Clinical Guide to Biomarkers in Colorectal Cancer

Colorectal cancer is common, increasingly showing up in adults under 50, and far more manageable when caught early. Biomarkers are the signals we measure to find cancer earlier, classify it more precisely, guide treatment choices, and track whether therapy is working. Think of them as the health dashboard behind the scenes. Some are simple blood or stool tests. Others are genetic fingerprints inside the tumor. Together they turn a one-size-fits-all diagnosis into something tailored and informed.

This guide walks through the biomarkers that matter most in colorectal cancer, how they are used in real care, and what their limits are. The goal is clear, practical understanding so results make sense and conversations with your care team feel grounded.

Screening biomarkers: finding cancer before it finds you

Screening tests look for silent disease in people who feel fine. In colorectal cancer, the workhorses are stool-based tests. They do not visualize the colon like colonoscopy. They look for molecular traces that cancer and advanced polyps shed into stool.

FIT and high-sensitivity gFOBT

FIT is the fecal immunochemical test. It uses antibodies to human hemoglobin in stool¹. In plain language, it checks for tiny amounts of blood from the lower gut. It does not react to animal blood in food, so you do not have to change your diet before collecting a sample. When FIT is positive, it signals bleeding that could be from a polyp, cancer, or another cause like hemorrhoids, and colonoscopy is the next step¹. Sensitivity for cancer is high in repeated yearly testing, while sensitivity for advanced precancerous polyps is moderate¹.

High-sensitivity guaiac fecal occult blood tests also look for blood but can be affected by diet and medications. Many programs favor FIT because it is specific to human hemoglobin and easier to use consistently¹.

Multi-target stool DNA

Multi-target stool DNA tests look for an upgraded set of clues. They combine FIT for blood with DNA changes and methylation patterns shed by colorectal tumors and advanced adenomas. The technology surveys abnormal methylation in genes like NDRG4 and BMP3², mutant KRAS, and an internal control to ensure enough human DNA is present. This design raises sensitivity for cancer and some advanced polyps compared with FIT alone, though it can generate more false positives². Negative results are reassuring for a longer interval than FIT in most screening programs. A positive test points to colonoscopy for diagnosis.

Blood-based screening

Blood tests that detect circulating tumor signals, often based on DNA methylation, are emerging. They are convenient and avoid stool collection, but current evidence shows lower sensitivity for advanced precancerous polyps compared with stool tests and colonoscopy. Some guidelines consider them an option when other screening methods are declined. Availability, insurance coverage, and exact performance vary by test and region, and practices continue to evolve as new data arrive.

What to know about screening test limits

Stool and blood tests are excellent entry points for early detection. They do not remove polyps and cannot directly visualize the colon. A positive screening test points to colonoscopy for confirmation and possible removal of precancerous lesions. A negative test reduces risk but does not reduce it to zero, which is why routine intervals matter in organized screening programs. Evidence from population studies shows that consistent participation in any high-quality screening strategy is what reduces mortality most³.

Diagnostic and staging biomarkers: defining the disease

When colorectal cancer is suspected or confirmed on colonoscopy, the next questions are what it is, where it is, and how it behaves. Tissue from a biopsy or surgery is the anchor. Pathologists establish the diagnosis and grade, and then a standard set of biomarkers is measured to classify the tumor more deeply.

MMR and MSI testing in all colorectal cancers

Mismatch repair proteins are tumor proofreading enzymes. When these proteins are lost, DNA replication errors accumulate in repetitive sequences called microsatellites. The result is microsatellite instability, often abbreviated MSI⁴. Testing can be done in two ways. Immunohistochemistry looks for the presence or absence of the MMR proteins MLH1, MSH2, MSH6, and PMS2 in tumor tissue. PCR or next-generation sequencing looks directly at instability in microsatellite regions⁵. If the tumor shows high microsatellite instability, it is called MSI-H or if proteins are absent, deficient MMR.

Why it matters. MSI-H or deficient MMR tumors have distinct biology. In early-stage disease, they tend to have a better prognosis and are less likely to benefit from certain chemotherapy regimens after surgery. In advanced disease, they are more likely to respond to immune checkpoint inhibitors⁶. There is also an important inherited angle. Loss of MLH1 with promoter methylation is usually sporadic, while loss of MSH2, MSH6, or PMS2 without another explanation suggests Lynch syndrome. Because this single test informs prognosis, treatment, and family risk, professional guidelines recommend universal MSI/MMR testing in all newly diagnosed colorectal cancers⁷.

