Genetic Mosaicism in the Embryo: An Invisible Cancer Threat?

Our Genetic Code Is Less Uniform Than We Think

The traditional view of genetics holds that all cells in our bodies have the same DNA sequence. However, research using next-generation sequencing technologies developed in recent years shows that this assumption is incomplete. The human body consists of groups of cells with slightly different genetic makeup that accumulate different mutations over time and throughout development. This biological patchwork is called “genetic mosaicism.”

Each cell division produces approximately 10 new mutations . A newborn carries an average of more than 120 mutations in each cell. Most mutations are harmless, but some can eventually lay the groundwork for serious diseases, including cancer.

What Is Genetic Mosaicism?

Mutations that arise early in embryonic development can spread to the tissues derived from the affected cell. This results in genetically distinct groups of cells within the same organism, a condition called “genetic mosaicism.” Just as mosaics in art form images from small, different stones, biological mosaics represent a whole made up of different cells.

A 3rd Mechanism After Environmental and Hereditary Factors: Mosaicism

The most common scenario in cancer development is the accumulation of DNA changes in cells throughout life, known as somatic mutations . These mutations arise through factors such as environmental exposures (smoking, obesity, alcohol, and certain viral infections such as HPV), aging, and cellular stress. However, this process may be accelerated from birth in some individuals, owing to hereditary (germline) mutations . Inherited mutations in tumor suppressor genes such as BRCA1/2, TP53, and APC predispose some individuals to cancer from early in life.

In recent years, a third category has attracted attention: mosaic mutations. These mutations are neither entirely hereditary (they are not present in all cells) nor conventional somatic mutations acquired later in life. Instead, they arise early in embryonic development and spread to all tissues derived from that cell. As a result, some of the individual's cells carry the mutation while others do not.

Mosaic mutations are particularly important for the following reasons:

• They may be clinically silent: Because the mutation is present only in some cells, signs of disease may appear late or diagnosis may be difficult.

• They are difficult to detect with tests: If the proportion of cells carrying the mutation is low (for example, <20%), conventional genetic tests may fail to detect the change.

• They can behave like inherited mutations: In particular, gonadal mosaic mutations (affecting reproductive cells) can be passed on to subsequent generations and cause recurrent cancer cases within a family.

• They can cause cancer: If a mosaic mutation affects, for example, TP53, tumor suppressor functions may be disabled in some cells. This increases the risk of uncontrolled proliferation in those cells.

For these reasons, mosaicismis emerging as a concept that was long overlooked in the genetic basis of cancer but could now fundamentally affect diagnosis and risk assessment.

What Does VAF (Variant Allele Frequency) Tell Us?

VAF (Variant Allele Frequency)indicates the proportion of cells carrying a particular mutation in the genetic material being examined, such as tumor tissue or blood. For example, a VAF of 10% means that the mutation is present in approximately 10% of cells in that tissue.

Genetic mosaicism is generally characterized by variant allele frequencies below 50% :

• Germline heterozygous: VAF ≈ 50%

• Mosaic mutation: VAF 5–40%. Mutations with low VAF therefore require careful analysis. Variants in noncoding regions require more complex interpretation of their biological effects.

Examples of Mosaicism Through Clinical Scenarios

Example 1: Genetic Test Is “Negative,” but the Clinical Picture Suggests Hereditary Risk

Scenario: The patient develops breast cancer at a young age . There is no strong family history, but factors such as age and tumor type, for example triple-negativedisease, suggest hereditary risk. A multigene panel reveals no significant mutation, including in BRCA1/2.

Possible explanation: This may be due to a mosaic mutation that conventional genetic tests cannot detect.

• If the mutation arose during embryonic development, only some of the individual's cells, such as those in breast tissue, may carry it. However, because genetic testing is usually performed on blood, the mutation may be “invisible” during testing.

• In particular, if the variant allele frequency (VAF) is low, for example below 10%, conventional tests may miss it.

• In these patients, detecting a mutation in tumor tissue but not in blood, or finding suspicious low-VAF mutations in cfDNA (circulating free DNA), may indicate mosaicism.

Clinically important point: Even if their genetic test result is “negative,” these patients should be considered at risk. Reassessment using advanced techniques, such as ultra-deep sequencing, tumor DNA analysis, or samples of other tissues from the individual, may also be necessary.

