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DNA Palindromes as a Novel Tumor Marker in Extracellular Vesicles from Liquid Biopsy

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[Technical Report, Annual Report]

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The goal of our project is to develop a novel, highly sensitive Next Generation Sequencing NGS-based assay to identify tumor-specific chromosome aberrations in plasma from liquid biopsies in women with very early stages of breast cancer. To accomplish the goal, we have developed a method to enrich DNA palindromes, a common form of structurally aberrant DNA in tumor cells. We have shown previously that we can identify cancer-specific DNA palindromes in breast tumors by sequencing the enriched DNA Genome-wide Analysis of Palindrome Formation, GAPF. In the first year of the grant period, we have optimized the procedure and established a pipeline for the sequencing data analysis. We also obtained 38 tumorbuffy coat normalplasma pairs from biobank and completed DNA extraction from tumors and buffy coat samples. We enriched DNA palindromes for the three sets of tumornormal pairs and constructed DNA sequencing libraries. We have submitted the libraries and are waiting for the data. We also rigorously investigated DNA contents that are circulating in plasma. We showed that most of the DNA plasma are in the large extracellular vesicles, which support the feasibility of our approach.

Subject Categories:

  • Genetic Engineering and Molecular Biology
  • Medicine and Medical Research

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[A, Approved For Public Release]