Clinical Cancer and Long Read Sequencing

Clinical Cancer and Long Read Sequencing  

Dr Jeffrey Rosenfeld

The clinical treatment of cancer has progressed greatly over the last several years. Instead of using a brute-force approach of chemotherapy or radiation, targeted therapies have better success rates and decreased side effects. In addition to targeted therapy, immunotherapy has been developed to harness the host immune system to attack the tumor. These treatments are enabled by genomics approaches and is one of the most prominent clinical applications of advances in genome knowledge. As the head of the Bioinformatics Core at the Rutgers Cancer Institute of New Jersey, I developed the computational infrastructure for our precision medicine testing. I will present how we developed this test and the relevant considerations along the whole pipeline of processing from the wet lab sample prep through the production of a signed clinical report that is returned to a physician. This report will tell a physician which therapies are indicated in a patient, as well as whether they would be a candidate or any clinical trial. In addition to the standardized clinical sequencing, I am investigating long read technologies to determine their utility. In particular, I have found that for certain applications, Oxford Nanopore Sequencing provides a fast cheap and accurate method for investigating cancer mutations. I will outline the benefits of nanopore sequencing and its potential for clinical sequencing.

What you will learn at the workshop

Cancer Sequencing

• Why sequencing is important for cancer treatment
• How sequencing is implemented currently for cancer treatment
• Tumor Mutation Burden
• Upcoming improvements in Cancer Sequencing

Long Read Sequencing

• Current techniques for DNA sequencing
• Long read techniques
  • Oxford Nanopore
  • Pacific Biosciences
• How the long read technologies are changing our understanding of biology and changing the questions that we can ask

The future outlook for sequencing