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Master of Advanced Studies in Precision Medicine Therapeutics in Oncology MAS in PMTO
  1. Precision Medicine Therapeutics in Oncology
  2. Curriculum
  3. Functional Precision Oncology Course

Functional Precision Oncology to Guide Diagnosis and Tailored Therapies

Course Information

Lukas Chavez

PMTO 206 Functional Precision Oncology to Guide Diagnosis and Tailored Therapies

  • 2 units
  • Quarter offered: Fall
  • Instructor:Lukas Chavez, PhD, Associate Professor, SBP Medical Discovery Institute

Course Description & Learning Objectives:

This course is an introduction to the theoretical, technical, and analytical methods for precision cancer diagnosis and for identifying individualized treatments.The course will provide participants with a critical understanding of the methods available for analyzing tumor biopsies to enable precision cancer diagnosis and individualized treatments. Methods include genomic, epigenomic, and transcriptomic characterization of tumors, bioinformatic and statistical analysis of the collected data, AI image analysis of tumor histology slides and MRI scans, and high-throughput cancer drug sensitivity testing. Using real-world examples, it will be demonstrated how the results of these multimodal analyses are used by a molecular tumor board consisting of physicians, pathologists, biologists, and bioinformaticians to identify individualized treatments. Learning objectives include:

  • Sequencing methods available for identifying DNA mutations, structural variants, and fusion genes in tumor biopsies.
  • Diagnostic yield and limitations of clinical tumor and germline DNA sequencing.
  • DNA methylation array technologies and machine learning methods for the molecular classification of tumors based on epigenetic fingerprints.
  • Bioinformatics methods, computational tools and statistical analysis of the different -omics data types.
  • Digital histopathology and AI methods for predicting cancer biomarkers from histological tumor images.
  • High-throughput drug screening in patient-derived tumor cells to determine individualized drug sensitivity.
  • Objectives and workflow of a molecular tumor board.
  • Critical parameters for precision medicine therapeutics in oncology, such as cost, technical and time constraints, and regulatory conditions including data de-identification and CLIA certification

Learning Outcomes & Skills Acquired from the Course

Upon completion of the course, students will be able to:
  • Critically evaluate a report of DNA mutations and the suggested treatment options.
  • Understand strengths and limitations of the different -omics assays and how they relate to each other.
  • Identify and explain analysis methods and results of bioinformatics tools for processing the different-omics data types.
  • Tumor type classification using DNA methylation array data and interpretation of confidence scores.
  • Work with CLIA certified high-throughput drug screening facilities to determine drug sensitivity of patient tumor material.
  • Coordinate a molecular tumor board that meets critical parameters for precision medicine therapeutics in oncology.