Abstract A009: Targeting Structural Variants (DNA palindromes) in plasma cell-free DNA for Liquid Biopsy-based Cancer Detection

Abstract

Abstract We aim to expand the utilities of our genome-wide detection method of chromosomal structural aberrations (structural variants, SVs) for blood-based cancer detection (liquid biopsy). SVs, such as genomic amplification, are prevalent DNA abnormalities and define tumor phenotypes. With cell-free DNA (cfDNA) in plasma, a genome-wide assay for SVs seems feasible for cancer detection. However, most current tests probe a part of the genome for cancer gene mutations and differential DNA methylation. Considering liquid biopsy's promise in clinics, approaches targeting SVs must be considered and developed. The low tumor fraction in plasma cfDNA is a major obstacle to developing liquid biopsy-based tests. Targeted assays overcome low signals by ultra-deep NGS, yet deep sequencing for the entire genome for SV detection would be costly and computationally challenging. In this regard, we have an established approach for enriching SVs (DNA palindromes or inverted repeats, also called fold-back inversions) from total genomic DNA to determine their frequency and genomic locations by sequencing (genome-wide analysis of palindrome formation, GAPF-seq). DNA palindromes arise from common events of genome instability, such as illegitimate repair of DNA double-strand breaks and telomere-telomere fusions, as an early step of genomic amplification. Therefore, a technique to identify DNA palindromes could serve as a tumor DNA detection test across tumor types, including breast cancer. The simple GAPF-seq procedure confers advantages over other methods because it simultaneously amplifies the target signal and reduces background noise. GAPF-seq exploits the inherent propensity of denatured DNA palindromes to form double-stranded DNA (dsDNA) by intra-molecular annealing. Genomic DNA will be denatured and quickly renatured to enrich DNA palindromes to favor intra-molecular annealing. Single-strand-specific nuclease S1 will eliminate the remaining single-stranded, non-palindromic DNA. The dsDNA from palindromes will be amplified by the process of preparing libraries for NGS, by which DNA palindromes appear as coverage peaks in the genome. As a proof-of-concept, we examined the read coverage of nearly 3 million 1-kb bins from low coverage NGS GAPF-seq data for 39 breast paired tumor/normal DNA. We found that the chromosomal distribution of the top 1000 high-coverage bins (GAPF profiles) could effectively differentiate breast tumor DNA, including all stage I tumor DNA, from paired normal DNA (AUROC=0.9885). Automated, three-fold cross-validation with machine learning (ML) algorithms from the STREAMLINE platform confirmed the highly accurate binary classification by GAPF profiles. The same approach was applied for 15 cfDNA from breast cancer patients and effectively differentiated cancer patients' cfDNA from healthy individuals' cfDNA (AUROC=0.900). These results support the potential of GAPF-seq as a unique, SV-targeting liquid biopsy approach for breast cancer. Citation Format: Fumie Igari, Hisashi Tanaka, Michael M Murata, Mitsue Saito, Armando E Giuliano. Targeting Structural Variants (DNA palindromes) in plasma cell-free DNA for Liquid Biopsy-based Cancer Detection [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A009.