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

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  • Full or part time
    Dr E Hollox
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

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.

Funding Notes

International students with sponsorship are also welcome to apply for this project.

References

Tslil Gabrieli, Hila Sharim, Dena Fridman, Nissim Arbib, Yael Michaeli, Yuval Ebenstein; Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH), Nucleic Acids Research, , gky411, https://doi.org/10.1093/nar/gky411

Miten Jain, Hugh E. Olsen, Benedict Paten and Mark Akeso. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community Genome Biology 2016 17:239 https://doi.org/10.1186/s13059-016-1103-0

Elizabeth Winzeler Glycophorin alleles link to malaria protection Science Vol. 356, Issue 6343, pp. 1122-1123
DOI: 10.1126/science.aan4184

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