New insights into intermediate CAG repeats: Mapping the expansion continuum

Why do some people with intermediate CAG repeats, a genetic “gray zone” in Huntington’s disease, develop neurological symptoms while others do not? This article covers a recent study that tackled this question by looking for somatic expansion, which is a tiny changes in DNA, in individuals across various CAG repeat sizes. Using ultra-sensitive research technology on blood samples, the team discovered that intermediate CAG repeats do experience expansion, but the changes are typically very small. While this confirms that intermediate repeats are part of a continuous spectrum of genetic instability, the research found no clear link between this expansion in blood and the presence of symptoms. This article covers what this new research reveals about the genetic landscape of HD.

The HD Gray Zone

Huntington’s disease (HD) develops when people have a repetition of the genetic letters C-A-G in their huntingtin gene. People with 40 or more repeats will develop the disease during their lifetime, while people with 36-39 repeats have what scientists call “reduced penetrance”, meaning some develop symptoms while others don’t. 

Repeat lengths of 27-35 are called “intermediate alleles”. “Intermediate” meaning the repeat falls between the range that will and won’t cause diseases, and “allele” being the copy of the huntingtin gene someone inherited from their mom or dad. While these repeat lengths are not considered disease-causing, they present uncertainty for families. These intermediate alleles can expand when passed from parent to child, potentially reaching disease-causing lengths in the next generation. Also, some people with intermediate CAG numbers develop neurological symptoms despite being below the traditional HD threshold. 

This situation places intermediate CAG lengths in a controversial “gray zone,” raising fundamental questions: What does this mean for the future? Do these DNA sequences change over time within a person’s lifetime? Could such changes explain why some intermediate allele carriers develop symptoms while others don’t?

The Research Question

Scientists have long known that DNA can change over a person’s lifetime, through various processes. Some are as simple as mutations caused by damage from sun exposure, and others are more complicated and less understood. A recent hot topic in HD research involving DNA changes is a process called “somatic expansion.” 

Somatic expansion is a biological process where CAG repeats can expand in different cells of the body over time in people with the gene for HD. Interestingly, these expansions tend to be largest in brain cell types that are most vulnerable to death in HD. Many researchers think these increasing CAG expansions may contribute to when and how symptoms develop.

A research team led by Dr. Maria Ramos-Arroyo tested the idea that people with intermediate CAG repeats might also experience somatic expansion, and that this could explain why some intermediate CAG repeat carriers develop neurological symptoms while others don’t. To test this idea, they used ultra-sensitive DNA sequencing to study 355 people across the entire CAG spectrum, including 191 individuals with intermediate repeat lengths.

The Study Results

Ultra-sensitive techniques reveal small changes

The team used a very sensitive test, called MiSeq (pronounced “my seek”) sequencing, on blood samples from people in this study. MiSeq is a technique sensitive enough to detect DNA changes that routine genetic testing would miss. From this, the team found that people with intermediate CAG repeats do experience somatic expansion. However, these changes are quite small. When expansion occurs, it is typically limited to just one or two additional CAG repeats in a small fraction of DNA molecules.

Inherited length matters more than time

The researchers also found an important pattern in what influences these expansions. The length of inherited CAG repeat size has a much stronger impact on somatic expansion than age does. For intermediate CAG repeats, each additional CAG repeat in the inherited sequence had about 40 times more impact on expansion than each additional year of age. That’s a huge difference!

A continuous pattern emerges

The results remind us that CAG length represents a continuous spectrum rather than distinct categories. The data revealed that somatic expansion behavior follows a clear continuum. People with longer inherited CAG repeats showed progressively more expansion, with intermediate CAG lengths fitting naturally between normal and disease-causing lengths. This confirms that intermediate length repeats are not a separate biological category, but part of this larger spectrum.

Brain shows higher expansion rates than blood

When researchers examined brain tissue from one person with 33 CAG repeats who had developed symptoms, they found that brain regions showed higher expansion rates than blood, with the movement-related area of the brain (putamen) showing the most change. This matches patterns seen in people with HD, but it’s important to remember that this analysis was limited to a single individual.

No clear link to symptoms

Importantly, this study found no clear link between somatic expansion and symptoms in intermediate CAG repeat carriers. The researchers studied 78 people with intermediate CAG lengths that had neurological symptoms (85% had movement, 27% had cognitive, and 29% had behavioral symptoms) but there didn’t seem to be a difference in their blood expansion levels compared to symptom-free carriers. This suggests that somatic expansion alone doesn’t explain why these people had symptoms of HD while others with similar intermediate CAG lengths did not.

What Do These Results Mean?

For carriers of intermediate repeat lengths and their families, these findings do not change the current state of clinical practice or predictive testing. Because there isn’t a clear link between the level of somatic expansion in blood and the presence of neurological symptoms, this means that measuring CAG expansions for people with intermediate lengths cannot be used to predict an individual’s future health. Furthermore, because the genetic changes involving somatic expansion are detectable only with advanced research methods, they would not be identified by the standard genetic tests available to families.

From a scientific perspective, the confirmation of a continuous spectrum of CAG lengths is a significant step forward. It shows that intermediate CAG lengths follow the same genetic processes as HD-causing repeat lengths, just at much lower levels. 

However, there are still hurdles in using these findings for HD families to help them know if intermediate length carriers will develop disease symptoms. The design of this study captures only a snapshot in time rather than following individuals over years, limiting our understanding of how these changes develop. Additionally, the difficulty of detecting these subtle expansions limits the scale of studies that can be conducted. 

But the added knowledge that CAG repeats, even in the intermediate range, 1) exist on a continuum, 2) also experience repeat expansions, and 3) are sometimes associated with symptoms, give researchers a better understanding of HD. With that information, scientists can work toward advancements that will eventually give us a better understanding of what influences symptom development. 

Future Research Directions

Researchers can build on these findings and ask questions about who will go on to develop symptoms and why. To do that, the scientists need to consider the research hurdles identified in this study. 

The path forward will likely require a combination of more detailed tracking of people over time and larger-scale studies. Following individuals over many years would allow researchers to track both genetic changes and symptom progression within the same people as they age. Expanding to larger numbers of people would also be valuable, though this remains challenging given the specific nature of the genetic sequencing tests used in this study. More accessible biomarkers could facilitate larger studies.

This study provides a more detailed map of the genetic landscape of the huntingtin gene, confirming that even people with intermediate CAG repeat lengths are part of a continuum of somatic instability. While it does not establish a link between this instability and symptoms, it clearly defines the challenges and priorities for the next research steps that could help scientists understand who will or won’t go on to develop symptoms.

Summary

• Somatic CAG expansion occurs across a continuum: Intermediate CAG lengths show small but detectable expansion that fits the same patterns we see in full HD expansions.
• There doesn’t appear to be a clear relationship between expansion and symptoms: Within the scope of this study, the level of somatic expansion in blood did not clearly explain why some people with intermediate CAG repeat lengths develop symptoms while others don’t.
• More research is needed: Larger studies that track people over time will be essential to better understand symptom development in people with intermediate CAG repeat lengths, potentially improved by more accessible biomarkers.

Learn More

Original research article, “Somatic CAG repeat instability in intermediate alleles of the HTT gene and its potential association with a clinical phenotype” (open access).