Complete Genomics-led Team Achieves Breakthrough in Cancer Diagnosis

Complete Genomics-led Team Achieves Breakthrough in Cancer Diagnosis

Tissue biopsy has long been the only way to make a definitive diagnosis for most cancer types, but the search for noninvasive yet comprehensive cancer diagnostic methods is yielding important results.

Analyzing genomes from a blood test reveals a new approach, according to a study published in Cancer Research August 15 that was led by a team from Complete Genomics. In this project, the team isolated 34 highly pure circulating tumor cells (CTCs) using immunomagnetic enrichment/fluorescence-activated cell sorting, and performed whole genome sequencing (WGS) based on long fragment read technology (LFR). Taking advantage of this combination approach, they were able to identify several driver mutations and the tissue of origin of these CTCs. The project has proved the concept of using advanced WGS of CTCs for high-resolution analyses of cancers, and will help to guide personalized therapy.

Brock Peters, Senior Director of Research at Complete Genomics who led the team along with Chief Scientific Officer Radoje (Rade) Drmanac, explained more about the significance of the project in this Q&A.

Q: When was the research project started?

A: The first discussions were all the way back in 2011. The lab work started in 2012. We generated data on the real samples in 2013 and started working on the informatics. The time since then has been writing the paper and performing confirmatory experiments. There were some reorganizations and people left the company which contributed to the work being published only recently.

Q: Can you tell us a bit about the background of this project, e.g. why you initiated this research project, any problems that your team had to overcome, and the roles of CG, UCSF, Advanced Cell Diagnostics in this project?

A: Emily Park, who was working at BD Biosciences at the time (she now works at Advanced Cell Diagnostics) had been working with John Park at UCSF on CTC isolation. She had worked with Rade in the past and thought we might be able to work together on some projects. We had a working version of LFR on isolated genomic DNA and wanted to apply it to projects involving a small number of cells. Using CTCs seemed like a great way to demonstrate the usefulness of LFR data. The main problem was adapting what was originally designed for genomic DNA into a process that could start from a small number of cells. This mostly involved changing volumes and pipetting steps to minimize loss of material during the process. The cell lysis step also needed to be optimized for our process.

Q: Compared to traditional diagnostic tests in oncology, what is the advantage of using WGS for circulating tumor cells (CTCs)?

A: Simply put, it’s more comprehensive.  Traditional diagnostic tests look at a few mutations or a few genes.  With WGS, we can look at the entire genome.

Q: Is this method of using WGS for CTCs only applicable to patients known to have cancer? How early can a tumor be detected using this method?

A: Most likely.  It comes down to the biology of CTCs.  The studies that have been performed suggest that very few CTCs exist in early stage cancers.  That said, it is possible that improved methods of CTC detection and a much lower cost of DNA sequencing could enable this to be used for cancer detection.  As we showed in the paper, based on the mutation spectrum it is quite possible to narrow down which tissue the tumor cells are likely to be derived from.

Q: For tumor detection, do we know how much blood would be needed?

A: In this study we did pretty standard blood draws (~10 ml) and for patients with advanced cancer that is all that should be needed. If you’re talking about detecting CTCs in an otherwise healthy individual, most likely you’ll need much more blood. In such a case you could expose your CTC capture system to the blood stream, such as by a thin wire or circulate the blood through a device. If this is to be used as part of a routine physical it will be important to develop something that is quick and minimally invasive, otherwise no one will want to do it. I think initially we would use this on individuals with advanced, tumor inoperative cancer for which getting a good tumor biopsy is difficult. In these instances, using CTCs is the best method for collecting comprehensive information about their tumor.

Q: In your paper, you said that this technique will help to guide personalized therapy. What is your vision for WGS for CTCs for personalized medicine?

A:  As we outlined in the paper, the data you get from this kind of analysis is extremely comprehensive. It gives you a list of every mutation, the percent of cancer cells harboring that mutation, and all of the possible therapies that could be used against those mutations. We envision a time when every patient gets a cocktail of drugs that has the most efficacy against their tumor with the least amount of side effects. Importantly, because the tumor is getting attacked by multiple different drugs; resistance to this combination therapy should be minimized.

Q: Are we getting close to commercializing this method? What are the next steps?

A: It could be commercialized in its current form.  However, we continue to work on reducing the cost and making the process more automation friendly.  One major improvement we are working on is using beads as compartments.  This will enable millions of compartments in a single vessel.  For this project we used 3,072 physically separated compartments.  Millions of compartments in a single tube will dramatically improve the data and reduce the cost.

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