Distinguishing sporadic MLH1 loss from Lynch syndrome

When MLH1 is absent on immunohistochemistry, the next step is to look for an MLH1 promoter methylation signal or a tumor BRAF V600E mutation. The presence of MLH1 methylation or a BRAF V600E mutation supports a sporadic origin rather than Lynch syndrome. If MLH1 is absent and these features are not found, germline genetic evaluation is appropriate because of the possibility of inherited mismatch repair deficiency⁷.

CEA at baseline

Carcinoembryonic antigen is a simple blood test that quantifies a protein many colorectal tumors shed. It is not specific enough to diagnose cancer, but at the time of diagnosis it provides a baseline that can be tracked⁸. After surgery or during treatment, trends in CEA can mirror response or recurrence. It should always be interpreted alongside imaging and clinical context.

Tumor DNA profiling

Next-generation sequencing of the tumor reveals mutations, amplifications, and fusions that guide therapy in advanced disease. In localized disease, a limited panel may still be done to establish MSI and help clarify Lynch syndrome risk. The scope of sequencing depends on the clinical scenario and the amount of tissue available.

Pivotal predictive biomarkers that guide therapy

Predictive biomarkers tell clinicians which treatments are likely to help or not help. In metastatic colorectal cancer, several have become standard.

RAS mutations

Mutations in KRAS or NRAS are the classic gatekeepers for anti-EGFR therapy. If the tumor carries an activating RAS mutation, blocking the EGFR pathway upstream is unlikely to slow the cancer³. If the tumor is RAS wild-type, especially in left-sided colon cancer, anti-EGFR therapy can improve outcomes. Large randomized trials developed this rule. Most modern reports specify the exact exon and codon because certain rare variants have nuanced behavior.

BRAF V600E

BRAF V600E is a powerful driver mutation with two practical implications. It generally signals a more aggressive course in metastatic disease and it predicts benefit from targeted combinations that inhibit the MAPK pathway more directly³. As above, BRAF V600E in a tumor with loss of MLH1 also helps distinguish sporadic tumors from Lynch syndrome associated tumors.

HER2 amplification

A subset of RAS wild-type metastatic colorectal cancers overexpress or amplify HER2. These tumors are less likely to respond to anti-EGFR therapy and can respond to HER2-targeted regimens³. Confirming HER2 status typically uses immunohistochemistry and in situ hybridization or sequencing copy number data, similar to workflows in breast cancer.

MSI-H or deficient MMR

MSI-H or deficient MMR status is both prognostic and predictive. In metastatic disease, it predicts increased likelihood of response to immune checkpoint blockade⁶. In earlier stages, it identifies tumors less likely to benefit from fluoropyrimidine-only adjuvant therapy. This dual role is why universal testing is a consensus standard.

TMB and PD-L1

Tumor mutational burden reflects the total number of mutations per megabase of DNA. MSI-H tumors are often high TMB, but not all high TMB tumors are MSI-H⁹. In colorectal cancer, MSI status is a stronger and more consistent predictor of immunotherapy response than PD-L1 expression¹⁰. PD-L1 alone has limited predictive value in this disease¹⁰.

Rare but actionable fusions

NTRK fusions and, less commonly, ALK or ROS1 fusions occur in a very small minority of colorectal cancers, often in MSI-H or right-sided tumors¹¹. When present, they can open the door to fusion-targeted therapy. Broad sequencing panels usually capture them.

Sidedness

Primary tumor location, left versus right colon, is not a biomarker in the lab, but it behaves like one in metastatic disease. Left-sided, RAS wild-type tumors are more likely to benefit from anti-EGFR therapy than right-sided counterparts. This observation is grounded in pooled analyses of randomized trials and is routinely considered in treatment planning.

Pharmacogenomic biomarkers: safety signals before therapy

Some biomarkers predict toxicity risk rather than tumor response. Checking them helps teams dose safely from the start.

DPYD variants and fluoropyrimidines

Dihydropyrimidine dehydrogenase is the enzyme that breaks down fluoropyrimidines, the backbone of many colorectal cancer regimens. Inherited DPYD variants reduce enzyme activity and raise the risk of severe, sometimes life-threatening toxicity¹². Genotyping or phenotyping can identify reduced function before treatment. Several professional groups support pre-treatment DPYD testing to guide initial dosing or consider alternatives¹³. When available, this is one of the clearest examples of precision safety in routine oncology.

UGT1A1 and irinotecan

UGT1A1 metabolizes SN-38, the active metabolite of irinotecan. Individuals with reduced function alleles such as UGT1A1*28 have a higher risk of neutropenia and diarrhea at standard doses¹⁴. Knowing UGT1A1 status helps anticipate and mitigate toxicity. Practices vary by center, but the concept is well established.

