Nanopore long-read sequencing of complex structurally variable human genomic regions involved in disease

Complex genomic structural variants are known to cause or contribute to disease. In somatic cells, complex rearrangements are a characteristic of cancer, and can promote tumorigenesis by generating novel fusion genes. In the inherited germline genome, structural variants are known to increase the risk of diseases such as psoriasis and schizophrenia. However, such complex variants are understudied partly because they are can be challenging to detect and analyse using short read Illumina genome sequencing.

New sequencing technologies, such as Nanopore sequencing, can generate many kilobases of DNA sequence in a single run, allowing structural variation to be discovered and assayed very effectively. However, Nanopore sequencing has a high sequence nucleotide error rate. This project will use new methods of targeting genomic regions to sequence using long read technology at high depth to minimise sequence errors.

The project will target the glycophorin gene region, which has numerous deletion, duplication and more complex alleles. One particular glycophorin variant, called DUP4, is protective against malaria. We will use an approach called CATCH, which uses the enzyme Cas9 to cut a particular region of the genome, to isolate the glycophorin region from well-established structural variation alleles to assess the ability of Nanopore sequencing to accurately discore and assay structural variation that has medical consequences.