An integrated approach to analyzing breast cancer at the proteomic and genomic level is presented using a cytometric readout. The approach analyzes fine needle aspirates to assess proteins, mRNA expression of HER2, and genomic integrity. Feasibility testing used a model system of mixed cell lines and analyzed 40 breast tumors and 10 normal tissues fixed in two solutions. The clinical performance relates to the model system and the cell-based assay could apply to xenograft models and circulating tumor cells.

1. An Integrated Approach to the Proteomic and Genomic Analysis of Breast Cancer
Using a Cytometric Readout
Keith Shults1
Amanda Chargin1
and Bruce K Patterson2
1 Penfold Patterson Research Institute Menlo Park, CA
2 IncellDx, Inc. Menlo Park, CA
Abstract: The most common approach in today’s world when faced with a complex question is
to apply the latest technology, most recently massively parallel sequencing. There has been an
explosion in genomic technology advancements which focus on one area of cellular detection
for cancer whether it be mRNA expression, DNA copy number analysis, or sequencing. In
contrast to this single minded approach, many years of research and a large literature base
suggests the disease of breast cancer is a multi-factorial system in which proteomic, genomic
and cell cycle alterations are implicated. In addition, it has been reported that approximately
20% of current HER2/ER/PR testing by immunohistochemistry or in-situ hybridization is
inaccurate. This inaccuracy drives a current need for the use of a better integrated approach for
breast cancer diagnostics using an all-encompassing platform with the ability to integrate
proteomic and genomic analysis of breast cells. This integrated platform may be applied to the
fields of therapeutic development as well as basic cellular research.
We wish to share our recent work utilizing an FNA(fine needle aspirate) mimic composed of
mixtures of WBCs, MCF-7, and SK-BR-3 cells that differ in multiple proteins, mRNA expression of
HER2, and genomic integrity (DNA indices and cell cycle alterations). This mimic served as our
model system for the development of our cytometric readout. Feasibility testing of this assay
was initiated through an IRB approved tissue repository designed to collect 40 breast tumors
during the normal course of treatment of breast cancer and 10 normal tissues obtained during
breast reduction procedures. To determine optimal the optimal fixation solution for this assay,
tissues were fixed in 2 different fixatives to emulate how this test may be used in the clinical
setting. We wish to share the clinical performance of our approach and how it relates to the
model system. In addition to the clinical application, the cell based nature of the assay provides
multiple avenues for future application in xenograft models and possibly circulating tumor cells.