Understanding Lynch Syndrome Cancer Risks by Gene, Age, and Gender: What 6,350 Carriers Taught Researchers

Table of Contents

• Key Points
• What Is Lynch Syndrome and Why This Research Matters
• How the Research Was Conducted
• Overall Findings: Cancers Observed in the Study
• Key Findings: MLH1 and MSH2 Gene Variants
• Key Findings: MSH6 Gene Variants
• Key Findings: PMS2 Gene Variants
• Survival After Cancer Diagnosis
• What These Findings Mean for Patients
• Study Limitations
• Recommendations for Patients and Families
• Frequently Asked Questions
• Source Information

Key Points

• In 6,350 Lynch syndrome carriers followed for 51,646 years, MLH1 and MSH2 mutations carried the highest cancer risks.
• MSH6 mutations caused high endometrial cancer risk in women but only 18% lifetime colorectal cancer risk in men.
• PMS2 carriers showed no significantly increased cancer risk before age 50 and only a nonsignificant increase later.
• Ten-year survival exceeded 80% for colon, endometrial, and ovarian cancers diagnosed before age 65.
• Management guidelines for Lynch syndrome may need revision to reflect gene-specific and gender-specific risks, authors concluded.

What Is Lynch Syndrome and Why This Research Matters

Lynch syndrome (LS) is the most common hereditary cancer syndrome, affecting an estimated 1 in 300 people. It is caused by disease-causing mutations (called pathogenic variants) in one of four genes known as the mismatch repair (MMR) genes: MLH1, MSH2, MSH6, and PMS2. Normally, these genes help repair errors that occur when DNA is copied during cell division. When one of these genes is faulty, cells can accumulate DNA damage that may lead to cancer.

Each of the four genes is associated with increased risks for cancers in specific organs, including the colorectum (colon and rectum), endometrium (lining of the uterus), ovaries, stomach, small bowel, bile duct, pancreas, and upper urinary tract. Accurate estimates of these risks are essential for planning appropriate approaches to cancer prevention and early diagnosis. However, previous studies have been limited by factors including retrospective designs (looking back at past data), lack of validation in independent groups of patients, and inconsistent classification of genetic variants.

Earlier findings from the Prospective Lynch Syndrome Database (PLSD) produced some surprising results. First, people with MLH1 and MSH2 mutations appeared to have a lifetime risk of colorectal cancer (CRC) of approximately 50% despite undergoing surveillance colonoscopy (regular scope examinations of the colon). Second, shorter intervals between colonoscopies did not seem to reduce the incidence of CRC in Lynch syndrome patients. These observations challenged the long-held assumption that colorectal cancer in Lynch syndrome usually develops from a non-invasive polyp precursor (adenoma) and that removal of these polyps during colonoscopy can reliably prevent cancer.

Previous PLSD analyses also showed no increase in cancer risk in PMS2 carriers before 40 years of age. Although observation years were limited in older PMS2 carriers, Lynch-associated cancers other than endometrial and prostate were not observed.

How the Research Was Conducted

This study was an international, multicenter prospective observational study (meaning researchers followed participants forward in time) conducted through the PLSD. It had no control group; instead, researchers counted cancers that developed during follow-up in carriers of pathogenic MMR gene variants.

Participants, including both initial patients (probands) and their relatives, were recruited for prospective follow-up at collaborating centers in 18 countries. Genetic variants were assumed to be inherited and were confirmed by genetic testing either before, at, or after inclusion in the study. To be included, each participant needed to have completed a first prospectively planned colonoscopy and had at least one year of follow-up afterward. Cancers diagnosed before or at the same age as that first colonoscopy were counted as "previous" cancers.

Only variants classified as class 4 or class 5 (clinically actionable, meaning definitively disease-causing) in the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) database were included. The study was conducted in two phases: first, a newly recruited validation cohort of 3,527 carriers contributed 26,682 observation years. Second, the previously published original cohort of 2,823 carriers contributed 24,964 follow-up years after updating. Before merging the two groups, all variants in the original cohort were reassessed to ensure consistent classification.

After merging, the combined data set comprised 6,350 carriers — 3,480 females and 2,870 males — who had been followed from a mean age of 46.8 years (range 25–74 years), providing 51,646 observation years. A total of 1,808 cancers were diagnosed during prospective follow-up.

For statistical analysis, researchers calculated annual incidence rates (the chance of developing cancer each year) in 5-year age groups from age 25 to 75. They also computed cumulative incidence — the overall risk of developing cancer by a given age — starting at age 25. Survival after cancer diagnosis was estimated using the Kaplan–Meier method, which measures the percentage of patients still alive at various time points after diagnosis. Survival calculations were limited to cancers diagnosed before age 65 to avoid the influence of other age-related factors, and follow-up was censored (cut off) at organ removal, last known contact, or death, whichever came first.

