Massively parallel next generation sequencing to investigate the cis- and trans-acting genetic modifiers of somatic instability in Huntington’s disease

Alshammari, Asma Mubarak (2018) Massively parallel next generation sequencing to investigate the cis- and trans-acting genetic modifiers of somatic instability in Huntington’s disease. PhD thesis, University of Glasgow.

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Huntington disease (HD) is an extremely variable inherited neurodegenerative disorder caused by expansion of an unstable CAG trinucleotide repeat in the huntingtin gene (HTT). Somatic instability in HD exhibits an age-dependent, expansion-biased and tissue-specific pattern, and the highest level of somatic instability is found in tissues that are most susceptible to the disease pathology. Therefore, the aim of this project was to test the hypothesis that somatic instability of the HD CAG repeat plays a major role in disease pathology by quantifying somatic instability in the number of CAG repeats by next generation sequencing (NGS) technology in buccal cell DNA.

We developed a method to sequence and genotype HTT alleles from blood and buccal swab DNA of the Scottish and Venezuelan populations respectively. A total of 210 individuals from the Scottish general population and 742 HD patients and unaffected individuals from the Venezuelan HD cohort were sequenced on the MiSeq platform. We established that it was possible to sequence and genotype the CAG repeats, the polymorphic CCG repeat and the flanking sequences. Our data highlight the utility of NGS technology as an approach to genotype HTT alleles, detect sequence variants and quantify somatic instability of the CAG repeat. Our data emphasise that the somatic instability in HD is age-dependent and expansion-biased, also could be a major factor in disease progression, and could be a potential therapeutic target in HD.

We also investigated the possibility that there are trans-acting modifier factors involved in determining the degree of somatic instability in HD patients. We genotyped polymorphisms in candidate mismatch repair (MMR) genes and examined their effect, if any, on the residual variation of somatic instability. Individuals carrying the minor allele of rs3512 in FAN1 have a higher level of somatic instability than average, suggesting that some of the variations in HD somatic instability could be accounted for by genetic variation in the DNA mismatch repair pathway. The search for modifier genes might have consequences in understanding the pathological process in HD, and may therefore provide therapeutic targets for future investigations.

Item Type: Thesis (PhD)
Qualification Level: Doctoral
Keywords: Huntington's disease, next generation sequencing, MiSeq, triplet repeat, microsatelite.
Subjects: Q Science > QH Natural history > QH426 Genetics
Colleges/Schools: College of Medical Veterinary and Life Sciences > Institute of Molecular Cell and Systems Biology
Supervisor's Name: Monckton, Professor Darren G. and Hamilton, Dr. Graham
Date of Award: 2018
Depositing User: Asma Mubarak Alshammari
Unique ID: glathesis:2018-30752
Copyright: Copyright of this thesis is held by the author.
Date Deposited: 28 Aug 2018 12:57
Last Modified: 02 Sep 2021 08:37
Thesis DOI: 10.5525/gla.thesis.30752

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