An Innovative, Multiomics Approach to Early Cancer Detection

Protein’s pivotal role in a multiomics approach executed by a fast-growing team aims to change the face of cancer detection

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Early detection of cancer has the potential to positively impact thousands of lives annually. To reinvent disease management through early detection and precision intervention, Freenome has built a multidisciplinary team with expertise in genomics, proteomics, computational biology, and machine learning.

A multiomics approach includes a strong focus on proteomics. “We look at DNA, RNA, proteins, and other biomolecules to derive information about the tumor as well as the environment,” explains Jimmy Lin, MD, PhD, MHS, Chief Scientific Officer at Freenome. “In fact, we actively seek out cutting-edge technologies to interrogate the full range of biological signals in blood.”

“We are excited by the many advances in understanding protein biology, such as post-translational modification, protein-protein interactions, heteromultimeric protein complexes, and even protein-corona signals,” adds Lyndal Hesterberg, PhD, Vice President, Development. “We are also exploring protein depletion methods and the peptidome to extensively understand how proteins contribute to cancer diagnosis.”

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Freenome’s cross-functional team is pushing the limits of molecular biology and machine learning to solve early cancer detection.

Other test developers have focused on nucleotides using NGS, says Lin, noting that often, even when assessing down to the single-molecule level, there simply is not enough tumor-derived DNA for an accurate analysis. Therefore, the needs extend beyond nucleic acids to include proteins.

A multiomics approach generates massive amounts of information for each patient. “If we look at DNA, RNA, and proteins, there are billions of pieces of information per patient. Such enormous datasets require machine-learning approaches in order to find patterns across large populations,” says Lin.

Machine learning algorithms interrogate signals and provide useful classification models. Interactions between different signals can differentiate between a cancerous and noncancerous sample. The goal of early detection is to identify the least amount of signal with the highest sensitivity and specificity.

Freenome is developing a blood test for multiple cancers, and its first indication is colorectal cancer (CRC). Their premarket approval (PMA) clinical trial, PREEMPT CRC®, will assess the early detection test’s effectiveness.

Diverse technology approach to science

“My background is in genomics, and I have helped launch multiple genomic-based products for tissue and blood. I joined Freenome because of the mission to detect cancer early, building an entire research platform that does not depend on specific technology,”  says Lin. “Combining signals from DNA, RNA, and protein provides a comprehensive look at all biological signals to optimize best clinical performance, so our talented, diverse team
of researchers has genomics and proteomics experience.”

“My PhD is in protein physical biochemistry. I have studied protein-protein interactions delving into how antibodies and other proteins work,” explains Hesterberg. “I have spent decades working in proteomics to understand these biological complexities in order to build immunoassays and other detection tests to measure proteins in human plasma and blood.”

The underlying clinical diagnostic question of whether early cancer exists in a patient requires a strong understanding of biology and a multiomics approach in order to get the full picture. “Otherwise we are using black-and-white film to try to make a color photograph. It just does not work,” says Hesterberg.

“We evaluate all the latest technologies,” inserts Lin, who adds the company is always looking to recruit talented scientists. “Freenome is a true playground for scientists who are enthusiastic about new technology.”

“The opportunity to save tens of thousands of people’s lives across the world annually with early detection and to build an exceptional team are some of the main reasons why I was excited to join the company. I think others will be excited to join as well,” points out Hesterberg. “No one else is doing what we are doing.”

By combining deep expertise in molecular biology, proteomics, and advanced computational techniques to recognize disease-associated patterns among billions of circulating, cell-free biomarkers, Freenome is developing simple and accurate blood tests for early cancer detection with plans to integrate the actionable insights into health systems to operationalize a feedback loop between care and science.


Freenome is actively hiring molecular scientists and more.