Overall Findings: Cancers Observed in the Study

Among the 1,808 cancers diagnosed during prospective observation, the most frequent were cancers of the:

• Colon — 580 cases (32.1% of all cancers)
• Skin — 215 cases (11.9%)
• Endometrium — 173 cases (9.6%)
• Rectum — 127 cases (7.0%)

Skin cancers were not reported consistently by all centers and were therefore excluded from the risk calculations presented in this study.

The combined data set included enough observation years and cancer events to calculate precise risks by age, gene, and gender from age 25 to 75. The validation cohort showed no statistically significant differences from the original cohort for either risk of any cancer or risk of colorectal cancer (P > 0.05 at all ages), confirming that the findings were reproducible.

Key Findings: MLH1 and MSH2 Gene Variants

Of the 6,350 carriers in the study, 2,607 (41.1%) carried pathogenic MLH1 variants and 2,495 (39.3%) carried pathogenic MSH2 variants. Together, these two genes accounted for more than 80% of all Lynch syndrome carriers in the study.

Pathogenic MLH1 and MSH2 variants caused high-penetrance dominant cancer syndromes — meaning that a very large proportion of carriers developed cancer during their lifetime. The two genes shared similar risks for colorectal, endometrial (uterine), and ovarian cancers. However, there were important differences:

• Older MSH2 carriers had higher risks of cancers of the upper urinary tract (ureter and kidney), prostate, upper gastrointestinal tract (stomach, small bowel, bile duct, gallbladder, pancreas), and brain.
• Male MLH1 carriers had higher risks than female MLH1 carriers for cancers of the colon, stomach, small bowel, bile duct, gallbladder, and pancreas.

In early adult life, MSH2 carriers of both genders had the same high risk for colorectal cancer. At older ages, MSH2 carriers (including those who had survived earlier cancers) remained at relatively high risk for the additional cancers listed above.

Key Findings: MSH6 Gene Variants

Pathogenic MSH6 variants were found in 841 carriers (13.2%) of the study population. The results for this gene were striking and have important implications for how families are identified and counseled.

MSH6 variants caused what researchers describe as a sex-limited trait: women had a high overall cancer risk driven largely by gynecological (female reproductive system) cancers, while men had only an 18% lifetime risk of colorectal cancer. The overall cancer penetrance (risk of developing any cancer) for MSH6 variants was significantly lower in males than in females — the difference was statistically significant at age 70 (p < 0.0001, meaning there is less than a 0.01% chance this difference occurred by random chance).

Specifically, MSH6 carriers of both genders had similar, modestly increased risks for colorectal cancer, while female carriers had high risks for endometrial cancer compared with other organs. The authors noted that this limited the usefulness of family history in identifying families with MSH6-associated Lynch syndrome — because many male carriers might not develop cancer, the condition could appear to "skip" generations on the male side of a family.

Key Findings: PMS2 Gene Variants

Pathogenic PMS2 variants were the least common in the study, found in 407 carriers (6.4%). Very importantly, the researchers reported that they did not demonstrate a significantly increased cancer risk in carriers of pathogenic PMS2 variants.

Several specific findings support this conclusion:

• The risk of cancer for PMS2 carriers was not increased at all before 50 years of age.
• At older ages, the risk was only nonsignificantly increased — meaning the increase was too small to be confidently distinguished from random variation.
• No colorectal, endometrial, ovarian, or urinary tract cancers were observed before age 50 in PMS2 carriers — giving even lower risk estimates than had been reported in previous studies.

The authors noted that the relatively limited number of observation years for older PMS2 carriers is a weakness of the current study, and they called for further expansion of this group in future PLSD research. They also pointed out that although PMS2 variants are known to cause a rare recessively inherited cancer syndrome of childhood and adolescence called constitutional mismatch repair deficiency (CMMRD) syndrome, the cancer risk for adult carriers of a single PMS2 mutation (heterozygotes) is not increased in young to middle-aged adults and remains uncertain in older individuals.

Interestingly, recent studies have suggested that PMS2 variants may not actually initiate colorectal cancer development. Instead, PMS2 protein deficiency may favor the progression of existing non-cancerous polyps (MMR-proficient adenomas) to full colorectal cancer. If this is correct, surveillance colonoscopy with removal of polyps (polypectomy) could be more effective at preventing colorectal cancer in PMS2 carriers than in carriers of other Lynch syndrome genes. This could help explain the low incidence of colorectal cancer seen in PMS2 carriers in this study — but it cannot explain the low incidence of the other Lynch-associated cancers observed.

