Precision medicine for advanced cancers through molecular genomics and analysis of circulating tumor DNA
The proposed project will harness the latest innovations in tumor genomics and ultrasensitive mutational profiling to address critical clinical questions facing patients with advanced solid cancers. Studies will be performed to develop prognostic and predictive signatures based on transcriptomic and genomic data, to improve risk stratification and patient selection for targeted therapies, to monitor therapy response non-invasively using “liquid biopsies”, and for dissection of the molecular mechanisms of treatment resistance.
The vast majority of cancer mortality is caused by progression to advanced metastatic disease. However, our understanding of the lethal clones and their biology is limited. In this translational project, the student will study cohorts of well-annotated and preserved tissue and liquid biopsy samples (such as circulating tumor DNA in blood plasma) from patients with advanced breast cancer, non-small cell lung cancer, and prostate cancer, to better understand the molecular drivers of each malignancy, the impact of intratumoral heterogeneity, identify determinants of sensitivity or resistance to treatment, and how these molecular portraits correspond to clinicopathological factors as well as patient survival. In particular, patient tumor material and RNA-sequencing data from the SCAN-B project with over 11,000 enrolled patients will be utilized (ClinicalTrials.gov ID NCT02306096). For the engaged student, training is offered in state-of-the-art genomic methods using massively-parallel DNA- and RNA-sequencing, digital PCR, bioinformatics, machine learning, and functional genomics. You will be joining the Translational Oncogenomics group, an interdisciplinary team with strong national and international collaborations and partnerships, including with the spin-out liquid biopsy company SAGA Diagnostics in Lund.
Special requirements: Previous experience in bioinformatics, programming, next-generation sequencing, and/or cancer research is desired