, Disease Stratification, and Chemotherapy Resistance with Cell-Free DNA
Abstract
Recent efforts to understand the mutational landscape of tumors has resulted in a detailed cataloguing of diagnostic, prognostic, and clinically actionable mutations. Previous studies have identified a number of driver mutations, thought to be responsible for tumor formation, present in a significant proportion of non-small cell lung cancer patients. Detection of these mutations can help in early cancer detection, guide treatment options, or alert to the emergence of chemotherapy resistance, all of which could be harnessed to significantly improve survival. As with most other cancers in the chest cavity, access to tumor tissue by biopsy or surgical resection is often extremely limited or unobtainable and, additionally, not necessarily representative of the entire tumor. For this reason, DNA shed by the tumor into the bloodstream, often referred to as circulating tumor DNA(ctDNA), holds the promise of yielding detailed information about a tumor using a simple, minimally-invasive, blood test. Unfortunately, ctDNA from cancer comprises only a small fraction of all the overall amount of cell-free DNA in the blood stream. This issue, in conjunction with the high error rates of NGS technology, has proven to be a major impediment in developing minimally invasive tests to look for rare tumor specific mutations in the sea of normal cell-free DNA. To overcome this issue, we previously developed Duplex Sequencing, which is capable of detecting these low frequency mutations. However, this method requires more DNA than is generally found as cell-free DNA in the blood. As part of previous funding from the Department of Defense, we recently developed a method we call Linked-Strand Anchored Multiplex PCR (LS-AMP), a simple PCR-based target enrichment method that maintains the accuracy of Duplex Sequencing while offering reduced costs with increased efficiency and scalability on low amounts of DNA frequently encountered with cell-free DNA applications.
Document Details
- Document Type
- Technical Report
- Publication Date
- Aug 01, 2020
- Accession Number
- AD1115244
Entities
People
- Scott R. Kennedy
Organizations
- University of Washington