Survival After Cancer Diagnosis

Survival after cancer diagnosis is a crucial piece of information for patients. The researchers calculated crude (actual observed) 5-year and 10-year survival for the most common cancers in MLH1, MSH2, and MSH6 carriers diagnosed after entering the study and before age 65.

Most patients survived ten years or more following cancers of the:

• Colon — 88% survived 10 years (5-year survival: 95%)
• Rectum and sigmoid — 70% (5-year: 75%)
• Endometrium — 89% (5-year: 89%)
• Ovary — 84% (5-year: 84%)
• Prostate — 70% (5-year: 96%)
• Breast — 82% (5-year: 92%)
• Ureter and kidney — 67% (5-year: 86%)
• Urinary bladder — 68% (5-year: 81%)
• Stomach — 72% (5-year: 72%)
• Small bowel — 71% (5-year: 81%)

However, survival was much poorer for several less common cancers:

• Pancreas — only 29% survived 5 or 10 years
• Biliary tract (bile ducts) — 42% survived 5 or 10 years
• Brain — only 15% survived 5 or 10 years

These survival figures reflect actual outcomes in patients who were undergoing surveillance and treatment at expert centers, providing realistic expectations for patients diagnosed with Lynch-associated cancers.

What These Findings Mean for Patients

This study provides the most precise cancer risk estimates to date for Lynch syndrome, broken down by gene, age, and gender. Each gene tells a different story, and the authors conclude that management guidelines for Lynch syndrome may require revision in light of these gene-specific and gender-specific risks.

For patients with MLH1 or MSH2 mutations, the high penetrance of cancer means that intensive surveillance remains essential. The colorectal cancer risk of approximately 50% despite colonoscopy surveillance challenges the assumption that colonoscopy alone is fully protective. MSH2 carriers, in particular, may benefit from vigilance for upper urinary tract, prostate, upper gastrointestinal, and brain cancers, especially at older ages.

For patients with MSH6 mutations, the message is more nuanced. Women face substantial endometrial cancer risk, underscoring the importance of gynecological surveillance. Men have a lower colorectal cancer risk, which may mean that less intensive colorectal surveillance could be appropriate — though this needs to be determined by future guidelines. The reduced utility of family history in identifying MSH6 families is also important for genetic counseling.

For patients with PMS2 mutations, the lack of demonstrated increased cancer risk before age 50 — and the only nonsignificant increase at older ages — raises questions about whether the intensive surveillance protocols designed for MLH1 and MSH2 carriers are appropriate for PMS2 carriers. The authors stopped short of recommending changes but suggested that further study of PMS2 carriers is urgently needed.

Finally, the generally good prognosis for the most common Lynch-associated cancers (colon, endometrial, and ovarian) is reassuring: more than 80% of patients survived at least 10 years after these diagnoses in this study.

Study Limitations

The authors acknowledged several important limitations of this study:

• No control group: The study was observational without a comparison group, so risk estimates are relative to general population data rather than directly measured controls.
• Selection bias: Participants were identified because of family or personal history of cancer, which could have selected for coexisting non-Lynch cancer-predisposing genetic variants or environmental factors that may have increased the observed cancer rates.
• Survivorship bias: The long follow-up of some participants may have introduced biases related to who survived long enough to be included in certain analyses.
• Limited PMS2 data: The relatively small number of PMS2 carriers, particularly at older ages, limits the certainty of risk estimates for this group.
• Skin cancers excluded: Skin cancers were not systematically reported by all centers and were excluded from the analyses.
• Variable surveillance protocols: Follow-up protocols, compliance with surveillance, and cancer stage at diagnosis were not study parameters and could influence the results.
• Right-censoring for severe cancers: For less frequent cancers with serious prognoses (gastric, small intestine, bile duct, pancreatic), survival was right-censored when those cancers were diagnosed, to avoid underestimating survival for the more common cancers.

Factors that might have reduced the observed cancer risks include colonoscopy with polypectomy and possible use of aspirin, including participation in clinical trials. Because the analysis was censored for therapeutic or prophylactic organ removal, these measures are less likely to have impacted the findings. The authors also noted that partial colectomy or rectal cancer surgery was previously shown to have little effect on the risk of subsequent colon cancer in the original cohort.

