New publication: A panel of genes methylated with high frequency in colorectal cancer

I’m pleased to announce an open-access publication with my name on it:

Mitchell, S.M., Ross, J.P., Drew, H.R., Ho, T., Brown, G.S., Saunders, N.F.W., Duesing, K.R., Buckley, M.J., Dunne, R., Beetson, I., Rand, K.N., McEvoy, A., Thomas, M.L., Baker, R.T., Wattchow, D.A., Young, G.P., Lockett, T.J., Pedersen, S.K., LaPointe L.C. and Molloy, P.L. (2014). A panel of genes methylated with high frequency in colorectal cancer. BMC Cancer 14:54.

If you’re thinking “but Neil never blogs about what he actually does at work anymore”, jump to this footnote [1].

Expression of MAMDC2 in cell lines HT29 and SW480 with (orange) or without (blue) 5-aza 2′deoxycytidine treatment

The title pretty much sums it up. Take a bunch of tissues and cell lines, subject them to a bunch of methods to detect methylation and select some promising methylation biomarker candidates based on consensus between methods.

My main contribution to the paper was analysis of the data from one of the experiments described in the abstract: “activation of gene expression in CRC cell lines following DNA demethylating treatment.” When the final version of the supplementary material appears, you should see plots similar to the one at right, showing increased expression of exon microarray probesets in some colorectal cancer cell lines when treated with a demethylating agent.

Biomarker discovery is our main goal, so to quote the conclusion verbatim:

This study has characterised a panel of 23 genes that show elevated DNA methylation in
>50% of CRC tissue relative to non-neoplastic tissue. Six of these genes (SOX21, SLC6A15,
NPY, GRASP, ST8SIA1 and ZSCAN18) show very low methylation in non-neoplastic
colorectal tissue and are candidate biomarkers for stool-based assays, while 11 genes
(BCAT1, COL4A2, DLX5, FGF5, FOXF1, FOXI2, GRASP, IKZF1, IRF4, SDC2 and
SOX21) have very low methylation in peripheral blood DNA and are suitable for further
evaluation as blood-based diagnostic markers.

[1] Despite the tagline for this blog, very few of my posts feature the details of my own day-to-day research. The reasons for this are many and sometimes complicated, but are often because (1) I work with confidential data that I don’t own and (2) I work for an organisation which has strict guidelines about discussing internal information on social media.

I get around this by writing about bioinformatics in general, rather than what I do in particular. I think this is more interesting anyway, so it suits me just fine.