Human Genome Analysis and Genetic Diversity: Most people are familiar with the idea that the sequence of the human genome has been determined. This "reference" human genome sequence does not match everyone exactly; in fact, it does not correspond to the genome of any one person, but is just a framework sequence for the human genome, patched together from different sources. Real individual genomes are different from this reference sequence in a variety of ways: there is variation in the exact sequence, due to single base changes, but also variation in the general structure of the genome, due to variation in the numbers of repeated regions, including even variation in whether a sequence is present or absent (or, if present, how many times). Although these differences are often neutral (irrelevant to a person's health and other characteristics) genome variation can also influence disease. Our research looks at how variation in the structure of the human genome arises, and investigates its possible influence on human disease.
Copy number variation in the human genome: 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. There are currently major efforts aimed at discovering links between substitutional ('SNP') variants and predisposition to disorders like type I diabetes, asthma and schizophrenia. However, many human genetic disorders can instead result from having the wrong number of copies of a gene, or parts of a gene, and variation in gene number has recently become widely appreciated as an important contributor to disease susceptibility. 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 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. People can have between 2 and 18 copies of the human salivary amylase gene, and it has been proposed that this variation may be important in human handling of dietary carbohydrate. Our work has defined the structural basis of this variation (Carpenter et al., 2015) and discovered new variants of the nearby pancreatic amylase genes (Shwan et al., 2017).
We have are currently investigating the structure and consequences of the copy number variation in the human alpha-defensin genes. Alpha defensins are expressed at high levels in neutrophils and appear to be important contributors to killing of microorganisms. The major neutrophil defensins are encoded by the DEFA1 and DEFA3 genes, which show high levels of variation between individuals. We have defined the main features of the variation at this locus (Khan et al. 2013, Black et al. 2014), and we are currently exploring the functional consequences. Genetic associations have been demonstrated between variation in this region and the inflammatory disorders IgA nephropathy (Ai et al. 2016) and periodontitis (Munz et al., 2017), suggesting that alpha-defensins play a key role in immune system variation underlying these disorders, and possibly variation in more general features of immune function.
Connecting the Biomphalaria genome
Infection with the parasite Schistosoma gives rise to the parasitic disease schistosomiasis, a condition affecting more than 200 million people in tropical countries. Schistosomiasis cannot be spread directly from human to human, but must pass through an intermediate water snail host (just as malaria is spread between humans via an intermediate mosquito host). Among the snail hosts, Biomphalaria glabrata has emerged as a prominent model organism, not only for studies of schistosomiasis but also for the understanding of gene function in molluscs more generally. We are working towards establishing genome-based biology in Biomphalaria glabrata, starting with improvements to the completeness of the genome assembly (Adema et al., 2017), and with the intention of moving towards germline transgenesis, necessary both for definitive analysis of gene function and to create novel control measures to limit the spread of schistosomiasis.
Inheritance of attractiveness to mosquitoes
We have established using studies of UK twins that there is a substantial inherited component in the tendency for different people to be more or less attractive to biting insects like mosquitoes (Fernández-Grandon et al., 2015). In work funded by a grant from the MRC, with colleagues at the London School of Hygiene and Tropical Medicine, Rothamsted Research, MRC Gambia, St George's University of London, and the University of Durham, we are now extending these observations to investigate the molecular basis of those inherited differences, and whether the same heritability can be found in people from West Africa.
Adema, C.M., et al., (2017). Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Nature Communications 8, 15451.
Ai, Z., Li, M., Liu, W., Foo, J.N., Mansouri, O., Yin, P., Zhou, Q., Tang, X., Dong, X., Feng, S., Xu, R., Zhong, Z., Chen, J., Wan, J., Lou, T., Yu, J., Zhou, Q., Fan, J., Mao, H., Gale, D., Barratt, J., Armour, J.A., Liu, J. and Yu, X. (2016). Low α-defensin gene copy number increases the risk for IgA nephropathy and renal dysfunction. Science Translational Medicine. 8, 345ra88.
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.
Black H.A., Khan, F.F., Tyson, J. and Armour, J.A.L. (2014) Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus. BMC Genomics 15, 614.
Carpenter, D., Dhar, S., Mitchell, L.M., Fu, B., Tyson, J., Shwan, N.A.A., Yang, F., Thomas, M.G. and Armour, J.A.L. (2015). Obesity, starch digestion and amylase: Association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes. Human Molecular Genetics 24, 3472-3480.
Fernández-Grandon, G.M., Gezan, S.A., Armour, J.A.L., Pickett, J.A. and Logan, J.G. (2015). Heritability of attractiveness to mosquitoes. PLoS ONE 10, e0122716
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.
Munz, M., Willenborg, C., Richter, G.M., Jockel-Schneider, Y. et al. (2017) A genome-wide association study identifies nucleotide variants at SIGLEC5 and DEFA1A3 as risk loci for periodontitis. Human Molecular Genetics, 26, 2577-2588.
Shwan, N.A.A., Louzada, S., Yang, F. and Armour, J.A.L (2017). Recurrent rearrangements of human amylase genes create multiple independent CNV series. Human Mutation 38, 532-539.