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. C. Toomes

Ben McClinton
I completed my Bachelors in Genetics in 2019 in Trinity College Dublin and will be undertaking ESR6, Long-Read Sequencing of the ABCA4 Locus in the University of Leeds. 

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.