Germline risk biomarkers: who might have an inherited syndrome

About 1 in 10 people with colorectal cancer carry a hereditary predisposition. Tumor testing often provides the first clue.

Lynch syndrome

Lynch syndrome is caused by germline pathogenic variants in MLH1, MSH2, MSH6, PMS2, or EPCAM¹⁵. It raises the lifetime risk of colorectal, endometrial, and several other cancers. Tumors lacking MSH2, MSH6, or PMS2 by immunohistochemistry, or MSI-H tumors without MLH1 promoter methylation or tumor BRAF V600E, flag a higher likelihood of Lynch syndrome. When these patterns appear, referral for genetic counseling and germline testing is appropriate¹⁵. Identifying Lynch syndrome informs surveillance for the individual and risk assessment for relatives.

Polyposis syndromes

Familial adenomatous polyposis due to APC variants and MUTYH-associated polyposis are less common but important¹⁶. Clues include hundreds of polyps, a strong family history at young ages, or specific histologic subtypes. A multigene germline panel is often used when clinical suspicion is high. The decision to test is based on established criteria and should be guided by clinicians with genetics expertise.

Monitoring biomarkers: after treatment begins

Once therapy is underway, biomarkers help track the road ahead. They do not replace imaging and exam. They complement them.

CEA trends

After surgery for localized colorectal cancer, a falling CEA is a good sign. A rising CEA can be an early clue to recurrence, sometimes before imaging changes⁸. In metastatic disease, CEA frequently mirrors tumor burden. The rate of change, not a single value, carries more weight. Interpreting CEA always involves context because other conditions can nudge it up or down.

Circulating tumor DNA for minimal residual disease

Circulating tumor DNA is tumor-derived genetic material released into the bloodstream. Highly sensitive assays can detect minute quantities after surgery. If ctDNA remains detectable after a curative-intent operation, the risk of recurrence is substantially higher in prospective studies¹⁷. If ctDNA is undetectable, risk is lower. This is called minimal residual disease testing¹⁷. Many centers are exploring how to use it to personalize postoperative care. The field is moving fast, but large, definitive trials are still clarifying when changing treatment based on ctDNA improves outcomes. Timing matters because ctDNA levels can be transiently affected by surgery and chemotherapy, and low-shedding tumors may evade detection.

Reading a molecular report without getting lost

Modern reports pack a lot into a few pages. A practical way to parse them is to separate what is prognostic from what is predictive, and what is germline risk from what is somatic and limited to the tumor.

• Look for MSI or MMR status at the top because it influences prognosis, treatment options, and inherited risk assessment
• Scan for RAS and BRAF results to understand eligibility for EGFR-targeted therapy and the need for MAPK-targeted combinations in advanced disease
• Check for HER2 amplification in RAS wild-type tumors and note any rare fusions like NTRK that could be actionable
• If a likely pathogenic variant is reported in a mismatch repair gene with a note that germline origin cannot be excluded, that is a cue to discuss genetic counseling
• Note tumor mutational burden but interpret it in light of MSI, which is a stronger predictor in colorectal cancer

Reports often include variant allele frequency, which is the fraction of sequencing reads carrying a mutation. This number can be influenced by tumor purity and copy number changes, so it is not a direct measure of how dominant a clone is. Copy number gains or amplifications are sometimes reported as fold change rather than a binary present or absent. The footnotes matter because they explain assay limits and quality flags.

Assay choices and limitations you should expect

No test is perfect. Knowing the quirks prevents over-interpretation.

MSI by immunohistochemistry versus PCR or NGS

Immunohistochemistry is fast and points to the affected gene, which helps with germline triage⁵. PCR or NGS-based MSI assays may catch instability patterns when protein staining is equivocal and allow the same tissue to yield a broader genomic profile. Rarely, discordance occurs. When results conflict with clinical expectations, repeat testing or an alternate method can resolve it.

CEA interferences and context

CEA can be modestly higher in smokers and can rise with liver disease, pancreatitis, inflammatory bowel disease flares, or hypothyroidism. A single elevated value in these settings should not be overcalled. Assay cutoffs are not identical across labs, and values from different platforms are not interchangeable. Trends within the same lab are most informative.

CA19-9

CA19-9 is not a standard marker in colorectal cancer, though it is sometimes measured. It can be elevated in benign conditions and is not reliable in people who do not express the Lewis antigen. Its role is limited compared with CEA.

Tissue versus liquid biopsy

Tissue remains the reference for diagnosis and initial comprehensive profiling. Liquid biopsy captures tumor DNA shed into blood and can identify targetable alterations when tissue is scarce or a new biopsy is not feasible. Sensitivity depends on how much DNA the tumor sheds. A negative liquid result does not guarantee absence of the alteration, and confirmation with tissue is ideal when a strong suspicion remains.

