Epidemiology and Population Biology

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

This theme explores how genes operating through an individual organism influence the behaviour and properties of populations, and the interactions between populations and between species. At the first level, the research in this theme develops the methods that update and enhance the well-established theories of quantitative and population genetics with state-of-the-art developments in genomics. The objectives of the theme are: To develop predictive models of genome-wide diversity, risk and merit. To develop predictive models in epidemiology and population biology. To quantify pathogen diversity and patterns of disease.

Publications

10 25 50

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Acosta-Jamett G. (2015) Echinococcus granulosus infection in foxes in Coquimbo District, Chile in ARCHIVOS DE MEDICINA VETERINARIA

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Allen AR (2010) Bovine tuberculosis: the genetic basis of host susceptibility. in Proceedings. Biological sciences

 
Description Predictive models for the accuracy of genomic selection for quantitative traits, including underlying disease risk in both population and case-control studies.

Predicting relative efficiency of genome wide analytical methods as a function of attributes of the species genome and trait architecture.

Prediction of the total genetic variation captured by dense SNP chip by the application of deterministic models for genome-wide accuracy in a meta-analysis of publically available data.

Estimating the impact of epidemiological parameters and processes on the genetic interpretations obtained from field data.

Estimation of epidemiological parameters that properly reflect diagnostic imperfection.

Establishing a field recording system for capturing epidemiological data in dogs.
Exploitation Route The methods developed in this programme are being used both in on-going academic research on the genetic control of complex traits and in selective animal breeding.
Sectors Agriculture, Food and Drink

 
Description The development of marker-assisted selection and specifically breeding salmon for resistance to Infectious Pancreatic Necrosis is an example of economic impact underpinned by research in this project. In recent decades, the viral disease infectious pancreatic necrosis (IPN) has been a major constraint on salmon aquaculture, spreading rapidly among salmon farms in Scotland, Norway, Chile, USA, Canada and other countries. Severe outbreaks are known to kill as many as 80-90% of farmed fish, and no vaccine is effective in the salmon fry stage. However, research at The Roslin Institute has demonstrated that not only is resistance (i.e. survival) a heritable trait, but through innovative application of genomic techniques it has been demonstrated that the observed genetic differences are almost entirely due to a single quantitative trait locus (QTL). Fish inheriting two copies of the resistant variant of the QTL from their parents have, on average, between 65 and 100% higher survival rates than those receiving the susceptible variant from both parents. This science led to the collaborating breeding company, Landcatch Natural Selection (LNS), implementing marker-assisted selection for IPN resistance in 2008, when selecting its elite and commercial salmon populations - the first successful documented example of marker assisted selection for a disease resistance trait in any livestock species. Our economic analysis suggests that once the resistant variant of the QTL is fixed in the population through MAS, the production cost of rearing salmon up to harvest size will reduce significantly leading to increased production efficiency. Based on an assumed 25% mortality, application of MAS would allow the production of an extra 672 tonnes of harvest fish per one million eggs, which is equivalent to approximately £2 million of extra income. In terms of the UK salmon market (which currently requires about 75 million eggs per annum) this translates to 50,400 tonnes of extra fish and £150 million of extra income. The improved production efficiency will provide benefits for LNS customers and for UK consumers, by contributing to the sustainable production of affordable food, and thus will also help to address food security issues and reduce the environmental footprint of salmon production. The wider salmon aquaculture industry will benefit from this innovation directly through enhanced commercial performance and improved health and welfare, since the technology itself is sellable to other parties. This innovation has been hailed as a highly successful example of the application of BBSRC research for industrial benefit, and led to an effective Knowledge Transfer Partnership (KTP). The innovation and related findings have been widely communicated through different media (including numerous press releases, scientific and industry publications and presentations etc.) to ensure widespread publicity. Further, the KTP associate (Dr. Almas Gheyas) won the KTP Centres in Scotland prize for Best Project Presentation.
First Year Of Impact 2008
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description Roslin GCRF Impact Accelerator Award - A genomic map for bovine tuberculosis susceptibility in Bos indicus breeds
Amount £30,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2017 
End 02/2018
 
Description Cameroon Infectious disease epidemiology links 
Organisation Cameroonian Academy of Sciences
Country Cameroon 
Sector Academic/University 
PI Contribution expertise in infectious diseases epidemiology and study design. We currently have 2 BBSRC GCRF Impact Accelerator Awards active in Cameroon as part of ongoing links and collaborations.
Collaborator Contribution expertise in infectious disease logistics local setting transport accommodation.
Impact Grant on HPAI in North Cameroon - no funded Grant on FMD in Adamawa Region Cameroon - not funded 1 month collection of FMD samples - paper in preparation use of samples from TB project to screen for RVF - 2 papers in preparation
Start Year 2011
 
Description Centre for tropical livestock genetics and health (CTLGH) 
Organisation International Livestock Research Institute (ILRI)
Country Kenya 
Sector Charity/Non Profit 
PI Contribution Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org)
Collaborator Contribution The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health.
Impact The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together.
Start Year 2016
 
Description Centre for tropical livestock genetics and health (CTLGH) 
Organisation Scotland's Rural College
Country United Kingdom 
Sector Academic/University 
PI Contribution Mick Watson is co-leading programme 5 (informatics and bioresources) programme of CTLGH which aims to collect data on genotype and phenotype into a central database which can subsequently be mined for useful associations. So far we have ensured that scientists have access to the latest high performance computing environment for research, we have analysed and continue to analyse hundreds of farm animal genomes from LMIC countries, and we have built the data portal (http://data.ctlgh.org)
Collaborator Contribution The partners are involved in all programmes, which include:Program 1: Harnessing genetic variability among indigenous and exotic breeds of cattle (as well as their crosses) to develop genetic and genomic tools that will be used to improve productivity under harsh tropical conditions and to mitigate the impact of cattle on climate change. Program 2: Harnessing genetic variability in tropical productivity and adaptation among various breeds of Chickens. Program 3: Development and application of precision breeding (through novel reproductive and germplasm technologies) to achieve step changes in livestock genetic improvement. Program 4: Understanding the genetic and molecular mechanisms underlying the tolerance of certain cattle and poultry breeds to tropical diseases and pests. Program 5: A shared global data and biological sample resource to support continued research and development on tropical livestock genetics and health.
Impact The data portal so far: http://data.ctlgh.org The collaboration is multi-disciplinary, bringing together geneticists, parasitologists, virologists, epidemiologists and data scientists together.
Start Year 2016
 
Description Mass Vaccination of Dogs for Rabies in Malawi and India 
Organisation Mission Rabies
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Roslin and R(D)SVS are providing statistical, epidemiological and logistic support and data analysis to Mission Rabies for their mass vaccination campaigns.
Collaborator Contribution Mission Rabies are supplying access to the data and 50% support for a PDRA post. We also supervise 1 PhD and 1 MSc student from the Mission Rabies charity.
Impact 2 research papers
Start Year 2016
 
Description The Evolution of Mycobacterium bovis evolution in Africa 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution We have made available a collection of Mycobacterium isolates from cattle from across Africa that the BBSRC funded plus one has coordinated.
Collaborator Contribution The USDA have sequenced these isolates using their WGS pipeline.
Impact work is still in progress
Start Year 2016