From the Guidelines
Microarray technology is not effective in detecting TSC1 and TSC2 gene mutations, and next-generation sequencing (NGS) or targeted gene sequencing is recommended for comprehensive detection of TSC-causing mutations. Chromosomal microarray analysis (CMA) is primarily designed to identify copy number variations (deletions or duplications) across the genome, but it cannot reliably detect small point mutations, insertions, or deletions that commonly occur in TSC1 and TSC2 genes in tuberous sclerosis complex (TSC) 1. For accurate diagnosis of tuberous sclerosis, a combination of clinical evaluation, imaging studies, and molecular genetic testing specifically targeting these genes is necessary. The limitation of microarray technology in detecting TSC1 and TSC2 mutations exists because most pathogenic variants in these genes are small-scale mutations that fall below the resolution threshold of standard microarray platforms 1.
Some key points to consider:
- Most pathogenic variants in TSC1 and TSC2 are small-scale mutations, including point mutations, insertions, and deletions 1
- Microarray technology can detect large deletions involving these genes, but would miss approximately 70-80% of disease-causing mutations in TSC patients 1
- Next-generation sequencing (NGS) or targeted gene sequencing can identify the full spectrum of variants, including single nucleotide changes and small indels 1
- Clinical evaluation, imaging studies, and molecular genetic testing specifically targeting TSC1 and TSC2 genes are necessary for accurate diagnosis of tuberous sclerosis 1
It is essential to note that the most recent and highest-quality study, published in 2024, supports the use of NGS or targeted gene sequencing for detecting TSC1 and TSC2 mutations 1. This study highlights the importance of accurate diagnosis and the limitations of microarray technology in detecting these mutations. Therefore, NGS or targeted gene sequencing is the recommended approach for detecting TSC1 and TSC2 mutations.
From the Research
Microarray Detection of TSC1 and TSC2 Gene Mutations
- The microarray can detect TSC1 and TSC2 gene mutations using various methods such as multiple ligation-dependent probe amplification (MLPA) and next-generation sequencing (NGS) 2, 3, 4, 5, 6.
- Studies have shown that a combination of MLPA and NGS can provide a simplified strategy and reasonably high detection rate for TSC1/TSC2 mutations 2.
- Targeted NGS of the TSC1 and TSC2 loci is a suitable method to increase the yield of mutations identified in the TSC patient population 3.
- The use of NGS has also enabled the identification of mosaic and intronic mutations, which are common in TSC patients 5.
- Quick genetic screening using targeted NGS has been shown to be less cost, labor, and time consuming compared with Sanger sequencing 6.
Detection Rates and Methods
- A study using MLPA and NGS detected TSC1 pathogenic or likely pathogenic mutations in 18% of patients and TSC2 mutations in 62% of patients 2.
- Another study using targeted NGS identified pathogenic mutations in 3 out of 7 individuals with definite TSC who had no TSC1 or TSC2 mutations identified using conventional screening methods 3.
- A study using DGGE, MLPA, and long-range PCR sequencing identified pathogenic mutations in 78% of patients 4.
- A study using NGS identified mutations in 85% of TSC subjects who were previously found to have no mutation identified by conventional testing 5.