Whole exome sequencing (WES) does not reliably detect Fragile X syndrome for the following reasons:

• Fragile X Syndrome Is Caused by a Repeat Expansion:
  • Fragile X syndrome is typically caused by a CGG trinucleotide repeat expansion in the 5' untranslated region of the FMR1 gene on the X chromosome.
  • WES focuses on capturing and sequencing the protein-coding regions (exons) of the genome and does not effectively sequence repetitive DNA regions like trinucleotide repeats.
• Limitations in Detecting Repeats:
  • The short-read sequencing technology commonly used for WES has difficulty accurately mapping and sequencing highly repetitive regions, making it unsuitable for detecting repeat expansions.
  • Special techniques, such as Southern blotting or repeat-primed PCR, are typically required to measure the number of CGG repeats in the FMR1 gene.
• Targeted Enrichment Bias:
  • WES enrichment protocols are designed to capture exonic sequences efficiently but often exclude or underrepresent non-coding regions, including the promoter and 5' untranslated regions where the CGG repeat expansion occurs.
• Epigenetic Modifications:
  • Fragile X syndrome also involves epigenetic changes, such as hypermethylation of the FMR1 gene.
  • These modifications silence the gene and contribute to the condition, but they are not detectable using WES, which focuses solely on DNA sequence.
• To diagnose Fragile X syndrome, specific tests such as FMR1 DNA analysis (e.g., Southern blot, repeat-primed PCR) are required, as they directly assess the repeat expansion and methylation status of the FMR1 gene