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Abstract 5390: Broad Genomics and Cancer Program development of comprehensive blood biopsy sequencing capabilities to support direct-to-patient cancer research initiatives
C. Cibulskis, Andrew Hollinger
Genomic profiling of cell free tumor DNA (Blood Biopsy) offers the potential to revolutionize cancer precision medicine. As a proxy for tumor tissue profiling, successful blood biopsy analysis can help select appropriate patients for clinical trials…
Genomic profiling of cell free tumor DNA (Blood Biopsy) offers the potential to revolutionize cancer precision medicine. As a proxy for tumor tissue profiling, successful blood biopsy analysis can help select appropriate patients for clinical trials, provide useful data for treatment monitoring, and discover genomic mechanisms of disease resistance. Recognizing these potential benefits, we aim to enable large-scale genomic data generation and analysis of cfDNA samples to support the patient driven Metastatic Breast Cancer Project (mbcproject.org) and many other such efforts. The widespread adoption of cfDNA sequencing technology in clinical research will require low cost, efficient, and in some cases clinically-validated processes. Commercial offerings in this field are focused on analysis of small targeted hotspot panels due to the challenges of more complete sequencing approaches for cfDNA (e.g. variability in the fraction of tumor present and high false positive rates). Working in collaboration with the Broad Institute Cancer Program, we have developed a process to overcome these challenges and provide high quality comprehensive exome analysis of cfDNA. Our process includes screening samples using ultra low pass, UMI-enabled whole genome sequencing to quantify the % of tumor DNA available for sequencing. Qualified samples are then moved into automated processes for exome sequencing and somatic mutation detection. In our initial validation study of 23 breast and prostate cancer patients with matched cfDNA and tumor tissue sequencing, we are able to identify 90% of clonal and 45% of subclonal mutations found in the matched tumor biopsy. In our effort to scale this process, and fully characterize the benefits and limitations of this technology we will present additional validation analysis. We will evaluate the relative importance of using paired sample analysis (tumors and matched normals) with analysis of tumor sequencing alone and assess sensitivity and specificity of somatic alterations as a function of tumor fraction and sequencing depth. Citation Format: Carrie Cibulskis, Andrew Hollinger. Broad Genomics and Cancer Program development of comprehensive blood biopsy sequencing capabilities to support direct-to-patient cancer research initiatives [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5390. doi:10.1158/1538-7445.AM2017-5390
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