Abstract CC07-01: Whole exome and whole genome methylation sequencing of low-input cfDNA to implement precision medicine in metastatic castration resistant prostate cancer
Authors: Kandimalla Raju , Xiang Binggang , Dai Chao , Wang Amy , Du Pan , Luo Shujun , Liao Debbie 
Published: December 2021

Purpose Liquid biopsy has become increasingly important in cancer diagnosis, personalized medicine, and disease progression monitoring. Conventional liquid biopsy relies on targeted cancer gene panels which often contain fewer than 500 genes. Despite the revolutionary impact of liquid biopsy on cancer research and patient care, targeted gene panels may miss key novel mutations involved in cancer development and drug response, and other novel genomic alternations underlining cancer development, such as whole genome structural or epigenetic changes. Additionally, current commonly used methodologies require relatively large amounts of cell free DNA (cfDNA) input material, thus limiting its application when only small amounts of cfDNA input is available. Experimental Design cfDNA was isolated from whole blood collected from commercially available prostate cancer patients or age-matched healthy donors and evaluated using Predicine’s platform for whole exome sequencing, plasma WES, and compared to the targeted 500 gene PredicineATLAS panel (cfDNA input 10 or 30 ng). Additionally, low-input cfDNA (cfDNA input 10 or 20 ng) was also evaluated for whole genome methylation sequencing using PredicineECM and compared with standard whole genome bisulfite sequencing (WGBS). Results Plasma WES profiling of 30 or 10 ng cfDNA detected variants with mutation allele frequency (MAF) of 1% and above in the entire exome region, which enabled more accurate genome wide copy number variation prediction. All mutations detected using the PredicineATLAS panel that were ≥1% allele frequency were also detected by plasma WES, although low input required greater depth (10 ng, 3,500x) compared with high input (30 ng, 2500x depth). Furthermore, plasma WES identified 1.5 to 15.3x additional mutations compared with the PredicineATLAS panel. PredicineECM methylation analysis was superior to WGBS in reducing DNA damage and GC bias, resulting in increased NGS read mapping rate and quality score. Profiling of 2.5, 5 and 10 ng cfDNA using PredicineECM showed higher mapping rate and quality compared with WGBS profiling of 10 ng cfDNA. Additionally, clustering analysis of CpG methylation using PredicineECM separated tumor samples from normal samples and may serve as additional markers for minimal residue disease (MRD) tracing or early cancer detection. Conclusion In conclusion, we have successfully developed a multi-omics analysis platform for low-input cfDNA that integrates whole exome mutation and whole genome methylation profiling to obtain a comprehensive picture of cancer genomics to enable precision medicine in prostate cancer. This technology can also be applied to other cancers.

Citation Format: Raju Kandimalla, Binggang Xiang, Chao Dai, Amy Wang, Pan Du, Shujun Luo, Debbie Liao. Whole exome and whole genome methylation sequencing of low-input cfDNA to implement precision medicine in metastatic castration resistant prostate cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr CC07-01.