Abstract 4701: Cancer-specific genomic rearrangements used to quantify disease burden in plasma from patients with colorectal cancer.

Abstract

Abstract Tumor-specific chromosomal rearrangements have the potential to serve as highly sensitive biomarkers for tumor detection. Such alterations are not present in normal cells and should be exquisitely specific. It is well recognized that some colorectal cancers (CRC) release small amounts of DNA into plasma. Accordingly, sensitive and specific assays targeting these tumor-specific rearrangements should enable quantification of changes in disease burden if applied to serial plasma samples. Here we report the establishment of efficient procedures for 1) identification of tumor-specific genomic rearrangements, 2) development of sensitive and specific assays to these, 3) quantification of these rearrangements in plasma, and 4) results from applying these procedures to quantify disease burden in serial plasma samples from CRC patients. The tumor-specific genomic rearrangements were identified using a combination of next generation paired-end sequencing of large-insert libraries and SNP array based DNA copy number analysis. Nested real-time PCR assays targeting the rearrangements were applied to plasma samples in order to quantify disease burden. Initially the approach was tested using the CRC cell line SW620 as a tumor model, and serial dilutions of SW620 DNA and normal human plasma DNA as models of patient plasma. Multiple cell line specific rearrangements were identified and nested real-time PCR analysis of these in the serial dilutions revealed an excellent linearity, recovery across three log scales. Also the sensitivity was very good. As little as 6.4 pg cell line DNA could be detected in a background 20 ng of normal plasma DNA, corresponding to DNA from 1-2 tumor cells circulating in 2 ml plasma. We are currently in the process of analyzing 25 CRC patients from which we have more than three years of follow-up and serial plasma samples collected every third month, starting the day before surgery and until month 36. The results from these analyses will be presented. In conclusion: We have shown that the combination of large insert paired end sequencing and copy number analysis readily identifies multiple tumor-specific rearrangements that can be targeted by sensitive and specific nested real-time PCR assays to quantify disease burden in plasma samples. Citation Format: Lone V. Schøler, Rune Thomsen, Heidi Tobiasen, Søren Vang, Hans Jørgen Nielsen, Søren Laurberg, Torben F. Ørntoft, Claus L. Andersen. Cancer-specific genomic rearrangements used to quantify disease burden in plasma from patients with colorectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4701. doi:10.1158/1538-7445.AM2013-4701