Chordoma is a rare bone cancer that grows from leftover cells of the notochord, a flexible rod-like structure that forms during embryonic development and eventually gets replaced by the spine. About 300 people are diagnosed with chordoma in the United States each year. These tumors grow slowly but are locally aggressive, meaning they tend to invade nearby bone and tissue rather than spreading quickly to distant parts of the body.
Where Chordoma Comes From
Before you had a spine, you had a notochord. This embryonic structure serves as the body’s first scaffolding during early development, guiding the formation of the vertebral column. In most people, the notochord disappears almost entirely as the spine takes shape. But small clusters of notochord cells can persist in the bones of the skull base, spine, or tailbone area. In rare cases, these remnant cells begin growing uncontrollably, forming a chordoma.
A gene called Brachyury plays a central role. Brachyury is essential for notochord formation during embryonic life, but it normally goes quiet after development is complete. In chordoma, the gene becomes overactive again. Researchers have found that extra copies of the Brachyury gene, or mutations that change how its protein interacts with DNA, can drive these remnant cells to become cancerous. The tumor cells that result share both the appearance and genetic signature of the original notochord cells they came from.
Where It Occurs in the Body
Chordomas only develop along the path where the notochord once existed, which limits them to three general locations. Skull base tumors are the most common, accounting for about 39% of cases. Sacral chordomas (near the tailbone) make up roughly 34%, and tumors in the mobile spine account for the remaining 27%.
The location matters enormously because it determines both the symptoms and the surgical options. Tumors at the skull base sit dangerously close to the brainstem, major blood vessels, and cranial nerves. Sacral tumors can grow very large before detection because the pelvis has room to accommodate them. Spinal tumors can compress the spinal cord or nerve roots.
Symptoms by Location
Chordomas often grow for months or even years before causing noticeable problems, partly because they expand slowly and partly because early symptoms can mimic more common conditions. What you feel depends on where the tumor is growing.
When a chordoma develops at the base of the skull, headaches and double vision are the hallmark symptoms. The tumor can press on nerves that control eye movement, swallowing, or facial sensation. Some people notice difficulty speaking or a change in their voice.
Chordomas near the tailbone typically cause pain that radiates down the legs, along with difficulty controlling the bladder or bowels. Because low back pain is so common in the general population, sacral chordomas are frequently misdiagnosed or dismissed for long periods before imaging reveals the true cause. Tumors in the middle spine can produce localized back pain, numbness, or weakness in the arms or legs depending on which nerve roots are affected.
How Chordoma Is Diagnosed
MRI is the primary imaging tool. On MRI scans, chordomas typically appear bright on certain sequences, often with a lobulated (grape-cluster-like) structure separated by dark internal bands. These internal dividers between lobules are a characteristic feature that helps radiologists distinguish chordoma from other bone lesions. CT scans add complementary detail, revealing the pattern of bone destruction and any calcification within the tumor.
Imaging alone isn’t enough for a definitive diagnosis. A biopsy is needed, and pathologists look for the presence of Brachyury protein in the tumor cells, which serves as a reliable biomarker. Confirming the diagnosis accurately is important because chordoma can resemble other bone tumors or cartilage-based cancers under the microscope, and the treatment approach differs significantly.
Surgery Is the Primary Treatment
The goal of chordoma surgery is to remove the entire tumor in one piece with a margin of healthy tissue surrounding it. This approach, called en bloc resection with wide margins, gives the best chance of preventing the tumor from coming back. When surgeons achieve wide margins, local recurrence rates drop to between 5% and 17%. When the tumor is removed piecemeal or the margins are too narrow, recurrence rates jump to 71% to 81%.
Previous surgery that cut through the tumor makes future operations significantly harder. Patients who had an initial surgery that inadvertently entered the tumor face higher recurrence rates, which is why chordoma experts strongly recommend that the first surgery be performed at a center with specific experience in this cancer. The anatomy involved, whether it’s the skull base or sacrum, demands highly specialized surgical skill. Sacral surgery in particular can carry risks to nerves that control leg function, bladder, and bowel.
Radiation Therapy After Surgery
Chordomas are relatively resistant to standard radiation. Conventional X-ray-based radiation struggles to deliver a high enough dose to the tumor site without damaging the brain, spinal cord, or other critical structures nearby. Proton beam therapy solves this problem by depositing its energy precisely at the tumor target, then stopping. This physical property allows doctors to deliver much higher radiation doses to the chordoma while sparing surrounding tissue.
A systematic review of studies covering 561 chordoma patients treated with proton therapy found local control rates of 97% at one year, 88% at three years, and 77% at five years. Overall survival rates were also encouraging: 89% at three years and 86% at five years. Most side effects were mild. The typical treatment dose is significantly higher than what conventional radiation can safely deliver to these locations, which explains the improved results. Proton therapy is most often used after surgery to target any microscopic disease left behind, though it can also be a primary treatment when surgery isn’t feasible.
Why Recurrence Is Common
Even with the best available treatment, chordoma has a strong tendency to return. The tumor’s location along the spine and skull base makes it nearly impossible to achieve perfect surgical margins in every case. Bone, nerves, and blood vessels that must be preserved sometimes limit how much tissue the surgeon can safely remove. The slow growth rate also works against patients in a paradoxical way: because the cells divide slowly, they are less vulnerable to treatments that target rapidly dividing cells.
Post-treatment monitoring is essential and continues for years. The Chordoma Global Consensus Group recommends MRI scans every six months for the first five years after treatment. These scans should cover both the original tumor site and areas where the cancer could potentially spread. While chordoma is less likely to metastasize than many other cancers, it can eventually spread to the lungs, liver, or other bones, particularly in cases of repeated local recurrence.
Targeted Therapies and New Approaches
Because chordoma is so rare, treatment options beyond surgery and radiation have been limited. However, the discovery that chordoma cells have overactive growth-signaling receptors on their surface led to the use of certain targeted drugs originally developed for other cancers. These drugs block specific enzymes the tumor cells rely on to grow, and some patients have experienced disease stabilization.
The Brachyury gene remains the most promising therapeutic target. Because Brachyury is highly active in chordoma cells but largely silent in normal adult tissue, it offers an opportunity to attack the cancer without causing widespread side effects. A phase I clinical trial tested a vaccine designed to train the immune system to recognize and destroy cells producing Brachyury protein. That trial, which included chordoma patients with unresectable or metastatic disease, has been completed, and the approach continues to inform ongoing research into immunotherapy for this cancer.
For patients with advanced disease, clinical trials represent an important option. The rarity of chordoma means that every new treatment takes longer to study, but dedicated research networks have accelerated progress over the past decade. Patients are often encouraged to seek care at specialized centers where multidisciplinary teams combine surgical expertise, advanced radiation technology, and access to the latest trials.