ESR6: Long-read sequencing of the ABCA4 locus
Partner
University of Leeds, United Kingdom (medhealth.leeds.ac.uk/info/311/ophthalmology_and_neuroscience) Supervisor Dr. Carmel Toomes |
Ben McClinton
I am originally from Dublin, Ireland and completed my bachelor’s degree in Genetics at Trinity College Dublin. After completing my bachelor’s, I was fortunate enough to have the opportunity to undertake a PhD project as part of the StarT Network at the University of Leeds. During my time in Leeds, I worked as part of the Vision Research Group and published three papers exploring the genetics of ABCA4 related disease and other retinal disorders (DOI: 10.3390/genes14010191, DOI: 10.1002/mgg3.2164, DOI: 10.1016/j.labinv.2023.100160). The StarT network was a life changing opportunity for me to develop my skills as a scientist, collaborate with the leading researchers in the field and to take part in the latest research in inherited retinal disease. I obtained my PhD in August of 2023 and am currently working as an Associate Medical Writer with nspm in Zurich, Switzerland." |
Abstract
The establishment and optimisation of novel enrichment and sequencing strategies are necessary to detect missing heritability of ABCA4. Technologies which enable allelic phasing of identified genetic variants are of paramount importance in the absence of additional family DNA, particularly when assessing cis-acting modifier alleles. ESR6 will design and optimise a CRISPR-Cas9 mediated enrichment method for the entire ABCA4 gene and surrounding DNA for use in long-read sequencing on a PacBio Sequel. In addition, ESR6 will employ Illumina TruSeq synthetic long-read phased sequencing. These approaches will be applied to 50 mono-allelic STGD1 cases. The data generated by ESR6 will be integrated with the smMIPs, TLA and HaloPlex data generated by ESR5 and ESR7. ESR6 will interrogate this data set, along with cases and controls from the UK 100,000 Genome data, to look for disease associated haplotypes, non-coding or mild hypomorphic or modifier variants. Where appropriate, potential modifier and hypomorphic variants or haplotypes will be investigated functionally, and their potential contribution to phenotype/genotype correlations will be investigated.
The establishment and optimisation of novel enrichment and sequencing strategies are necessary to detect missing heritability of ABCA4. Technologies which enable allelic phasing of identified genetic variants are of paramount importance in the absence of additional family DNA, particularly when assessing cis-acting modifier alleles. ESR6 will design and optimise a CRISPR-Cas9 mediated enrichment method for the entire ABCA4 gene and surrounding DNA for use in long-read sequencing on a PacBio Sequel. In addition, ESR6 will employ Illumina TruSeq synthetic long-read phased sequencing. These approaches will be applied to 50 mono-allelic STGD1 cases. The data generated by ESR6 will be integrated with the smMIPs, TLA and HaloPlex data generated by ESR5 and ESR7. ESR6 will interrogate this data set, along with cases and controls from the UK 100,000 Genome data, to look for disease associated haplotypes, non-coding or mild hypomorphic or modifier variants. Where appropriate, potential modifier and hypomorphic variants or haplotypes will be investigated functionally, and their potential contribution to phenotype/genotype correlations will be investigated.
