Long-read genomic analyses to elucidate hidden structural variations associated with MECP2 duplication syndrome

Area of Science:

• Genomics
• Molecular Biology
• Human Genetics

Background:

• MECP2 duplication syndrome is caused by duplication of the MECP2 gene.
• Short-read sequencing struggles to resolve complex structural variations in repetitive genomic regions like Xq28.
• Accurate delineation of genomic architecture is crucial for understanding MECP2 duplication syndrome.

Purpose of the Study:

• To investigate hidden structural variations in MECP2 duplication syndrome.
• To precisely map breakpoints within the Xq28 region encompassing the MECP2 gene.
• To evaluate the utility of optical genome mapping and long-read nanopore sequencing for complex structural variant detection.

Main Methods:

• Optical genome mapping was employed to detect structural variations.
• Targeted long-read nanopore sequencing was utilized for high-resolution analysis.
• These methods were combined to identify and characterize breakpoints in affected individuals.

Main Results:

• Four individuals with MECP2 duplication syndrome were analyzed, revealing 14 breakpoints in the Xq28 region.
• The integrated approach precisely identified most breakpoints, with challenges in resolving inversions within highly repetitive sequences.
• Long nanopore reads successfully spanned difficult low-copy repeats, GC-rich segments, and interspersed nuclear elements, enhancing breakpoint accuracy.

Conclusions:

• Combining optical genome mapping and long-read sequencing offers a powerful approach for resolving complex genomic architectures.
• This study provides the most precise delineation to date of structural variants in MECP2 duplication syndrome.
• These findings advance the understanding of the genomic basis of MECP2 duplication syndrome and highlight advanced sequencing capabilities.