Birney group

Intraspecies variation in medaka fish and humans

Summary

The Birney group studies between-individual differences in both Japanese rice fish (medaka) and humans. We also explore novel algorithms in bioinformatics opportunistically.

We are interested in the interplay of natural DNA sequence variation with basic biology from molecular and cellular processes to complex physiology and behaviour. Over the past five years there has been a tremendous increase in the use of genome-wide association to study human diseases. However, this approach is very general and need not be restricted to the human disease arena using SNP genotypes. Association analysis can be applied to nearly any measurable phenotype in a cellular or organismal system where an accessible, outbred population is available. We are pursuing association analysis for a number of both molecular (e.g. RNA expression levels and chromatin levels) and organ physiology levels (heart function, retinal function), in particular in humans and Japanese rice fish. We have established the first vertebrate near-isogenic wild panel in Japanese rice fish (medaka, Oryzias latipes), which allows for exploration and dissection of gene × environment effects and aspects of variance in phenotypes, in ways which is impossible in any other vertebrate.

We also have interest in new algorithms and methods around new sequencing techniques, such as Oxford Nanopore.

Image of heart
Figure showing exploration of human heart physiology. Panel A shows a dissected human heart open on the left ventricle, showing the complex rough surface facing the blood pool. Panel B shows an idealised heart and the 2D MRI scans done in the UK BioBank. Panel C shows the results of a deep learning technique to find the muscle wall and then the follow-on derivation for the fractal dimension of the ventricle. This was later used for human genetic investigation, including causal analysis of the role of trabeculation in heart function.

 

Future plans

The Birney group will continue to work on intraspecies variation, in particular in Japanese rice fish and humans, exploring the interaction between genes and environment. We will also continue work into association-testing method development in relation to a variety of genome variation types and complex phenotype representations. We have a long track record of recognising opportunities for new algorithm development, and will continue to opportunistically develop methods when desired.