New XCI-ONT method could revolutionize clinical analysis

A team of SciLifeLab researchers has developed a new method called XCI-ONT that helps us understand a specific genetic phenomenon called X-chromosome inactivation (XCI). XCI is important for diagnosing certain genetic traits, but it’s difficult to do accurately using current methods. XCI-ONT will be important for both clinical diagnosis and research related to X-linked genetic traits.

XCI-ONT is a novel approach that combines Cas9 enrichment and long-read sequencing using Oxford nanopore technologies sequencing to investigate XCI without the need for DNA amplification. XCI-ONT allows us to study XCI in two specific genes: the human androgen receptor gene (AR) and the human X-linked retinitis pigmentosa 2 gene (RP2).

“This method shows great potential to be used in the clinic for improving diagnostics of X-linked traits and especially diagnostics of females manifesting X-linked disorders,” says Josefin Johansson, first author of the paper, PhD student in Bondeson research group at Uppsala University at the time, now a senior researcher at AstraZeneca.

XCI-ONT looks at the methylation of DNA at 116 specific sites inARand 58 specific sites in RP2 and can directly tell us the parental origin of the X-chromosomes. The study shows that XCI-ONT is more useful than the traditional golden standard PCR-based method, which only examines one or two specific sites in these genes. This is especially true when the XCI pattern is not perfectly balanced and when quantification of the XCI pattern is needed. XCI-ONT provides a more rigorous way to measure XCI.

“This research introduces a new, broadly applicable method for studying X-chromosome inactivation in DNA. XCI-ONT has important implications for both clinical diagnosis and research related to X-linked genetic traits,” says Associate Professor Maria Wilbe, last author of the paper.

The potential for this method is far-reaching, and it could even replace traditional analyses.

“Long-read sequencing has the potential to replace many traditional analyses in the clinical setting, increasing cost-effectiveness. In the long run, this method has the potential to entirely replace short-read sequencing and provide a comprehensive analysis that can address all genetic questions related to hereditary diseases, including methylation as demonstrated here,” says Marie-Louise Bondeson, Professor and Clinical Molecular Geneticist at Clinical Genetics, Uppsala University Hospital and active at the Clinical genomics facility in Uppsala.


Last updated: 2023-10-25

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