Uploaded March 2023 | Updated September 2026, 2 weeks ago
The goal of Kevin's project is to characterize a biobank of metastatic melanoma samples from patients in WA. The samples have been fresh-frozen and transplanted to immune-compromised mice to generate so called patient-derived xenograft (PDX) mouse models. Tumors growing in the PDXs can be used to study genetics of the disease, as well as serve as source of tumor cells for drug discovery in vitro as well as in vivo. An overarching goal is to couple genetics to the pharmacological response to drugs by metastatic melanoma, to gain insight into potential biomarkers of response. To that end, we will sequence the RNA and DNA (exome) of PDX tumors and DNA of matching normal cells. The sequencing data will be 1) aligned to a reference genome, 2) used for mutation and 3) copy number analyses, as well as, 4) sample clustering analyses based on gene expression. These analyses will be suitable for a ten week project student supervised by an experienced bioinformatician in the group.
The goal of Kevin's project is to characterize a biobank of metastatic melanoma samples from patients in WA. The samples have been fresh-frozen and transplanted to immune-compromised mice to generate so called patient-derived xenograft (PDX) mouse models. Tumors growing in the PDXs can be used to study genetics of the disease, as well as serve as source of tumor cells for drug discovery in vitro as well as in vivo. An overarching goal is to couple genetics to the pharmacological response to drugs by metastatic melanoma, to gain insight into potential biomarkers of response. To that end, we will sequence the RNA and DNA (exome) of PDX tumors and DNA of matching normal cells. The sequencing data will be 1) aligned to a reference genome, 2) used for mutation and 3) copy number analyses, as well as, 4) sample clustering analyses based on gene expression. These analyses will be suitable for a ten week project student supervised by an experienced bioinformatician in the group.
