Mismatch Repair (MMR) and Microsatellite Instability (MSI) in Colorectal Cancer

by Jason Wasserman MD PhD FRCPC
March 23, 2026

Mismatch repair (MMR) and microsatellite instability (MSI) testing are among the most important biomarker tests performed on colorectal cancers. Every colorectal cancer — whether found on a biopsy or in a surgical specimen — should be tested for this biomarker. The results tell your doctor whether your cancer’s DNA repair system is working normally or has broken down. That distinction matters for two reasons: it determines whether a class of cancer drugs called immune checkpoint inhibitors is likely to help you, and it may reveal whether your cancer developed because of an inherited condition called Lynch syndrome, which can affect other members of your family.

What the test looks for

Every cell in your body contains DNA — the genetic code that controls how cells grow and divide. When a cell copies its DNA to make a new cell, small errors called mismatches can occur. Your cells have a built-in repair system — the mismatch repair (MMR) system — whose job is to find and fix these errors before they cause problems.

The MMR system is made up of several proteins that work together. The four most important ones are MLH1, PMS2, MSH2, and MSH6. These proteins work in pairs: MLH1 pairs with PMS2, and MSH2 pairs with MSH6. If any one protein in a pair is lost or stops working, the entire repair system for that pair fails. When that happens, DNA copying errors begin to accumulate inside cancer cells. Over time, these errors pile up in particular regions of the DNA called microsatellites — short, repetitive sequences scattered throughout the genome. When microsatellites become unstable due to accumulated errors, the tumour is called microsatellite instable (MSI-H, meaning MSI-high).

A tumour with a broken MMR system is called MMR-deficient (dMMR). A tumour with a normally functioning MMR system is called MMR-proficient (pMMR). These two terms — dMMR and MSI-H — describe the same underlying problem and are often used interchangeably, although they come from different test types (see “How the test is performed” below).

The key clinical meaning of a dMMR/MSI-H result is this: when a tumour’s DNA repair system is broken, it accumulates an unusually large number of mutations. This makes the cancer cells look very abnormal to the immune system. The immune system then sends a large number of immune cells to attack the tumour — but those immune cells are often blocked from doing their job by molecular “brakes” called immune checkpoints. Drugs called immune checkpoint inhibitors work by releasing those brakes, allowing the immune system to destroy the cancer. This is why dMMR/MSI-H colorectal cancers tend to respond well to immunotherapy, while MMR-proficient tumours generally do not.

How common is dMMR/MSI-H in colorectal cancer?

Approximately 15% of colorectal cancers that have not yet spread to distant organs are dMMR/MSI-H. In cancers that have spread (metastatic disease), the proportion is lower — around 4 to 5% — because dMMR colorectal cancers caught at an early stage may behave differently than their metastatic counterparts (more on this in the prognosis section).

Of all dMMR colorectal cancers, roughly 25 to 30% are caused by Lynch syndrome — an inherited condition. The remaining 70 to 75% arise sporadically, meaning the MMR system failed not because of an inherited gene change but because of a chemical change in the tumour itself called MLH1 promoter methylation. Differentiating Lynch syndrome from sporadic dMMR is critically important and is explained in detail in the section below.

Certain subtypes of colorectal cancer are more likely to be dMMR/MSI-H. Mucinous adenocarcinoma and medullary carcinoma of the colon have higher rates of MMR deficiency than standard adenocarcinoma. dMMR/MSI-H colorectal cancers also tend to occur more often in the right side of the colon (the ascending colon and cecum) than in the left side or rectum.

Why is the test done

MMR/MSI testing is now performed on virtually all colorectal cancers, regardless of stage, for three important reasons.

