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Impact of Low-Burden TP53 Mutations in the Management of CLL

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Frontiers in Oncology
February 8, 2022:


  • Chronic Lymphocytic Leukemia (CLL) is a heterogeneous illness with a variable clinical course primarily determined by the disease’s underlying genetics, which is not the same for each affected individual. However, one gene that is highly important in predicting the natural history of CLL and response to chemoimmunotherapy is TP53, which resides on chromosome 17. TP53 is a beneficial tumor suppressor gene that encodes the p53 protein known as the “guardian of the genome.” When DNA damage occurs, this protein can either stop a cell’s normal cell cycle from allowing for the repair of damaged DNA or instead cause the cell to die, a process known as apoptosis, thus preventing the replication of genetic anomalies that could lead to malignancy.
  • The loss of functional TP53 through either deletion of the short arm of chromosome 17, known as del(17p), or from a mutation of the gene rendering that gene ineffective will result in more aggressive CLL and disease that is resistant to the chemotherapeutic regimen of Fludarabine, Cyclophosphamide, Rituximab (FCR) which was the first successful therapy for CLL and many years was the standard of care. Because of that resistance to FCR, it is now known that patients with a TP53 mutation should be treated with B-cell receptor inhibitors (BCRi) and/or BCL2 inhibitors (BCL2i).

Definition of a Low-Burden TP53 Mutation or Minor Clone

  • It is important to understand that an individual with CLL may have more than one type of malignant cell, known as a clonal population. Instead of just one significant population, there may also be smaller numbers of additional populations of malignant cells known as subclonal or minor populations with a different genetic makeup than the larger clonal cell population.  
  • Currently, the threshold for reporting a minor TP53 defective clonal cell population is 10%. However, with the advancement in detection by next-generation sequencing technology (NGS), populations of subclonal TP53 mutated cells can now be detected at a level of 3 mutant cells per 1,000 wild cells, also known as a 0.3% mutant allele fraction detection level or variant allele frequency (VAF). This paper reviews the justification to set the threshold for reporting minor populations of TP53 mutated cells to a lower level than the current 10% threshold to provide clinical and prognostic treatment guidance better.

Clonal Evolution of Low-Burden TP53 Mutation After Chemotherapy

  • TP53 mutations are found in 10% of treatment naïve patients and about 40% of fludarabine-refractory-CLL. The TP53 mutation confers a survival advantage to the CLL cells when under treatment with a fludarabine-based therapy. Studies have shown that low-level clones before fludarabine therapy have increased following chemotherapy resulting in clonal expansion, which may lead to persistent disease and/or relapse. This response of TP53 mutated cells to chemotherapy demonstrates that the low allele frequency mutations of <10% are real with clinical import and are not background artifacts inadvertently found by the newer technology. Therefore, justifying a change in the threshold of detection to a lower level than the currently accepted value of 10%.
  • TP53 variant allele frequency is stable in many patients, particularly those with mutated IGHV and indolent disease, when not treated with chemotherapy. However, over time, a natural clonal evolution of CLL and TP53 mutations may arise spontaneously without fludarabine treatment. Therefore, TP53 mutation testing should be done with NGS technology periodically at follow-up and before a new line of treatment is initiated.

Impact of Targeted Agents on Low-Burden TP53 Mutations

  • Targeted treatments with BCRi and BCL2i inhibitors are now being used for patients with TP53 mutations. Research has shown VAF stability of TP53 mutations following second-line treatment with targeted therapy in patients with persistent disease. However, the fact that cells are still present for testing means that there has been residual disease and not complete eradication.  
  • Research has also shown that in some patients with progressive disease, the TP53 clone has changed from a major to minor clone, but a BTK mutation or BCL-2 mutation has developed.  
  • Data from an additional study looking at targeted therapy in treatment naïve and relapsed/refractory patients with a BTKi found complex TP53 dynamics with most mutations decreasing or becoming undetectable. However, some remained stable, and a small number increased. However, after two years of follow-up, the overall stability of low-burden TP53 mutations was observed. 
  • These results are promising but additional research isolated to the front line setting to evaluate the effect of targeted therapy on TP53 clonal populations of < 10% is still needed.

Low- and High-Burden TP53 Mutations Have the Same Unfavorable Prognostic Impact

  • Studies using a threshold of 10-12% for detecting minor clones have been done to look at the effect of low- vs. high-burden-TP53 mutated clones on overall survival (OS). A decrease in OS has been found in untreated individuals with TP53 mutated clones regardless of whether they are low- or high-burden clones compared to those with wild-type or unmutated TP53.
  • The CLL-International Prognostic Index (CLL-IPI) combines five parameters of age, clinical stage, TP53 status based on the standard VAF of high-burden clones, IGHV mutational status, serum b2-microglobulin to predict survival, and time to first treatment in CLL patients. When the CLL-IPI was recalculated incorporating both low- and high-burden TP53mutations, there was greater accuracy in detecting high-risk or more aggressive disease.  
  • Studies have shown a decreased OS in chemoimmunotherapy patients harboring either low- or high-burden TP53 mutations.   
  • There is limited data available on the impact of targeted therapy on OS in the presence of minor TP53 clones though available research has shown that OS response to targeted therapy with BCRi and BCL2i did not differ between patients with wild-type TP53 or those with TP53 mutations regardless of the VAF.  

Ongoing Research and the Future

  • The European Research Initiative on CLL (ERIC) is currently conducting a multicenter study with the following three goals: To look at the standardization of NGS testing methodologies among laboratories performing TP53 mutations with a detection limit of £ 1% VAF; to assess the predictive impact of TP53 mutations with a low-burden VAF in patients entering first-line therapy; and to re-evaluate the threshold reporting level for of TP53 mutations in patients with CLL.
  • Pending the outcome of ongoing research, it may be best to adjust the VAF reporting threshold of TP53 mutations, which may have important implications for managing CLL patients.

This article reminds us of the ongoing importance of the need for CLL Society’s campaign to Test Before Treat™.

To learn more about TP53, see:

To read the full original review article from Frontiers in Oncology, click on Impact of Low-Burden TP53 Mutations in the Management of CLL.

We share in this journey together.

Kim Davidson, MD

Kim Davidson received her Doctor of Medicine degree from the Medical College of Virginia. Following training in Obstetrics and Gynecology and Family Medicine, she provided medical care and taught for over thirty years until recently retiring. She is a CLL patient and shares this journey with all of you.