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Genomic and functional analysis of gene copy number variation

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  • Full or part time
    Prof J A L Armour
    Prof O Hanotte
  • Application Deadline
    Applications accepted all year round
  • Self-Funded PhD Students Only
    Self-Funded PhD Students Only

Project Description

Understanding the genetic basis of human health involves determining how the different genetic variants present in human populations contribute to health and disease in individuals. Variation in gene copy number is extensive in humans - and there are many examples of important genes that show variation in number; for example, people who are "Rhesus negative" completely lack any copies of the RHD gene, whereas "Rhesus positive" individuals have one or two copies.

Our current research on human CNVs investigates the difficult question of how copy number variation affects function. It is often assumed that gene expression is simply proportional to copy number, but several examples show that the truth is often more complicated. In particular, expression can also be simultaneously affected by gene sequence variants, trans-acting factors, and position within a repeat array. We are using our high-precision approaches to measuring gene copy number to underpin investigation of these questions for the human alpha-defensin genes, and the copy-variable human amylase genes.

We have also recently begun to apply our methods for high-resolution measurement of gene copy number to analyse variation in gene number in the genomes of chickens. There appears to be extensive copy-number variation in the chicken genome, including many genes of importance in the immune response (see, for example, Crooijmans et al., 2013). These variants may therefore be of importance in determining susceptibility or resistance to infectious disease. Projects may be available either in the study of human or chicken CNVs.

Funding Notes

Home and EU applicants should contact the supervisor to determine the current funding status for this project. International applicants should visit our page for information regarding fees and funding at the University


Armour, J.A.L., Palla, R., Zeeuwen, P.L.J.M., den Heijer, M., Schalkwijk, J. and Hollox, E.J. (2007). Accurate, high-throughput typing of copy number variation using paralogue ratios from dispersed repeats. Nucleic Acids Res., 35, e19.
Crooijmans, R.P.M.A., Fife, M.S., Fitzgerald, T.W., Strickland, S., Cheng, H.H., Kaiser, P., Redon, R. and Groenen, M.A.M. (2013). Large scale variation in DNA copy number in chicken breeds. BMC Genomics, 14:398.
Hollox E. J., Huffmeier U., Zeeuwen P. L. J. M., Palla R., Lascorz J., Rodijk-Olthuis D., van de Kerkhof P. C. M., Traupe H., de Jongh G., Heijer M. d., Reis A., Armour J. A. L., and Schalkwijk J. (2008). Psoriasis is associated with increased [beta]-defensin genomic copy number. Nature Genetics 40, 23-25.
Khan, F.F., Carpenter, D., Mitchell, L., Mansouri, O., Black, H.A., Tyson, J. and Armour, J.A.L. (2013). Accurate measurement of gene copy number for human alpha-defensin DEFA1A3. BMC Genomics 14(1), 719.

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FTE Category A staff submitted: 90.86

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