Every cancer is unique because every person is unique, and information is one of the most important weapons in any cancer battle. Isabel offers that in abundance through rapid sequencing of the entire genome of cancer cells, potentially showing within days which therapies will and will not be effective. The company has received a groundbreaking designation from the FDA and has raised $3 million to market its approach.

The past ten years have brought many medical advances thanks to the commoditization of genomic processes, from sequencing to analysis, and cancer treatment is no exception. Because cancer (although it’s a simplification) is a genetic mutation that’s gotten out of hand, understanding those genes is a particularly promising line of research.

Panel tests look in the DNA of cancer cells for mutations in a selection of several hundred genes known to influence prognosis and clinical strategy. For example, cancer may have certain modifications that make it susceptible to radiation but resistant to chemo or vice versa — it’s incredibly helpful to know which ones.

Isabel co-founder and CEO Elli Papaemmanuil explain that as useful as panel tests are, they are only the beginning.

cancer treatment

“These tests have been carefully designed to look for the most common mutations, andshe said that  they have revolutionized cancer diagnosis for patients with common cancers,” she said. “But patients with rare cancers — and what we define as a rare cancer is still a third of patients — don’t benefit from it.”

Even many with common cancers may find their condition does not involve mutations of these most predictive genes. The relevant genes are somewhere between the other two billion base pairs – current tests look at only about 1% of the genome.

While the technology exists to look at that other 99%, it was historically expensive and slow compared to panels, and analyzing the resulting large amount of data was likewise difficult and time-consuming. But Isabel’s tests show that it is worth it.

Image Credits: Isabel

“It turns out that whole genome sequencing can detect many more clinically relevant findings – results that we can act on today. And what we’ve done is develop a platform that allows us to summarize it in a way that doctors can read in a day and use,” Papaemmanuil said, calling it a “clinically useful whole genome and transcriptome assay,” or cWGTS.

The company grew out of research Papaemmanuil did at Memorial Sloan Kettering, a New York-based cancer care and science partnership. “They collected and combined three different data sets: the germline genomes (ie, the patient); the tumor’s genome and also its transcriptome, essentially what the body produces by transcribing the DNA. You could see all these successes in panel trials and then all these patients who weren’t benefiting. But in my lab, we had the technology and the know-how,” she recalls.

“This gives a complete picture of the profile of the tumor,” she said. “Instead of having a classifier or a model that annotates the mutations [i.e., an automated panel test], we have analyzed integrating those three layers to interpret the role of the mutation and its relevance to each tumor type.”

Although Isabel owns the entire process from sampling to reporting, Isabel’s major advancement is data-base,d and therefor,e “there is no technical obstacle to making this solution available today. And we’ve shown that we can do it on a large scale,” Papaemanuil said. But just because it’s possible doesn’t mean it’s allowed in the medical world. The FDA has granted the technology “breakthrough” status, which is a fast track, but even the quick way is slow in the federal government.

While full clinical approval is likely 3-5 years away, that is much faster than the 5-10 years estimated by the industry for these types of applications. But research for validation and other purpose is underway, having just published the lead article demonstrating the process in Nature Communications today. (While this study focuses on childhood and young adult cancers, the technique is not limited to those demographics.)

“The seed round is mainly about letting us do the roadmap — it’s a good starting point for getting the necessary evidence and approvals,” Papaemmanuil said. “We’re already working with cancer centers to do studies, especially to hear from oncologists what they need and how they want the data.”

From left to right are Isabel Andrew Kung’s co-founders, Elli Papaemmanuil and Juan Santiago Medina. Image Credits: Isabel

The $3 million round was led by Two Sigma Ventures, with participation from Y Combinator, Box, one, and other companies. Papaemanuil’s co-founders are CTO Juan Santiago Medina and Andrew Kung.

She also clarified that Isabel’s research would be conducted openly: “We have a very strong scientific base and will be active in publishing the work. The data should be both published and made accessible in a form that allows for further research,” she said. The self-reinforcing game of producing and identifying predictive data could be an incredibly valuable resource across many disciplines.

Isabel exemplifies the power of a more or less pure data game in an industry more often associated with lab progress – alalthought took a lot of lab work to produce in the first place. But when automation of key processes, in this case, DNA transcription, enables a massive increase in data capture, there is always value to be found. In this case, that value could save many lives.


I have been blogging since August 2011. I have had over 10,000 visitors to my blog! My goal is to help people, and I have the knowledge and the passion to do this. I love to travel, dance, and play volleyball. I also enjoy hanging out with my friends and family. I started writing my blogs when I lived in California. I would wake up in the middle of the night and write something while listening to music and looking at the ocean. When I moved to Texas, I found a new place to write. I would sit in my backyard while everyone else was at work, and I could write all day.