The focus of this group's work encompasses two major, inter-related areas.
First, the Principal Investigator is the Director of Research and Development for clinical diagnostic assays in the Minnesota Health Molecular Diagnostics Laboratory. This lab is working on the following major projects:
- Validation of an optimized clinical pipeline for detection of variants in the highly homologous regions of PMS2
- Development and validation of focused UMI-enabled NGS methods for the detection of clinically relevant variants in solid and hematologic malignancies
- Characterization of two comprehensive genomic profiling assays (parallel DNAseq/RNAseq focused captures) for solid tumor molecular diagnostics
Second, the PI works with a multi-disciplinary team of other clinician scientists, bioinformatics scientists, and basic scientists to analyze breast and gynecologic cancers with multiple molecular/genomic techniques to study biologic mechanisms of cancer progression and therapy resistance. There are three current projects in this area:
- Identification of stromal based mechanisms of carcinogenesis and progression in breast carcinoma using Nanostring analysis of patient samples
- Characterization of transcriptional differences between classic and pleomorphic LCIS
- Study of RHAMM contributions to breast cancer progression using RNAseq analysis of RHAMM+ and RHAMM- in vivo xenograft models
Finally, work with the UMN Ovarian Cancer Precision Medicine Initiative uses somatic full exome DNA-seq, germline DNA-seq of ~5000 medically relevant genes, RNA-seq, and Nanostring analysis to characterize patients with ovarian cancer. The researchers are completing sequencing of the first 32 samples currently. They hope to continue patient accrual and sequencing of 32 additional samples in 2019.