Forging Forward - Our Progress in Biopharmaceutical Partnerships and Outlook for Success in 2025

Precision medicine is an ecosystem built on collaboration. Innovation in testing is critical to discovering new biomarkers to advance the development of medicines and clinical trials, and the insights gained from the real-world use of those medicines fuel progress and further advances in care.

Foundation Medicine has forged the path for high-quality diagnostic testing since its founding. As of the end of 2024, Foundation Medicine has 98 approved companion diagnostic indications,¹ has published over 1,000 peer-reviewed publications² and has supported more than 950 clinical trials.³ As a result, we bring deep scientific and regulatory expertise to our biopharmaceutical partners, enabling us to meet their needs for high-quality diagnostics as they arise.

As 2024 draws to a close, I want to reflect on how our key achievements over the past 12 months provide us with the strongest foundation to continue delivering value and innovation to our partners in 2025.

Leadership in companion diagnostics

Companion diagnostics are important high-quality diagnostic tests that are clinically proven and undergo rigorous review by the U.S. Food and Drug Administration (FDA) to accurately and reliably identify patients likely to benefit from an FDA-approved therapy. Foundation Medicine is the global leader in approved companion diagnostic indications, with 50% of all approved companion diagnostic (CDx) indications for next-generation sequencing (NGS) testing across the United States and Japan.⁴  

With our proven regulatory, CDx development and clinical trial expertise, along with the strength of our Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB), our biopharmaceutical partners trust us to support the development of their investigational therapies.

In 2024 alone, we added seven CDx approvals^5,6 to our portfolio across non-small cell lung cancer (NSCLC), breast cancer and prostate cancer, making ours the only comprehensive genomic profiling portfolio that includes seven FDA-approved CDx indications in breast cancer, seven in prostate cancer and more than 19 in NSCLC.⁷

By increasing the applicability and actionability of high-quality biomarker testing not just in lung, breast and prostate cancer but for rare cancers and pan-tumor indications, we can further demonstrate biomarker testing’s value and broaden uptake to more clinicians, and, ultimately, help more patients.

Fusion detection done right

Foundation Medicine's ability to detect gene fusions and rearrangements on our FDA-approved DNA-based tests stands out. FoundationOne®CDx is the only tissue-based test with FDA-approved companion diagnostic claims to detect ROS1, NTRK, ALK, FGFR2, and RET fusions across multiple tumor types⁵ and FoundationOne®Liquid CDx is the only liquid biopsy test with FDA-approved companion diagnostic claims for multiple fusion biomarkers, including ALK, ROS1 and NTRK1/2/3.^8,9

Building on that expertise in fusion detection, we added FoundationOne®RNA¹⁰ to our testing portfolio this year, continuing our commitment to providing truly comprehensive diagnostic tools that support the evolving research landscape. FoundationOne RNA is a tissue-based RNA sequencing test for detecting cancer-related gene fusions and rearrangements that can be added to orders of FoundationOne CDx. Adding FoundationOne RNA offers a robust layer of fusion detection that can support our biopharmaceutical partners with clinical trial optimization and the development of treatments targeting rare fusions and rearrangements. 

Equipped to accelerate the precision revolution in hematological cancers

Hematological cancers, including leukemia, lymphoma and myeloma, account for around 10% of new cancer diagnoses in the U.S. each year.¹¹ They represent a complex and heterogeneous group of diseases that are often difficult to treat and can be associated with poor patient outcomes.

The wider hematological cancer landscape has so far not experienced anywhere near the transformation that precision medicine has brought to solid tumors. The limited number of targeted treatments in hematological cancers has prevented the widespread adoption of comprehensive genomic profiling for patients with hematological malignancies.

But the hematological cancer landscape is now approaching a long-overdue tipping point. There are currently over 40 unique biomarkers being studied in hematological cancer clinical trials,¹² with a growing number of targeted treatments on the horizon.

Foundation Medicine launched FoundationOne®Heme¹³ in 2013 to help bring the benefits of precision medicine to patients with hematological cancers. FoundationOne Heme is currently available as a laboratory-developed test that combines DNA and RNA sequencing to detect known, novel and complex fusion events and other common genomic alterations (substitutions, indels, and copy number variations) in patients with hematologic malignancies.

With over a decade of clinical use detecting genomic alterations for patients, we’re uniquely placed to support our partners in accelerating the development of new targeted treatment options for these patients.

Earlier this year, we entered our first few partnerships to develop our FoundationOne Heme platform as a companion diagnostic for targeted hematological cancer treatments.¹⁴ This is an important milestone as it sets the foundations that will place high-quality, FDA-approved diagnostics at the heart of the precision medicine revolution in hematological cancers.

Delivering advances in clinical trials and the real world

Our collaborations with biopharmaceutical partners span the entire development journey, from early-stage research that helps to shape medicine discovery to the identification and introduction of new biomarkers that help optimize clinical trials and refine patient targeting in the clinic.

To help our biopharmaceutical partners advance their clinical trials, we offer our tissue-naïve circulating tumor DNA (ctDNA) monitoring assay, FoundationOne®Monitor,¹⁵ for investigational use only. Incorporating FoundationOne Monitor into clinical trials allows us to deliver deeper insights into molecular response and the mechanisms of treatment resistance to complement standard imaging, giving our biopharmaceutical partners the ability to optimize early clinical research and accelerate the development of new treatments.

Drawing on the wealth of genomic data in our CGDB, we can also identify new biomarkers to inform clinical trials and aid with medicine development. This year, we launched several new innovative biomarkers that are currently available for research use only, including clonal hematopoiesis prediction, expanded liquid biopsy copy-number loss detection, and AmpRatio to quantify copy-number amplifications.¹⁶ Additionally, we introduced our proprietary HRD signature biomarker,¹⁷ a next-generation sequencing scar-based genomic signature that does not rely on detecting homologous recombination repair (HRR) alterations in genes like BRCA or PALB2 to detect HRD, but instead identifies genome-wide copy number (CN) features. This novel approach offers benefits in both the trial setting and the clinic. For our biopharmaceutical partners, it can help refine their clinical trial enrollment, allowing the enrollment of patients with HRD from non-genomic sources but excluding patients with HRR mutations that do not lead to HRD. In the clinic, it can help healthcare providers identify more patients who are likely to benefit from PARP inhibitors and avoid treatment for patients who are less likely to respond. 

New partnerships and new directions in 2025 

What makes Foundation Medicine the partner of choice is our passion and strong commitment to our mission – to bring deep molecular information to the point of care for every patient living with advanced cancer.

This is what drives us, and as we move into 2025, we are excited at the prospect of forging partnerships and the potential of exploring innovative offerings in new areas, such as gene expression profiling, whole exome sequencing, whole genome sequencing, molecular residual disease testing and more, that will allow us to support our partners in new ways that further revolutionize the way we diagnose and treat advanced cancer.