To determine whether immunotherapy is an option

Immune checkpoint inhibitors — specifically pembrolizumab (Keytruda) and nivolumab (Opdivo) — are approved for colorectal cancers that are dMMR/MSI-H. These drugs work by releasing the molecular brakes on the immune system, allowing it to recognize and attack cancer cells. They are not effective in MMR-proficient (pMMR) colorectal cancers. The result of your MMR/MSI test is one of the first things an oncologist looks at when planning treatment for colorectal cancer.

To provide prognostic information

In early-stage colorectal cancer (Stage II, meaning the cancer has grown through the bowel wall but has not spread to lymph nodes), a dMMR/MSI-H result is associated with a better prognosis than pMMR at the same stage. Patients with Stage II dMMR colorectal cancer generally have a lower risk of the cancer returning after surgery. There is also evidence that Stage II dMMR tumours do not benefit from — and may actually be harmed by — a common chemotherapy drug called 5-fluorouracil (5-FU) when used on its own. This makes the MMR result particularly important when planning adjuvant (post-surgery) treatment.

In metastatic colorectal cancer, the picture is more complicated. Historically, patients with metastatic dMMR colorectal cancer did not do as well as those with early-stage dMMR disease. However, the introduction of immunotherapy has substantially changed outcomes in this group.

To identify Lynch syndrome

Because dMMR colorectal cancer can be caused by Lynch syndrome — a hereditary condition — MMR testing serves as the first step in screening for this inherited cancer risk. If Lynch syndrome is identified, your biological relatives may also carry the same inherited gene change and would benefit from genetic testing and increased cancer screening. This hereditary dimension of MMR testing is so important that it has its own detailed section below.

How the test is performed

There are two main methods for testing MMR/MSI status in colorectal cancer, and many labs use both to make sure results are accurate.

Immunohistochemistry (IHC)

Immunohistochemistry (IHC) uses specially designed proteins called antibodies to stain for the four MMR proteins — MLH1, PMS2, MSH2, and MSH6 — in a thin slice of tumour tissue. Under the microscope, a pathologist can see whether each protein is present (retained) or absent (lost) in the cancer cells. Normal cells surrounding the tumour serve as a built-in control — they always show staining, confirming the test worked correctly. IHC is quick, inexpensive, and widely available.

Microsatellite instability (MSI) testing by PCR

PCR-based MSI testing directly measures the lengths of microsatellite sequences in tumour DNA and compares them with those in normal DNA from the same patient. If the microsatellite lengths in the tumour are different from those in normal tissue, the tumour is classified as MSI-H (microsatellite instability — high). If the lengths are the same, the tumour is microsatellite stable (MSS). This test measures the downstream consequence of MMR protein loss rather than the proteins themselves.

IHC and PCR-based MSI testing agree in the vast majority of cases. When they disagree, or when the IHC result is uncertain, the other test is often performed to confirm the result. Next-generation sequencing (NGS) panels can also assess MSI status as part of broader molecular testing, and this approach is increasingly common.

How results are reported

Your pathology report will describe the MMR result in one of two ways, depending on which test was used.

If immunohistochemistry was performed, the report will describe the staining result for each of the four MMR proteins (MLH1, PMS2, MSH2, and MSH6) and then summarize the overall result:

MMR-proficient (pMMR). All four proteins are present in the tumour cells. The DNA repair system is intact. This result is also called MSS (microsatellite stable) when tested by PCR.
MMR-deficient (dMMR). One or more proteins are absent from the tumour cells. The DNA repair system is not functioning properly. The report will also specify which protein or proteins are missing — for example, “loss of MLH1 and PMS2” or “loss of MSH2 and MSH6.”

If PCR-based MSI testing was performed, the result will be described as:

MSS (microsatellite stable) or MSI-L (microsatellite instability — low). The tumour’s microsatellite sequences are stable. This corresponds to MMR-proficient (pMMR).
MSI-H (microsatellite instability — high). The tumour’s microsatellite sequences show significant instability. This corresponds to MMR-deficient (dMMR).

In most cases, the report will use one set of terms or the other, but some reports will include both.

