Breathtaking genes: A ‘Circos’ plot depicting how chronic obstructive pulmonary disease (COPD) has become a global concern – the 3rd biggest killer, defined by poor lung function. Our work shows that many parts of our DNA play a role in our lung health. Peaks in red are newly discovered regions, and the blue ones were previously identified by other groups. Millions of genetic variants from tens of thousands of individuals were analysed in this study. The identified genes will help us understand why some of us have better lung function, and lead to the identification of drug targets of potential relevance to COPD.
A press release was issued by the University of Leicester Press Office on 6 February 2017 about a study that I was also heavily involved in (please click on links below for details):
“Breakthrough advance offers the potential to defuse a ‘ticking timebomb’ for serious lung disease, including for over 1 billion smokers worldwide (source: World lung health study allows scientists to predict your chance of developing deadly disease — University of Leicester)”
The study has received a lot of attention from the media, with articles appearing in large media outlets such as BBC News, The Independent and MSN News. If you’re interested in the details, please read the paper published in Nature Genetics.
If interested in reading about the area of Genetic Epidemiology itself, please have a look at my (previously published) blog post about the matter: Searching for “Breath taking” genes. Literally!
Details on Circos plot* (above): FEV1: Forced expiratory lung volume in 1 second; FVC: Forced lung volume capacity; FEV1/FVC: the ratio of the two measurements. Labels in the outer circle show the name of the nearest gene to the newly identified (red) variants. X-axis: Genomic position of variant in genome (chromosome number in the outer circle), Y-axis: Statistical significance of variant in this study (higher the peak the greater the significance).
Love the circular manhattan plot from Louise Wain presenting her recent @NatureGenet paper. Elegant way of showing many plots at once #SEGEG pic.twitter.com/MAHaoTowrF
— Lynsey Hall (@LS_Hall) March 10, 2017
*The figure is a more artistic version of Figure 1 (Manhattan plot) in the above mentioned academic paper. It did not make it into the final manuscript published in Nature Genetics (6th Feb 2017) as it was found to be “confusing” by one of the reviewers – and the editor agreed. 😦 However, the plot was shortlisted (title: Breathtaking genes) and displayed in the Images of Research exhibition (9th Feb 2017) organised by the University of Leicester. 😉
My role in the Wain et al paper mentioned above: I led the ‘functional follow-up’ of the identified associated variants (e.g. mining eQTL datasets, biological pathway analyses, identify druggable genes, pleiotropy, protein-protein interactions) and appropriately visualise the GWAS results (various Manhattan and Circos plots). I was part of the core bioinformatics team of three in Leicester – alongside Dr. Nick Shrine and Dr. Maria Soler-Artigas.
References:
Wain LV et al., Published online 6th Feb 2017. Genome-wide association analyses for lung function and chronic obstructive pulmonary disease identify new loci and potential druggable targets. Nature Genetics. URL: https://www.nature.com/articles/ng.3787
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