Recommendations for Patients and Families

Based on this research, the following points may be helpful for patients living with Lynch syndrome and their families:

1. Know your specific gene. This study shows that cancer risks differ substantially between MLH1, MSH2, MSH6, and PMS2 mutations. Ask your doctor which gene you carry and what that means for your specific surveillance plan.
2. Follow gene-appropriate surveillance. MLH1 and MSH2 carriers face the highest risks and typically need the most intensive monitoring. MSH6 carriers should pay particular attention to gynecological screening. PMS2 carriers may be advised that their risks appear lower, though guidelines are still evolving.
3. Discuss family history limitations. If you carry an MSH6 mutation, be aware that cancer may appear to "skip" generations, particularly through male relatives. A clear family history is not always present in Lynch syndrome families.
4. Take colorectal surveillance seriously. Even though colonoscopy with polypectomy may not fully prevent colorectal cancer in MLH1 and MSH2 carriers, it remains the cornerstone of care and enables early detection, which is associated with a 95% 5-year survival for colon cancer in this study.
5. Be aware of prognosis. If you are diagnosed with colon, endometrial, or ovarian cancer, the 10-year survival rates in this study exceeded 80%, which offers important perspective and hope.
6. Consider speaking with a genetic counselor. Genetic counseling can help you understand your specific risks, discuss testing for at-risk relatives, and coordinate appropriate surveillance with your medical team.
7. Participate in research registries. The authors emphasized that further expansion of the PLSD — particularly for PMS2 carriers — would help refine risk estimates and improve care for future generations.

Frequently Asked Questions

What is Lynch syndrome and which genes are involved?

Lynch syndrome is the most common hereditary cancer syndrome, affecting about 1 in 300 people. It is caused by mutations in one of four mismatch repair genes: MLH1, MSH2, MSH6, and PMS2. These genes normally repair DNA copying errors, and faulty versions can lead to cancers of the colon, uterus, ovaries, stomach, and other organs.

How was this study of Lynch syndrome cancer risks conducted?

Researchers followed 6,350 people with Lynch syndrome mutations for over 51,000 total years at centers in 18 countries. Participants had a first colonoscopy and at least one year of follow-up. Researchers counted cancers that developed during follow-up, calculated risks by gene, age, and gender, and compared findings between a validation group and an original group.

What did the study find about PMS2 carriers?

Among 407 PMS2 carriers, researchers did not demonstrate a significantly increased cancer risk. No colorectal, endometrial, ovarian, or urinary tract cancers were observed before age 50. At older ages, the risk increase was too small to be confidently distinguished from random variation. The limited number of observation years for older PMS2 carriers is a noted weakness.

What are the survival rates after Lynch-associated cancers?

For cancers diagnosed before age 65, 10-year survival was 88% for colon cancer, 89% for endometrial cancer, and 84% for ovarian cancer. Survival was poorer for pancreatic cancer at 29%, biliary tract at 42%, and brain at 15% for both 5 and 10 years. These figures reflect outcomes at expert centers.

Should surveillance differ depending on which Lynch syndrome gene I carry?

This study suggests cancer risks differ substantially by gene. MLH1 and MSH2 carriers typically need the most intensive monitoring since their risks are highest. MSH6 carriers should pay particular attention to gynecological screening. PMS2 carriers may have lower risks, but guidelines are still evolving. Always discuss your specific gene and surveillance plan with your doctor.

I have Lynch syndrome with a PMS2 mutation, but my doctor recommends the same intensive screening as for MLH1. Should I seek a second opinion about my surveillance plan?

Cancer risks in Lynch syndrome vary greatly by gene. In a large prospective study of 6,350 carriers, PMS2 mutations showed no significantly increased cancer risk before age 50 and only a nonsignificant increase later, while MLH1 and MSH2 carriers had much higher risks. MSH6 carriers, especially men, had lower colorectal cancer risk, but women had high endometrial cancer risk. Because guidelines may not fully reflect these gene-specific differences, a second opinion can help you confirm that your surveillance plan matches your specific genetic risk. Diagnostic Detectives Network provides independent expert second opinions.

Source Information

This patient-friendly article is based on peer-reviewed research published in Genetics in Medicine (2020), Volume 22, pages 15–25.

Original title: "Cancer risks by gene, age, and gender in 6350 carriers of pathogenic mismatch repair variants: findings from the Prospective Lynch Syndrome Database"

Authors: Mev Dominguez-Valentin, Julian R. Sampson, Toni T. Seppälä, and colleagues (a full list of authors and affiliations appears at the end of the original paper). The first three authors contributed equally.

DOI: https://doi.org/10.1038/s41436-019-0596-9

Key words: Lynch syndrome; MLH1; MSH2; MSH6; PMS2

Funding and ethics: The study adhered to the principles of the Declaration of Helsinki and was approved by the Oslo University Hospital ethical committee (ref. S-02030) and the Norwegian Data Inspectorate (ref. 2001/2988-2). All genetic testing was performed with informed consent according to local and national requirements.

Note: This patient-friendly article is based on peer-reviewed research and is intended for educational purposes. It does not constitute medical advice. Patients should discuss their individual risks and surveillance plans with their healthcare providers.