CSF Digital Droplet PCR Analysis for Pediatric High-Grade Glioma Diagnosis and Therapy Response
Background
Pediatric brain tumors have become the leading cause of cancer-related deaths among the population of child patients. With no effective cures or treatment options, researchers have been looking into newly developed "targeted" therapies which utilize the unique molecular biology of each child's tumor to combat the cancer. However, the selection of a targeted treatment plan requires a surgical biopsy of the tumor to profile its genetic mutations. This is often dangerous and risks severe neurological injury due to the location of the tumor within the child's brain. The Koschmann Lab has recently been developing a safer, more non-invasive approach that uses tumor DNA from cerebrospinal fluid (CSF) to assess the genetic makeup of the tumor. We have a working hypothesis that the levels of tumor DNA within CSF are correlated with the tumor's growth or shrinkage, aiding in a more accurate treatment monitoring of pediatric brain tumors.
Project Goal
My project aims to study the ratio of tumor to wildtype DNA (allele fraction) in cell-free DNA collected from spinal fluid and analyze how it fluctuates in response to targeted therapies. The Koschmann lab has established a bank of spinal fluid samples from dozens of children with high-grade glioma who have undergone matched tumor/germline sequencing. Over the course of this program, I will design and validate probes specific to the unique mutational profile of 10 of these samples. I will then perform ddPCR assays and compare the allelic fraction from the samples to the sequenced tumor results. If time allows, I will perform ddPCR on paired samples (pre- and post-treatment) that are being collected through a clinical trial for which the Koschmann lab is performing the correlate research. Additionally, I will continue a project I have begun designing with a neurosurgery resident in the lab to help develop an in vitro based system of measuring cell-free DNA in the media of growing human pediatric glioma cell lines. The field of pediatric oncology is in desperate need of a minimally invasive approach to analyzing the treatment response of brain tumors. This project will elucidate the correlation between tumor growth and tumor DNA in CSF as it changes over the course of treatment and outline an approach to better monitor future targeted therapy clinical trials for pediatric brain tumors. I am hopeful that this will establish a groundwork upon which future studies can build to improve outcomes for patients with this horrible disease.
Mentored by Dr. Carl Koschmann
University of Michigan, Ann Arbor, MI