What the result means

MMR-proficient (pMMR) / MSS

This is the most common result — approximately 85% of colorectal cancers are pMMR/MSS. It means the cancer’s DNA repair system is functioning normally. This result has two main implications. First, immunotherapy drugs such as pembrolizumab or nivolumab are not expected to work in your cancer as a first-line treatment — they are reserved for dMMR/MSI-H tumours. Second, Lynch syndrome is not likely to be the cause of your cancer (though it cannot be completely ruled out based on this test alone in rare cases). Your treatment plan will focus on surgery, chemotherapy, targeted therapies (such as anti-EGFR or anti-VEGF drugs), and radiation, depending on the stage and location of your cancer.

MMR-deficient (dMMR) / MSI-H

Approximately 15% of non-metastatic colorectal cancers are dMMR/MSI-H. A dMMR result has several important implications:

Immunotherapy eligibility. Pembrolizumab (Keytruda) is approved as a first-line treatment for metastatic dMMR/MSI-H colorectal cancer. Nivolumab (Opdivo) is also approved in this setting. For early-stage disease, immunotherapy is being studied in clinical trials. If your cancer is metastatic, a dMMR result opens the door to immunotherapy as part of your treatment plan.
Better prognosis in early-stage disease. If your cancer is Stage II (grown through the bowel wall but not spread to lymph nodes), a dMMR result is generally associated with a better long-term outcome than a pMMR result at the same stage.
Reconsideration of 5-FU chemotherapy. There is evidence that Stage II dMMR colorectal cancers may not benefit from 5-fluorouracil (5-FU) chemotherapy alone after surgery, and your oncologist will factor this into decisions about adjuvant treatment.
Possible Lynch syndrome. A dMMR result means that Lynch syndrome must be considered. Further testing is needed to determine whether the MMR deficiency is hereditary (caused by Lynch syndrome) or sporadic. This is explained in detail in the section below.

Which proteins are lost — and why it matters

The pattern of protein loss in the IHC result provides important clues about the cause of the MMR deficiency:

Loss of MLH1 and PMS2 together. This is the most common pattern in sporadic (non-inherited) dMMR colorectal cancer. When MLH1 is lost, its partner PMS2 is usually lost as well. This pattern often results from a process called MLH1 promoter methylation — a chemical change that silences the MLH1 gene in the tumour. This is usually a sporadic event, not inherited. Additional tests are usually ordered to confirm this (see below).
Loss of MSH2 and MSH6 together. When MSH2 is lost, its partner MSH6 is usually lost as well. This pattern is strongly associated with Lynch syndrome and should prompt genetic counselling and germline testing.
Loss of MSH6 alone. Isolated MSH6 loss is more strongly associated with Lynch syndrome than sporadic disease, though it can occasionally occur sporadically.
Loss of PMS2 alone. Isolated PMS2 loss is associated with Lynch syndrome (specifically, a germline PMS2 mutation), though it can also occur sporadically.
Loss of MLH1 alone (without PMS2). This is an unusual pattern. It may indicate an MLH1 germline mutation (Lynch syndrome) or, less commonly, a somatic MLH1 alteration, and warrants further investigation.

Distinguishing Lynch syndrome from sporadic dMMR: MLH1 promoter methylation and BRAF testing

When the IHC result shows loss of MLH1 and PMS2, the next step is to determine whether this is due to Lynch syndrome or a sporadic, non-inherited process. This distinction is critical because Lynch syndrome has major implications for the patient’s health and that of their family members.

MLH1 promoter methylation testing

The most common sporadic cause of MLH1 and PMS2 loss is MLH1 promoter methylation — a chemical change called methylation that “turns off” the MLH1 gene in the tumour cells. This is not a genetic mutation that can be inherited; it is a chemical modification that happens only in the cancer. If MLH1 promoter methylation is detected, the MMR deficiency is almost certainly sporadic, and Lynch syndrome is much less likely. If methylation is absent, the likelihood of Lynch syndrome increases significantly, and germline testing is typically recommended.

