Identification and characterisation of genetic variation that modifies age at onset in Huntington’s disease

Abstract

Huntington’s disease (HD) is a progressive and ultimately fatal neurodegeneration caused by a CAG repeat expansion in the huntingtin gene (HTT). The length of the CAG repeat is strongly inversely correlated with disease onset, but there remains considerable onset variation that is unexplained, even between individuals with the same repeat length. This thesis details the investigation of genetic modifiers of HD onset using next-generation sequencing (NGS), with an emphasis on rare coding variant identification. Chapter 1 gives a general introduction. Chapter 2 details the experimental procedures used in this study. Chapter 3 explores several HD onset phenotypes in the Registry-HD study, derived using the clinician’s estimate of onset and the HD clinical characteristics questionnaire. An extreme HD onset cohort (N=500) is then selected using residual age at motor onset. Chapter 4 uses whole-exome sequencing to sequence the 500 HD patients selected in the previous chapter. I identified rare damaging variation in several DNA repair genes associated with altered disease onset, including FAN1, EXO1, MSH3, LIG1 and PMS1. Unbiased whole-exome burden and SKAT(-O) analyses identified NOP14 as an exome-wide significant gene. Investigation revealed NOP14 strongly tagged HTT allele structure, identifying it as a major modifier of disease onset. Chapter 5 confirms the HTT allele structures using an independent NGS method. HTT alleles possessing additional interruptions were associated with late disease onset; whereas alleles lacking interruptions were uniformly found in early onset individuals. I also detail three novel HTT alleles associated with extremely delayed onset and explore MiSeq-based instability measurements. In Chapter 6, I discuss the study generally. I give an overall model describing genetic factors that modify HD onset, and present my two-fated pathway model for somatic instability. I then highlight future studies and approaches in HD given what we have learned from this work. The results presented here have important implications for understanding the mechanisms underlying HD onset, underscoring DNA and DNA repair as critical components in HD