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Characterising the dynamics of repeat expansion in Huntington’s disease
Huntington’s disease (HD) is an autosomal dominant neurodegeneration caused by an expanded CAG repeat in HTT. It generally has onset in mid-life, progresses inexorably and has no available disease-modifying treatments. While it is known that the number of CAG repeats explains ~50% of the variation in age-at-onset, other genes, particularly those in the DNA damage response networks, also modulate age-at-onset. It is likely that this is mediated through expansion of the repeat in somatic cells. Recent work conducted here suggests that the somatic expansion is driven by the exact sequence of the repeat and variants in the DNA damage response. To build a picture of repeat expansion dynamics, which would complement our existing exome sequence data, we would like to sequence and determine the epigenetic status of the HTT locus in the lymphocytes and lymphoblastoid cell lines of a cohort of HD subjects at the extremes of age of onset. Well-established sequencing technologies are unable to sequence through the repeat region. In contrast, third-generation sequencing technologies produce reads which are long enough to span the entire repeat region. We intend to sequence and quantify the transcripts of the HTT locus across our cohort, to see how HTT CAG repeat sequence variants and loss of function or predicted damaging changes in the DNA damage response network affect HTT DNA sequence, and to examine how methylation and transcript production are altered by this. Because third-generation sequencing technologies are capable of sequencing long, unamplified nucleic acids and can determine base modifications, we believe they are well suited to this task. Characterising how such variation affects expansion in pluripotent stem cell models and brain-tissue will enable further insight into somatic expansion in the most susceptible cell-types in HD. Ultimately single cell sequence data is desirable in order to track these variations on a cell-by-cell basis. This should allow us to build a much clearer picture of repeat expansion dynamics and determine whether and how they underpin somatic expansion and HD pathogenesis.