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The University of Southampton
Institute for Life Sciences

Genomics

Advances in sequencing technology have the potential to effect a step change in our approach to medical genetic research and clinical diagnostics. Processing and interpretation of large scale genomic data from patient samples has the potential to reveal common and rare genetic changes that predispose to disease. The development of new tools and skills necessary to analyse, interrogate and understand the importance of genomic variation is an essential prerequisite. The vast nature of the data necessitate analytical pipelines, variant annotation and variant prioritisation in order to extricate biologically relevant variation from background noise.

Genetics of Paediatric Immune Disease

Housed in University Hospital Southampton NHS Foundation Trust is the Wessex regional referral centre for children diagnosed with inflammatory bowel disease (IBD).  The University of Southampton have teamed up with clinical colleagues in UHS and recruited these children to a study looking at the genetics of paediatric IBD.

We are applying Next Generation Sequencing (NGS) to the genetic analysis of patient DNA. NGS is the cutting edge technology that enables us to take a DNA sample from a patient and read ALL the letters of that person's genetic code. In any human genome there are approximately three billion base (A,T,C,G) pairs. Only about one percent of these lie in regions (genes) that contain recipes for the proteins that our bodies required to develop and function.  Up to only a few years ago, it was prohibitively expensive to get continuous sequence reads for individual patients and researchers tended to analyse only intermittent letters that were known to be commonly varied in the population. NGS enables us to look at all of the letters across either the entire length of the genome, or as for the study reported in Gut, concentrate on just those gene sequences that code for proteins- the exome. As well as being cheaper - because most genetic variation that causes disease lies within genes - this study design represents the most cost efficient way of taregting the analysis to the highest risk regions of the genome. Even with this frugal approach, this type of analysis costs approximately one thousand pounds per sample.

Recently we have published a paper describing individual profiles of genetic changes across a panel of genes known to influence IBD risk. For each patient we produced a profile of their individual variation across these genes. We found that despite having common diagnoses, each individual presents with a unique profile of genetic variants. In the second phase of this project we are analysing forty two more samples. By using very detailed clinical information, we plan to build on this work to identify which specific clinical characteristics are shared by patients with similar genomic profiles. Ultimately, this may help us give much more specific diagnoses to individuals rather than the "umbrella terms" that are currently used, and this in turn may help inform clinicians of the best treatments for their patients. We expect our findings will translate into adult medicine as well as aiding screening in relatives of those affected by this familial disease.  As new drugs and therapies emerge, knowing which specific biological pathways are impaired on a case-by-case basis will lead to targeted treatment tailored to individual patients.

 

Epigenetics in Asthma

We have been studying the origins of asthma and allergies for over twenty years in a group of people born on the Isle of Wight in 1989. We know that the chances of someone developing an allergy depends on both the genes they inherit from their parents and also on the exposures they encounter in their environment. One way the environment can alter the risk of disease by altering what is known as the 'epigenome'. The epigenome is a series of chemical modifications to DNA which is important for controlling turning genes on and off .

Our study has shown that one of the strongest risks of developing allergy is whether your mother has allergies if you are a girl, or if your father has allergies if you are a boy. One possible explanation for this lies in one specific chemical mark in the epigenome called DNA methylation. To study whether DNA methylation is the factor that is transmits risk from parent to child we are revisiting study participants on the Isle of Wight that are now having their own children. We are measuring DNA methylation in all 23,000 genes in the genome in the mother and father and also in their children. From this we can see if there are specific DNA methylation marks that are transferred from an allergic parent to a child. By following the children of the next generation as they grow up, we can also see whether these DNA methylation marks will increase the chances of these children developing allergies and asthma themselves.

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