The focus of this group's work encompasses five broad areas.
- Ovarian Cancer Precision Medicine Initiative (OCPMI): This is a prospective, on-going research program funded by the UMN Grand Challenges Research mechanism. The group's objective is to study resistance to standard, identify new therapeutic targets, and develop molecular signatures for patient stratification in ovarian cancer. This is a multi-PI project. Data sets for ~50 patients have been generated with funding to acquire up to 100 patients total. This group is using MSI for:
- Bulk somatic exome and targeted (TSO500) DNAseq
- Bulk somatic RNAseq
- Bulk germline medical exome DNAseq
- cfDNA targeted DNAseq
- Multiplex Immuno Fluorescence (mIF)
- Endometrial Cancer Translational Research This researchers are studying genomic correlates of disease outcome and therapy response in endometrial cancer using moderately sized targeted DNAseq panels in two projects:
- Using a high-depth, ultra-sensitive UMI panel for diagnostic applications to characterize early stage disease and response to exemestane
- Using a moderately sized capture panel (TSO500) for molecular stratification of surgically resected endometrial cancer to guide adjuvant chemotherapy
- Breast Cancer Translational Research: The group's breast cancer research encompasses several projects:
- Investigating the biology of lobular carcinoma in situ (LCIS) and normal breast tissue to determine molecular signatures of low grade and high grade LCIS that can be translated into diagnostic methods through multiple analysis methods of bulk somatic RNA-seq data.
- Investigating gene expression in human invasive breast cancers using both Nanostring and Affy array data.
- Performing mechanistic breast cancer invasion/progression research for which the researchers will generate RNA-seq data from 3D culture models and in vivo xenograft tumors.
- In a new project, starting to explore spatial transcriptomics using the newly implemented Nanostring GeoMx Digital Spatial Profiling instrument newly installed at the University of Minnesota Genomics Center.
- Molecular Diagnostics Laboratory Research and Development: As the Director of Research and Development for the M Health Fairview Molecular Diagnostics Laboratory, the PI directs and provides MSI resources for pre-clinical characterization of new diagnostic assays/pipelines for the laboratory. This is separate from the routine clinical work which routes through ClinicalMDL. They have numerous development projects across both germline genetics and oncology diagnostics. Current work includes development and implementation of a new focused solid tumor NGS molecular diagnostic assay as well as a comprehensive genomic profiling assay for cancer.
SARS-CoV-2 Genomic Sequencing: This PI led the development group that created the first Laboratory Developed Test for COVID-19 clinical diagnosis at M Health Fairview and oversaw clinical testing from March-August 2020. This group (in collaboration with UMGC and MDH) continues to perform genomic sequencing of positive clinical samples to elucidate patterns for viral spread and understand the biology and natural course of the virus.
Research by this group was featured on the MSI website in August 2020: Improving Treatments for Breast Cancer.