BRAF V600E testing

Testing for a specific BRAF gene mutation, V600E, is another way to distinguish sporadic from hereditary dMMR. A BRAF V600E mutation is found almost exclusively in sporadic dMMR colorectal cancers and is extremely rare in Lynch syndrome-associated cancers. If a BRAF V600E mutation is present alongside dMMR (particularly loss of MLH1 and PMS2), this strongly suggests the cancer is sporadic rather than Lynch syndrome-related. If BRAF is wild-type (normal), the likelihood of Lynch syndrome increases, and germline testing should be considered.

In practice, many laboratories perform MLH1 promoter methylation testing and/or BRAF testing automatically whenever MLH1 and PMS2 loss is found on IHC, to streamline the Lynch syndrome evaluation without requiring an extra step. Your oncologist or genetic counsellor will explain which tests were done and what the results mean for your situation.

Lynch syndrome: what it is and why it matters

Lynch syndrome — also called hereditary non-polyposis colorectal cancer (HNPCC) — is an inherited condition caused by a germline mutation in one of the MMR genes (most commonly MLH1, MSH2, MSH6, or PMS2). “Germline” means the mutation was present from conception and is carried in every cell of the body, including cells that can be passed on to children. A person with a Lynch syndrome mutation has a significantly elevated lifetime risk of developing colorectal cancer and several other cancers, including endometrial cancer, ovarian cancer, stomach cancer, urinary tract cancer, and others.

Approximately 25 to 30% of all dMMR colorectal cancers — and roughly 3 to 5% of all colorectal cancers — are caused by Lynch syndrome. For patients whose dMMR result cannot be explained by MLH1 promoter methylation or BRAF V600E mutation, referral to a genetic counsellor and germline testing is recommended. Germline testing is a blood or saliva test that looks for inherited mutations in the MMR genes.

What a Lynch syndrome diagnosis means for you

If germline testing confirms Lynch syndrome, this information will shape your ongoing cancer care in several ways. Your surgical team may discuss more extensive surgery (such as removal of a larger segment of the colon or, for women, consideration of the uterus and ovaries) to reduce the risk of a second cancer. Your follow-up surveillance schedule will be intensified to catch any future cancers early. And you will be counselled about the other cancer types associated with Lynch syndrome.

What it means for your family

Each biological child, sibling, and parent of someone with a confirmed Lynch syndrome mutation has a 50% chance of carrying the same mutation. This is called cascade testing — the process of testing family members once a hereditary mutation has been identified. Family members who test positive for the Lynch syndrome mutation can begin earlier and more frequent screening for colorectal and other Lynch-associated cancers, which substantially reduces their risk of developing an advanced cancer. If Lynch syndrome is suspected or confirmed in your case, your genetic counsellor can help facilitate this process and guide conversations with your family.

It is important to understand that Lynch syndrome does not cause cancer with certainty — it raises the risk. Many people with Lynch syndrome live long, healthy lives when they follow appropriate screening protocols.

Treatment implications of dMMR/MSI-H in colorectal cancer

Metastatic (Stage IV) disease

The arrival of immune checkpoint inhibitors has transformed the treatment of metastatic dMMR/MSI-H colorectal cancer. Pembrolizumab (Keytruda) is now approved as the preferred first-line treatment for patients with metastatic dMMR/MSI-H colorectal cancer, based on data from the KEYNOTE-177 trial, which showed that pembrolizumab produced significantly longer progression-free survival than standard chemotherapy in this group. Response rates to pembrolizumab in dMMR/MSI-H metastatic colorectal cancer are approximately 43%, and some patients achieve durable, long-lasting responses.

Nivolumab (Opdivo), alone or in combination with ipilimumab (Yervoy), is also approved for previously treated metastatic dMMR/MSI-H colorectal cancer. These drugs work by blocking immune checkpoint proteins (PD-1 and CTLA-4) that cancer cells use to evade the immune system.