Example 2: Strong Family History and Breast Cancer, but a Negative Genetic Test

Question: The patient developed breast cancer at a young age and has a family history of multiple cancers. However, a multigene panel reveals no significant mutation. Should mosaicism be considered?

Answer: Yes, mosaicism may be a possible explanation.

• The patient may carry a germline mutation as a mosaic . In other words, the mutation is present in some cell lineages, such as breast tissue or the germline, but may not have been detected by genetic testing because the VAF in peripheral blood is very low.

• In such cases of a “negative test but clinically high risk,” additional testing of epithelial tissues, such as tumor tissue, ultra-deep sequencing or cfDNA analysis may make it possible to detect mosaicism.

• Other considerations include an inadequate testing panel, for example one that does not screen for epigenetic changes, and variants reported as “VUS.”

Conclusion: In this situation, the possibility of mosaic BRCA1/2, TP53, or other predisposing gene mutations is strong, and mosaicism may explain the clinical picture.

Example 3: The Patient Carries a BRCA1 Mutation, but There Is No Family History of Cancer

Question: Genetic testing detects a BRCA1 mutation, but there is no family history of breast or ovarian cancer. Is this mutation inherited? Could it be mosaicism?

Answer: Yes, this too may indicate mosaicism.

• This mutation may be de novo , meaning that it may have arisen after the patient's zygote formed and affected some germline and somatic cells.

• Alternatively, one of the individual's parents may have gonadal mosaicism : In this case, the mutation is detectable in the individual's blood but not in the parents when the family is screened through blood testing, because it arose only in the parent's gonadal cells during early embryonic development.

• If the mutation's VAF, for example 20–30%, is below the usual level for heterozygosity, somatic mosaicism becomes more likely.

• The absence of an inherited pattern in the family may suggest that this mutation is an individual mosaic event rather than a familial one .

Conclusion: Although a BRCA1 mutation detected in the absence of a family history may resemble a conventional inherited mutation, it may represent a mosaic event or a de novo mutation .

Summary for Clinical Practice:

How Common Is Mosaicism in Cancer?

A Study Reporting a Low Frequency

In a study published in 2022 in Cancer Discovery , researchers from Memorial Sloan Kettering Cancer Center examined more than 35000 patients with cancer using MSK-IMPACT, an FDA-approved broad-panel genetic test. Pathological mosaic mutations arising during embryonic development were detected in only 36 patients (0.1%). The genes most frequently affected included TP53 and RB1 . This low rate suggests that mosaic mutations are rare or that current tests have limited ability to detect them.

A Study Reporting a High Frequency

Published in 2024 in the International Journal of Colorectal Disease , this systematic review and meta-analysis assessed the frequency and clinical significance of genetic mosaicism in colorectal cancer (CRC) and polyposis syndromes. Through a comprehensive search of PubMed, Scopus, and Web of Science, the researchers identified 27 eligible studies and analyzed their data.

In this analysis involving a total of 2272 patients, somatic mosaicism was detected in 108 patients. The overall frequency of mosaicism in this disease group was calculated as 8.79% (95% confidence interval: 5.1% – 14.7%). These findings suggest that genetic mosaicism may be more common in this disease group than previously thought.

Subgroup analyses highlighted higher rates of mosaicism in certain genes.

• APC had a mosaicism rate of 13.43%,
• MLH1 of 2.75%, and
• MSH2 of 9.69%.

These rates suggest that these genes may be particularly associated with mosaic mutations.

The study concluded that somatic mosaicism is an important contributor to genetic diversity in colorectal cancer and polyposis syndromes and warrants greater attention in clinical practice. In particular, in patients whose diagnosis cannot be established through conventional germline tests , evaluating mosaicism may directly affect diagnosis and treatment. The authors therefore recommended including mosaicism screening in genetic testing algorithms.

Other Studies Highlighting the Clinical Significance of Mosaicism

1. TP53 Mosaic Mutations and Bilateral Breast Cancer – A Chinese Study (2024)

In August 2024, a study published in Breast Cancer Research and Treatment assessed

the frequency and phenotypic characteristics of TP53 mutations in 420 Chinese patients with breast cancer. Arguing that current genetic testing criteria exclude some patients, the researchers proposed a new criterion: patients diagnosed with synchronous or metachronous bilateral breast cancer should be assessed for TP53 mutations.

