DNA methylation analysis in Kabuki syndrome: reclassification of germline KMT2D variants

Background

Kabuki syndrome (KS) is a rare multiple congenital anomaly/neurodevelopmental disorder caused by heterozygous inactivating variants or structural rearrangements in the KMT2D gene. Although KS is recognizable due to its distinctive facial features, diagnosis remains challenging due to its clinical variability. Additionally, somatic mosaic variants have been identified in KS, but the complete germline characteristics of these variants have not been fully determined.

DNA methylation (DNAm) analysis as a tool has been successfully used to classify variants in genes associated with various neurodevelopmental disorders, including KS. In this study, we applied KS-specific DNAm markers to classify 13 individuals carrying KMT2D variants and tested the ability of DNAm analysis to identify pathogenic variants in different degrees of mosaicism.

Article Information

This study was conducted by Marcello Niceta, Andrea Ciolfi, and a team of other experts. The researchers come from several renowned institutions, such as the Catholic University of the Sacred Heart in Italy, Copenhagen University Hospital in Denmark, and the Bambino Gesù Children’s Hospital in Rome. The article was published in the European Journal of Human Genetics, Volume 32, pages 819-826, 2024, with DOI: 10.1038/s41431-024-01597-9.

Research Process and Results

The research was conducted in several steps. First, DNAm markers with the best discriminatory power for KS were identified and further validated in another group of KS patients. Then, a trained machine learning model was used to classify KS patients and controls.

The study tested 13 individuals carrying KMT2D VUS, confirming 3 VUS as consistent with KS diagnosis while excluding 10 VUS from KS association. The research also provided evidence that DNAm analysis can identify pathogenic variants at different mosaic levels and determined 15% as the minimum threshold for DNAm analysis to serve as a diagnostic tool in KS mosaicism.

Research Significance

The scientific and practical value of this study lies primarily in providing a more accurate diagnostic method for KS, while also offering reference for methylation analysis of other neurodevelopmental disorders. The research also emphasizes the importance of correctly classifying VUS in clinical practice to develop more precise treatment plans for patients.

Research Highlights and Uniqueness

The highlight of this study is the use of KS-specific DNAm markers to reclassify VUS, which is recognized as a new advancement in the field of molecular diagnosis of KS. Additionally, the study confirmed the ability of DNAm analysis to identify pathogenic variants at different mosaic levels, a finding crucial for studying somatic mosaic variants and improving diagnostic accuracy for rare diseases.

Conclusion

By applying specific DNAm markers, we successfully distinguished cases from controls and reclassified VUS, which is of great significance for the diagnosis of KS and other hereditary neurodevelopmental disorders. The results indicate that DNAm analysis provides highly sensitive KS diagnosis but may have limitations in identifying low-percentage mosaic variants.