If your metastatic colorectal cancer is dMMR/MSI-H, your oncologist will likely discuss immunotherapy as part of your first-line treatment. Standard chemotherapy regimens (such as FOLFOX or FOLFIRI) may still play a role in some cases, particularly if the tumour progresses on immunotherapy.

Early-stage (Stage II) disease

In Stage II colorectal cancer (cancer that has grown through the bowel wall but has not spread to lymph nodes), dMMR/MSI-H status has an important influence on decisions about adjuvant chemotherapy — treatment given after surgery to reduce the risk of recurrence. Multiple studies have shown that Stage II dMMR colorectal cancers are unlikely to benefit from adjuvant 5-fluorouracil (5-FU) chemotherapy and may actually do worse with it compared to surgery alone. Current guidelines generally recommend that Stage II dMMR patients be treated with surgery alone, reserving chemotherapy for cases with other high-risk features. Immunotherapy in early-stage dMMR colorectal cancer is being actively studied in clinical trials.

Stage III disease

In Stage III colorectal cancer (spread to nearby lymph nodes but not to distant organs), adjuvant chemotherapy with oxaliplatin-based regimens (such as FOLFOX or CAPOX) is standard of care for most patients, regardless of MMR status. The benefit of adjuvant chemotherapy appears to be retained in Stage III dMMR patients, unlike in Stage II. Immunotherapy in the adjuvant setting for Stage III dMMR disease is currently under investigation in clinical trials.

Locally advanced rectal cancer

For rectal cancers that require treatment before surgery (neoadjuvant therapy), the MMR/MSI result is increasingly relevant. Early trial data suggest that dMMR/MSI-H rectal cancers may respond exceptionally well to neoadjuvant immunotherapy — in some cases, achieving complete tumour disappearance, potentially allowing patients to avoid surgery altogether. This is an evolving area, and your treatment team will be best placed to discuss whether you might be eligible for relevant clinical trials.

What happens next

If your MMR/MSI result has just come back, the steps that follow will depend on whether your cancer is early-stage or metastatic, and on the pattern of protein loss.

If your result is pMMR/MSS, your treatment planning will proceed based on the stage and other features of your cancer. Immunotherapy is generally not indicated, and your oncologist will discuss surgery, chemotherapy, targeted therapy, or radiation as appropriate.
If your result is dMMR/MSI-H, your care team will likely order additional tests — MLH1 promoter methylation and/or BRAF V600E testing — if these were not already performed. If metastatic, immunotherapy will likely be discussed as a treatment option. If Lynch syndrome has not yet been ruled out, referral to a genetic counsellor will be arranged.
If Lynch syndrome is confirmed by germline testing, you will be connected with a genetic counselling team for guidance on your own ongoing surveillance and to facilitate testing of family members. This process takes time, and it is reasonable to ask your care team what to expect at each step.

If you are waiting for results, or if you have received a result that you do not yet fully understand, it is entirely appropriate to ask your oncologist or pathologist to explain what was found and what it means for your specific situation. You do not need to understand all of this at once.

Questions to ask your doctor

Was my colorectal cancer tested for MMR/MSI status, and what were the results?
If my cancer is dMMR/MSI-H, which proteins are missing — and what does the pattern of loss suggest?
Has my tumour been tested for MLH1 promoter methylation or BRAF V600E to help distinguish Lynch syndrome from a sporadic cause?
Based on my MMR/MSI result, am I a candidate for immunotherapy?
How does my MMR/MSI result affect decisions about chemotherapy after surgery?
Should I be referred to a genetic counsellor to discuss Lynch syndrome?
If Lynch syndrome is confirmed, what does that mean for my surveillance going forward?
Should my family members be tested for Lynch syndrome?
Are there any clinical trials I should be aware of based on my MMR/MSI result?