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In genetic studies of human disease it is now routine for studies to collect genetic data on thousands of individuals with and without a particular disease. However, the genetic data collected is incomplete, with many millions of sites of the genome unmeasured. The novel methods and software (IMPUTE) developed by researchers at the University of Oxford predict unobserved genetic data using reference datasets.
IMPUTE has been adopted by the company Affymetrix in the design of custom genotyping chips. Affymetrix recently won the tenders by the UK Biobank and UKBiLEVE studies to genotype >500,000 participants, with a total study cost of ~£25M. The company states that IMPUTE gave their project bid a significant competitive advantage. Affymetrix also purchased the IMPUTE source code for £250,000. In addition, Roche Pharmaceuticals have used the software in their research on the genetic basis of drug response. The use of imputation has saved Roche ~$1,000,000.
Age-related macular degeneration (AMD) is the most common cause of blindness in Western populations and reduces the quality of life of tens of millions of older people worldwide. In 2007 a research group at Cambridge University led by Professor John Yates in the Cambridge Institute for Medical Research discovered that a common genetic variant in the complement C3 gene was associated with an increased risk for AMD. This finding is now being used in a genetic test in North America and Europe to estimate individual risks for AMD. Those found to be at high risk are offered regular eye examinations to detect early development of the wet form of the disease before symptoms arise. This can be treated with anti-VEGF therapy. Early treatment gives the best chance of preserving sight by preventing irreversible damage to the retina.
Targeted Projection Pursuit (TPP) — developed at Northumbria University — is a novel method for interactive exploration of high-dimension data sets without loss of information. The TPP method performs better than current dimension-reduction methods since it finds projections that best approximate a target view enhanced by certain prior knowledge about the data. "Valley Care" provides a Telecare service to over 5,000 customers as part of Northumbria Healthcare NHS Foundation Trust, and delivers a core service for vulnerable and elderly people (receiving an estimated 129,000 calls per annum) that allows them to live independently and remain in their homes longer. The service informs a wider UK ageing community as part of the NHS Foundation Trust.
Applying our research enabled the managers of Valley Care to establish the volume, type and frequency of calls, identify users at high risk, and to inform the manufacturers of the equipment how to update the database software. This enabled Valley Care managers and staff to analyse the information quickly in order to plan efficiently the work of call operators and social care workers. Our study also provided knowledge about usage patterns of the technology and valuably identified clients at high risk of falls. This is the first time that mathematical and statistical analysis of data sets of this type has been done in the UK and Europe.
As a result of applying the TPP method to its Call Centre multivariate data, Valley Care has been able to transform the quality and efficiency of its service, while operating within the same budget.
During the last 10 years Cardiff University researchers have developed and applied a range of genetic and molecular analysis techniques to inform conservation and biodiversity policy and practice in regions around the world where specific species and biodiversity are under threat. Genetic research on orang-utans and elephants in the Kinabatangan Wildlife Sanctuary in Borneo has guided strategic action plans for these species. Cardiff's molecular censusing and genetic analysis of giant panda populations in China have directly informed the strategic relocation of individual animals into isolated populations in the wild to preserve the genetic diversity of the species.
Research in the School of Mathematics & Statistics in the University of Glasgow has been influential in answering a long-standing question: where do we come from? The fleshing-out of the 'out of Africa' theory has been the focus of two documentary series, The Incredible Human Journey and Meet the Izzards, and has generated income for DNA testing companies in the UK and US by enabling them to offer `deep DNA' tests revealing one's roots from far back in history. The Incredible Human Journey aired on BBC 2 in 2009, reaching 10.2 million viewers altogether, has been watched 100,000 times on YouTube and was broadcast in shorter format in Australia and Canada before being released as a DVD. Meet the Izzards was broadcast on BBC 1 in 2013 to over 3 million people.
OxCal is the most popular software package world-wide for calibrating and analysing dates within the carbon dating process, enabling the accurate dating of objects from the past. The brainchild of Prof. Christopher Bronk Ramsey, Director of the Oxford Radiocarbon Accelerator Unit (ORAU), OxCal is based on chronologies refined by the use of Bayesian statistical methods, and provides users with access to high-quality calibration of chronological data, now the basis for global chronologies. It is available online and free to download, and has played a highly significant role in establishing the ORAU as one of the pre-eminent international radiocarbon dating facilities. Funded by the NERC, and used widely within professional archaeology as well as other disciplines, OxCal has also played a key role in research projects (within Oxford and beyond) brought to the attention of the general public by the media.
The Stonehenge Riverside Project was carried out between 2003 and 2010, to determine the purpose of Stonehenge by investigating both the monument and the surrounding landscape. The project's reach and importance have been considerable, from training and inspiring the next generation of professional archaeologists to stimulating people worldwide with new knowledge about Stonehenge, providing artistic inspiration and changing perceptions and beliefs about the use of the site, leading to significant economic, cultural and technological benefits.
Impact: BEAST software has widespread applications with impacts on public health policy, service provision and awareness, and in other contexts such as commercial disputes and criminal cases.
Beneficiaries: Public agencies such as health bodies and criminal courts; ultimately, global and local populations subject to infectious disease epidemic and pandemic outbreaks in which BEAST is used to inform the response.
Significance and Reach: BEAST is critical software that has been used to understand the spread of and to inform the response to global pandemics such as H1N1 swine-flu. It is also used to determine disease origin and transmission issues in specific situations (e.g. in criminal cases). The reach of this software is therefore both global and local.
Attribution: Rambaut (UoE) co-led the phylogenetic research and developed BEAST with Drummond (Auckland, NZ). The subsequent epidemic and pandemic analyses were variously led by Rambaut and Pybus (Oxford) and by Ferguson (Imperial College London).
Research carried out by the University of Southampton into the genetic causes of diseases, and the gene mapping techniques and applications derived from this research, has benefited patients worldwide through improved prediction, diagnosis and treatment for common diseases with a complex genetic basis. A particularly striking example is age-related macular degeneration which is a common cause of blindness. Commercially, the research provides cost-effective strategies for genotyping DNA samples, and marker-based selection strategies for economically relevant animal species, such as cattle. The work underpins the development of the personal genomics industry, which specialises in individual genetic risk profiling.
Research by Professor David Brook on inherited disorders has made a major contribution to the human genetics field. The work involved gene identification and mutation detection for genotype/phenotype correlation analysis in patients, which has led to the development of diagnostic tests for inherited conditions including myotonic dystrophy type 1 (DM1), Holt-Oram Syndrome (HOS), and campomelic dysplasia (CD). The tests have benefitted patients in the UK and throughout the rest of the world and in many cases they have been used as the definitive diagnostic measure. The assays developed have also been used in affected families for prenatal diagnosis to enable informed reproductive decisions.