Abstract 5382: The evaluation of the DEPArray NXT™ as a clinical application for somatic tumor profiling from FFPE tissue
Authors: Jasmina Uvalic, Kevin Kelly, Daniel Bergeron, Yadwinder Deol, Claudio Forcato, Honey Reddi
Journal: Cancer Research (2018)

Abstract Introduction: Current methods of somatic tumor profiling involve the use of FFPE tissues from tumor biopsies, which present challenges in clinical testing due to poor qualities and overall availability of tissue. The use of the DEPArray allows one to address some of the issues that come with the use of FFPE samples by allowing for isolation of pure tumor and pure stromal populations for downstream tumor analysis. Here we evaluate the use of the DEPArray NXT™ to complement current clinical somatic testing workflows as a means to reduce the tumor content requirement for clinical samples as well as to isolate pure tumor populations to accompany and build on our current clinical offerings. Methods: Thirty micron sections were prepared from 10 FFPE samples from varying tumor types. The samples had tumor contents ranging from 20-75% used to determine clinical specificity. Immunostaining was performed on individual cell suspensions of the samples, with vimentin and cytokeratin to be able to isolate and recover pure populations of stromal and tumor cells respectively, using the DEPArray NXT workflow. Pure populations were recovered and libraries were prepared using an amplicon panel for NGS, targeting over 60 genes that are known to be associated with cancer. Samples were sequenced using the Illumina MiSeq and NextSeq. Results: On average two hundred pure stromal and pure tumor cell populations were recovered from each of the samples evaluated and an average of 2.5 million reads were generated per sample. A subset of the sequenced samples underwent in-depth comparative analysis of stromal, tumor and unsorted cell populations. Results show that even from ~200 cells recovered, CNA's and SNV's were still able to be called within the pure tumor population compared to that of the stromal. The unsorted cell population mimicked more of the stromal population, further highlighting the need for cell selection prior to library preparation. Conclusion: The DEPArray NXT was successfully able to isolate pure tumor and stromal cells which generated adequate libraries for sequencing and downstream analysis which allows for greater reliability and precision in making accurate variant calls compared to current best practices. The DEPArray aids in lowering the tumor content sample requirements as we are able to target and recover pure cell populations as opposed to current methods of extraction which extract all cells present, resulting in analysis of DNA that is not relevant to the tumor. Overall, cells isolated purely from the underlying tumor will provide the physician and the patient clearer test results to help manage and treat the patient with a more specific course of treatment based on the identified variants. This also enables the offering of testing for those specific cases that would have been turned away due to poor quality and quantity of tissue obtained from the tumor biopsies. Citation Format: Jasmina Uvalic, Kevin Kelly, Daniel Bergeron, Yadwinder Deol, Claudio Forcato, Honey Reddi. The evaluation of the DEPArray NXT™ as a clinical application for somatic tumor profiling from FFPE tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5382.