How a sample is collected, stored, and processed affects quality. For stool tests, adequate sample collection and timely mailing matter. For blood and tissue, correct tubes, fixation times, and handling influence downstream performance. These details live behind the scenes but explain why occasional tests need to be repeated.

Special situations across age and life stage

Early-onset colorectal cancer is rising. For adults under 50 with a new diagnosis, germline risk assessment is considered more often because the chance of an inherited syndrome is higher than in older adults¹⁸. Tumor biology can also differ subtly by age, but treatment principles and biomarker use are largely the same.

During pregnancy, CEA is not a reliable decision-maker. Imaging choices and procedures are tailored, and multidisciplinary care is essential. In inflammatory bowel disease, chronic inflammation can raise background CEA and increase colorectal cancer risk after years of colitis¹⁹. Surveillance colonoscopy with targeted biopsies is the cornerstone in that context, and pathologic assessment includes dysplasia grading rather than the typical adenoma pathway.

Lifestyle, biology, and biomarkers

Lifestyle does not treat cancer, but it does influence the biology that biomarkers measure. Two small examples make the point. Exercise contracts skeletal muscle, which draws glucose into cells without insulin and lowers circulating insulin-like growth signals that some tumors exploit. Sleep and circadian rhythm shape cortisol and inflammatory cytokines, which can nudge systemic inflammation and liver metabolism and subtly affect markers like CEA. These effects are modest and indirect. They are reminders that the numbers we track sit in a living system where whole-person habits matter alongside precision tests, though biomarker-driven decisions always rely on clinical trial evidence.

Putting it together across the care continuum

Here is how the pieces usually flow. Screening identifies risk through stool or blood tests. Colonoscopy confirms and, in many cases, prevents cancer by removing polyps. If cancer is found, baseline imaging and CEA establish the starting line. The tumor is tested for MSI or MMR to set prognosis, identify immunotherapy-sensitive biology, and screen for inherited risk. In metastatic disease, a genomic panel clarifies RAS, BRAF, HER2, and rare fusions to match therapy. Pharmacogenomics like DPYD and UGT1A1 tune safety. During and after treatment, CEA trends and, increasingly, ctDNA provide additional signals about response and recurrence. Each step adds information. The art is integrating it without overweighting any single number.

Quick reference: what each common biomarker tells you

• MSI-H or deficient MMR indicates immunotherapy-sensitive biology, favorable prognosis in early stages, and possible Lynch syndrome
• RAS mutation status indicates eligibility for EGFR-targeted therapy in metastatic disease
• BRAF V600E indicates poorer prognosis in metastatic disease and potential benefit from MAPK-directed combinations
• HER2 amplification indicates potential benefit from HER2-directed regimens in RAS wild-type disease
• CEA trend indicates approximate tumor burden dynamics in context with imaging
• ctDNA minimal residual disease indicates recurrence risk after surgery and may detect progression earlier than scans
• DPYD and UGT1A1 indicate risk of chemotherapy toxicity and guide safer dosing

Credibility cues and where the evidence stands

Universal MSI/MMR testing is a consensus standard endorsed by major oncology guidelines because it shapes therapy, prognosis, and familial risk assessment all at once⁷. RAS testing as a gatekeeper for anti-EGFR therapy comes from multiple randomized trials³. BRAF V600E and HER2 pathways have been mapped in large cohorts and validated in prospective studies for targeted treatment selection³. Prospective cohorts show that postoperative ctDNA positivity predicts recurrence risk much more strongly than traditional clinicopathologic features¹⁷, although its role in changing therapy is still being tested in randomized trials. DPYD-guided dosing reduces severe fluoropyrimidine toxicity in real-world and trial settings¹². These signals are robust, but every assay has technical limits and not all findings are actionable. That is why interpretation sits within multidisciplinary care.

What changes and what stays stable

Biomarkers can be stable or evolve as the tumor evolves. MSI status and most germline-driven features are stable. Under treatment pressure, acquired resistance can emerge in pathways like EGFR, and liquid biopsy can detect new RAS mutations at progression. This is one reason why repeating molecular testing at key clinical turning points can be informative when treatment choices depend on current tumor biology.

Final takeaways

Biomarkers in colorectal cancer are tools that help at every step. They flag silent disease in screening, reveal tumor behavior and inherited risk at diagnosis, prioritize the right therapies in advanced disease, and track treatment response over time. Each test answers a different question. The clearest picture emerges when those answers are stitched together by a care team that knows the strengths and limits of each assay. Results are not the decision by themselves. They are the map. The route still depends on the terrain, the evidence, and the goals you set with your clinicians.