Category Archives: Papers

Author post: A hybrid SNP/qPCR approach for large scale association testing in KIR

SNP arrays are a great way of cheaply genotyping a large number of individuals for genome-wide association studies.

This is what you expect a typical SNP to look like:


There are three clearly distinguishable clusters representing the three possible genotypes at that locus (TT, TC and CC).

But some SNPs look like this:


What is going on here?

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Increased IFN signalling is a risk factor for the development of the first autoimmune events in T1D

Our group has a manuscript just out in Diabetes in which we have investigated the role of type 1 interferon signalling in the pathogenesis of the autoimmune disease T1D. The work was led by Ricardo Ferreira and Hui Guo. Type 1 interferon (IFN) signalling is a evolutionarily conserved biological pathway that plays a major role in the defense against viral infections. Every mammal expresses IFN genes and birds, amphibians and fish also express functionally homologous molecules. However, a side effect of the IFN responses is that they can also cause bystander tissue damage and can also lead to the activation of an autoimmune response. In fact, in humans chronically activated IFN signalling has been recently implicated in the aetiology of several systemic autoimmune diseases such as systemic lupus erythematosus (SLE) or vasculitis. Importantly, in T1D, genetic evidence from genome-wide association studies has pointed to an important role of this biological pathway in this disease, including the identification of IFIH1, a major sensor of viral infections, as a susceptibility gene.

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Another colocalisation paper

I am a co-author on another paper about colocalisation posted on arXiv. It’s a novel approach, using Bayesian inference based on Approximate Bayes Factors derived from p values, making colocalisation testing much more practical when data is not often as open access as claimed. My co-author, Vincent Plagnol, has written a nice post about it on Haldane’s Sieve. The software to conduct these tests is in the coloc package, v2.0 now available on CRAN.

New paper on colocalisation testing

We have a new paper on arXiv detailing some work on colocalisation analysis, a method to determine whether two traits share a common causal variant. This is of interest in autoimmune disease genetics as the associated loci of so many autoimmune diseases overlap 1, but, for some genes, it appears the causal variants are distinct. It is also relevant for integrating disease association and eQTL data, to understand whether association of a disease to a particular locus is mediated by a variant’s effect on expression of a specific gene, possibly in a specific tissue.

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