CancerFind: Low-Cost Liquid Biopsy for Breast Cancer
This is an interdisciplinary, multi-institution collaborative research effort, jointly pursued by VAVlab (Bogazici University, TR), Dr. H. Torun (University of Northumbria, UK), Dr. Zeynep Madak-Erdogan Lab (UIUC, USA). The fundamental goal is to develop low-cost, highly sensitive liquid biopsy technology targeting biomarkers for diseases.
The CancerFind project is the first initiative of this research collaboration. It aims to develop a hand-held spectroscopy-based detector to predict breast cancer susceptibility. The project involves wet-lab data collection, statistical data analysis, machine learning, hardware design and sensor signal analysis. The discovered biomarkers and application of signal processing techniques to derive the relevant information from low-cost detectors are the major contributions of this project.
The collaborative group's scope will be widened, with new technologies and applications, as the potential of liquid biopsy (in the form of CTC, ctDNA, cfDNA, exosomes) grows.
Core Collaborators
A Computational Statistics Approach to Evaluate Blood Biomarkers for Breast Cancer Risk Stratification
Kaan Oktay, et al.
In this study, we systematically evaluated metabolites and proteins in blood to develop a pipeline to identify potential circulating biomarkers for breast cancer risk. Our aim is to identify a group of molecules to be used in the design of portable and low-cost biomarker detection devices. We obtained plasma samples from women who are cancer free (healthy) and women who were cancer free at the time of blood collection but developed breast cancer later (susceptible). We extracted potential prognostic biomarkers for breast cancer risk from plasma metabolomics and proteomics data using statistical and discriminative power analyses. We pre-processed the data to ensure the quality of subse- quent analyses, and used two main feature selection methods to determine the importance of each molecule. After further feature elimination based on pairwise dependencies, we measured the performance of logistic regression classifier on the remaining molecules and compared their biological relevance. We identified six signatures that predicted breast cancer risk with different specificity and selectivity. The best performing signature had 13 factors. We validated the difference in level of one of the biomarkers, SCF/KITLG, in plasma from healthy and susceptible individuals. These biomarkers will be used to develop low-cost liquid biopsy methods toward early identification of breast cancer risk and hence decreased mortality. Our findings provide the knowledge basis needed to proceed in this direction.
Off-the-Shelf Low-Cost Interferometer
Kaan Oktay, et al.
We proposed a Fabry-Perot (FP) interferometer-based spectroscopic biomarker analysis setup to quantitatively detect specific molecules in their environments. Our proposed setup was considered as a cheap and portable alternative to common Fourier Transform Infrared Spectroscopy which is a large and expensive device. For this purpose, we used Fabry-Perot interferometers and their evaluation boards (InfraTec GmbH), which takes the output of the interferometers and process it to make the measurements readable and interpretable. For the surface on which we drop our samples for the measurements, we used CaF2 windows. To make measurements robust, we firstly designed a constant-thickness hole on a window and sandwiched it with another window manually after dropping sample on processed window. However, because our initial design failed to give robust measurements, currently we are proposing a microchannel-like structure between two windows to make the thickness of the hole, in which dropped samples fill, always constant. In addition to hardware parts, we developed a reconstruction method on computer generated spectra to overcome the inherited blurring problem of the interferometers. We will then apply this method to properly collected spectra taken by our measurement setup.
Figure: The experimental setup for the Fabry-Perot interferometer measurements.
