Tuesday, 22 May 2012

Resources for the public understanding of cancer genomics

We have just had an open day at our institute, we had Science Week here in the UK a month ago and I went to my son's school to talk about why people have differently coloured eyes. I like communicating science to other people; at work, in the pub, on the train, at school, etc, etc, etc. I am a science nerd and an happy to be known as one. Most of the time.

Public understanding of science (PUS) is important and we need to make sure the people funding us, and hopefully benefiting from the work we do, realise why we do what we do. However it is not always easy to find the time to put together something everyone will understand and engage with.

There are surprisingly few resources out there to get PUS materials and examples from. This post outlines the work I've done for our open day and discusses some of the resources that are out there to offer some inspiration. I'd also like to enthuse others about the idea of Creative Commons licensing of your PUS materials so others can use them. Then we just need to find somewhere to put them and organise them. Does anyone fancy writing a grant to Wellcome to get some funding for a web-resource?

Why bother with PUS in a genomics core facility: I wanted to share the recent posters I put together to show visitors to our open day what we do in a genomics core facility lab and how those shiny Illumina HiSeq, MiSeq and GAIIx (a little old and not so shiny!) machines can help us help patients.
Mutations in Cancer: The PUS poster comes as a pair which have huge Sanger style sequence traces of the Braf V600E mutation in normal and mutant versions. The visitors are asked to "spot the difference" and identify the mutation, which is a very difficult thing to do by eye. We explain that finding this kind of mutation is what we are doing on our instruments about 1000 times a day. Of course this is a massive over-simplification of the possibilities offered by cancer genome sequencing but hopefully it shows why we spend so much money on cancer genomes. Braf V600E was chosen as it is one of a few mutations that can be tested for to determine treatment. Tests we are developing in out institute will hopefully mean every cancer patient in the UK is screened for mutations like this from a tumour biopsy and, maybe one day, a simple blood sample.

Can you spot the difference between normal (left) and mutant (right) Braf sequences?
How can I tell other scientists about my posters: I wanted to make these posters available to others to use or modify for their own PUS events. The posters can be downloaded here under a creative commons license. However there does not appear to be a central repository of resources like this. A few sites do offer material under creative commons, like the University of Oxford maths department podcasts. I wonder if the resource we need today is somewhere to upload materials with keywords and abstracts in a searchable form. If these were available as shared documents then the community could work on them together. I am thinking something like GoogleDocs or a Wiki for PUS. This would be a wonderful thing for someone like Wellcome or MRC to fund. If your materials became widely used then they could also become something that was worth adding to your CV, demonstrating additional skills outside of research experience.
PUS sites I liked: There are people out there communicating about PUS. There is even a journal called "Public Understanding of Science" that has an interesting editorial blog post about open access publishing. PUS is a subscription journal and they appear to lean away from a PLoS model of open access which seems totally at odds with the journals remit to promote public understanding. How can the scientists better learn to help communicate science if we have to subscribe to a journal to hear about the best ways to do it? PUS covers all kinds of interaction between science and the public, they cover topics such as: "science, scientific and para-scientific belief systems, science in schools, history of science, education of popular science, science and the media."

A post on Diffusion summarises a seminar from martin Rees. He advocates scientists doing more communications work and making sure the public and politicians get access to the very best explanations of science possible.

Marie Boran has some wonderful blog posts at The Strange Quark about public understanding of science. I'd also recommend her posts on what science is, science journalism and what communication means. She communicates things in a way people are likely to remember them. I particularly liked her way of presenting the scale of cells, apparently if you use an M&M to represent a red blood cell then a single grain of sugar would be about the same size as a bacterium.

Lastly I'd like to point everyone to Small Science Zines. This is a site that promotes the use of "Zines", small, easily and cheaply reproduced magazines. They provide instructions (zine-folding directions) to help you produce a simple eight page zine for easy distribution. The zine on DNA computing is an interesting if wordy read. I think I'll give one a go for Illumina sequencing so watch this space. Perhaps we can produce a series of NGS "how to" comics?

The site discusses how to communicate science and how to design zines. It does not all have to be about well honed presentations or laminated A0 posters. PUS could simply be the last time you told someone a science fact. Making a zine to show people is much more personal than pointing them to a website or asking them to visit the lab. All you need is "to know and care about your topic, and want to share this with others".


  1. Hey James,

    Very nice work - although it would be great to update the capillary trace example to be relevant in the NGS era.

    One idea: a whole bunch of magnetic short reads, and people need to slide them around on a magnet board to align them to a reference genome to find the mutation.

    Oh, and please, please, let's find a better abbreviation than PUS!

  2. I crossed my eyes so the two images would overlap, and found the difference. I don't think it is too scalable of an approach both for the human genome, and for the long term health of my eyes! Great post!

  3. Just one problem. Mutant Braf sequence is on the left and WT on the right. You have display a reverse complement sequence.
    WT rev compl: aga ttt CAC tgt agc
    Mutant p.V600E (c. 1799G>T): aga ttt CTC tgt agc

    1. I've done a mistake for V600E. It's c.1799T>A....