The results were noteworthy:

• In 1.4% of patients, a pathogenic or likely pathogenic TP53 germline mutation was detected.

• TP53 mutation carriers: 33.3% developed cancer at a young age, (before age 30).

• In the same group of carriers, 33.3% had bilateral breast cancer .

• Pedigree analyses did not identify these mutations in the parents, suggesting that the mutations could be de novo or mosaic .

The researchers emphasized that these findings were inconsistent with current genetic testing protocols and that testing criteria should be updated .

2. Interpreting TP53 Mutations: Mosaicism, Clonal Hematopoiesis, and Ambiguous Findings (2023)

Published in 2024 in the Journal of Genetic Counseling , this study discusses how to interpret TP53 findings detected by next-generation sequencing that do not match the clinical picture, through a case series of eight patients. Although these variants produced presentations resembling classic Li-Fraumeni syndrome (LFS) , most patients' family or personal histories did not match LFS.

The origins of such TP53 variants were categorized as follows:

• Inherited mutations with low penetrance

• Mosaic mutations (the mutation is present in some groups of cells but absent in others)

• Clonal hematopoiesis (CHIP) -related mutations

Using case examples, the study illustrated the difficulty of interpreting these findings and the need for a multidisciplinary approach + bioinformatics support . It also noted that VAF (Variant Allele Frequency) values below 50% were interpreted as supporting mosaicism in some cases.

3. Mosaic Chromosomal Alterations and Cancer Risk – UK Biobank Data (2023)

In 2023, a large-scale study published in Nature Geneticsexamined blood samples from approximately 500000 individuals in the UK Biobank database. The aim was to establish the frequency, mutation rate, and effects on cellular selection of mosaic chromosomal alterations (mCAs), namely chromosome gains, losses, and copy-neutral loss of heterozygosity.

Key findings:

• mCAs generally have low mutation rates but confer moderate to substantial cellular advantages (fitness effects) .

• Compared with single-nucleotide changes, mCAs are 10 times less common, although some mCAs can become dominant.

• The most striking finding: Losses of the X and Y chromosomesoccur, compared with autosomal mCAs, approximately 1000 times more frequently .

• Some mCAs increase at a constant rate with age, whereas others expand at variable rates depending on genetic predisposition or environmental factors.

The study argues that mCAs may arise before cancer develops and could be biological indicators that should be considered in cancer risk scoring .

Implications for Clinical Practice

• Diagnosis: Individuals with “negative” conventional test results may have mosaicism.

• Treatment: Mosaic mutations in genes such as BRCA2 or TP53 may influence decisions about targeted therapy.

• Screening and Counseling: These individuals' family members may also be carriers at a low level of risk.

A Brief Summary of the Key Points

• Genetic mosaicism is the presence of different genetic makeup in different cells of an individual.

• An average of 10 mutations occur with each cell division; each cell in a newborn may carry an average of more than 120 mutations.

• Mosaic mutations may arise during embryonic development, spread to different body tissues, and escape conventional genetic tests.

• In a study published by AACR, only 36 (0.1%) mosaic mutations were detected in 35000 patients with cancer.

• A 2023 meta-analysis reported a mosaic mutation rate of 8.79%, with rates of APC 13.43% in this gene, MLH12.75% in this gene, and MSH29.69% in this gene.

• TP53 mosaic mutations were detected in 1.4% of Chinese women with bilateral breast cancer. Among these patients, 33.3% developed cancer before age 30 (Breast Cancer Res Treat, 2024).

• TP53 variants may originate from clonal hematopoiesis or mosaicism and may be inconsistent with the clinical picture (J Genet Couns, 2024).

• An analysis of approximately 500000 individuals in the UK Biobank reported that mosaic chromosomal alterations increase with age and, in some cases, occur 1000 times more frequently than autosomal mCAs (Nature Genetics, 2023).

• Mosaic mutations generally have a variant allele frequency (VAF) of 5–40% and therefore require sensitive analytical methods and careful interpretation.

• Mosaicism can directly affect diagnosis, treatment, and screening decisions, particularly in individuals with “negative” genetic test results but high clinical risk.

Final Thoughts

Genetic mosaicism marks a new era in cancer genetics. Cases that appear “negative” with conventional methods may be explained by mosaicism. It is therefore no longer possible to overlook mosaicism in diagnosis, treatment, and risk assessment.