The focus of this group's work encompasses four 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; anticipate generation of 20-30 datasets in 2020
- Using a moderately sized capture panel (TSO500) for molecular stratification of surgically resected endometrial cancer to guide adjuvant; currently generating 48 data sets as this time at the University of Minnesota Genomics Center
- Breast Cancer Translational Research: The group's breast cancer research encompasses three current projects:
- LCIS: The group has previously performed bulk somatic RNAseq on clinical samples 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. Although older data (some of which has not been accessed since 2017), they have renewed their effort to push this to publication. Active work on this project (on existing analyzed data) should occur through the first half of 2020 which may require re-analysis of the existing datasets in storage. This data will be archived after publication.
- Invasive Ductal Carcinoma: Nansotring and Array data from clinical patient cohorts at UMN and the University of Nebraska Medical Center (UNMC). Ongoing analysis is planned through 2020 for publication and also for preliminary data generation for grant proposals.
- Mechanistic breast cancer invasion/progression research: The researchers have mouse models examining the impact of RHAMM/HMMR on breast cancer progression for which they are planning whole transcriptome RNAseq in 2020, with approximately 20-40 datasets.
- 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. There are two anticipated projects for 2020:
- Clinical validation of TSO500, a moderately sized capture for DNAseq and focused RNAseq for human cancer genomic profiling; anticipating 60 new datasets
- Clinical validation of Ampliseq Focus and Ampliseq BRCA1/2: small sized amplicon enrichments for DNAseq and focused RNAseq for standard of care cancer testing in an array of solid tumors; anticipating 80-100 new datasets