MICA: Application for a Mental Health Data Pathfinder award (Oxford)

Lead Research Organisation: University of Oxford

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

Making data findable and interoperable, adding value to existing datasets and enriching data collection from person-centric and patient reported measures represents the most valuable opportunity to accelerate understanding and improved treatment of mental health conditions.
Building on our experience of leading national and international programmes enabling access, interoperability and reuse of data for mental health - including the platform enabling use of Electronic Medical Records for mental health across England (CRIS), the platform for data aggregation for dementia (DPUK) and the pan-European platform to enable data interoperability from cohort and real-world data (EMIF) we propose here a programme of work including
underpinning themes and four indicative projects. These projects will gain from the linkage we propose to establish between routine care data and primary, secondary, schools and cohort data and will use devices to collect data remotely ranging from patient reported outcome measures to cognition, sleep and behaviour. To these enormous volumes of data, including the full mental health medical records from 10k people we have already linked to UK Biobank and the generation of 10k proteomes linked to mental health records, plus the streaming data from connected devices, we will bring advanced analytics from the Mathematics Institute and Natural Language Processing from computer scientists using neural networks. All our work will be enveloped in a governance and ethics stream with patient and public involvement. We leverage more than £40m in existing grant funding plus new cash and in-kind contribution from industry partners of over £12m. The outcome will be an informatics supported platform for experimental
medicine, increased understanding and development of novel therapeutics for depression and a bold drive to determine the relationship between intervention and outcome in mental wellbeing in young people. These themes and proposed projects will work with our proposed partners to establish the preparatory work for a platform for Mental Health Data capitalising on the unique opportunities presented by the NHS, by strengths in mental health research and by outstanding
digital sciences in the UK and in Oxford.

Publications

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Cipriani A (2019) Providing the most appropriate care to our patients. in Evidence-based mental health

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Gligic L (2020) Named entity recognition in electronic health records using transfer learning bootstrapped Neural Networks. in Neural networks : the official journal of the International Neural Network Society

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Goodday SM (2020) The True Colours Remote Symptom Monitoring System: A Decade of Evolution. in Journal of medical Internet research

 
Description Collaboration between Oxford MRC Pathfinder Colleagues and Oxfordshire County Council - collected and provided data (and gave advice) to the council on pupils' mental health from participating schools in the region
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Gave evidence to a government review
Impact The local authority will contribute to future data collections and liaise with the MRC Pathfinder team to understand the mental health of pupils in Oxfordshire, and use the data and advice from experts in the field to guide policy. Report to be published this month (February 2020) on the Joint Strategic Needs Assessment website, summarising the mental health of students in Oxfordshire
URL http://insight.oxfordshire.gov.uk/cms/joint-strategic-needs-assessment
 
Description AI for the discovery of new therapies in Parkinson's (JBCF)
Amount £200,000 (GBP)
Funding ID A2926 (Rosetrees) 
Organisation John Black Charitable Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2020 
End 04/2023
 
Description Alzheimer's gut microbiome project (NIH)
Amount $5,200,000 (USD)
Funding ID 1U19AG063744-01 
Organisation National Institutes of Health (NIH) 
Sector Public
Country United States
Start 07/2019 
End 06/2024
 
Description Deep learning of genomic associations with Alzheimer's Disease (J&J)
Amount £400,000 (GBP)
Funding ID No reference number yet 
Organisation Johnson & Johnson 
Sector Private
Country United States
Start 06/2020 
End 05/2023
 
Description Rising Start Initiative - stage 2
Amount £99,000 (GBP)
Funding ID No reference number 
Organisation Ono Pharmaceutical 
Sector Private
Country Japan
Start 03/2020 
End 06/2021
 
Description Unlocking evidence from electronic patient records for smart intervention of mental health disorders (EPSRC)
Amount £45,000 (GBP)
Funding ID EP/N026977/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 03/2019
 
Description Virtual Brain Cloud (H2020)
Amount € 15,000,000 (EUR)
Funding ID H2020-SC1-DTH-2018-1 
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2019 
End 12/2022
 
Title EMIF1000 
Description We have collected 1200 blood samples of psychiatric patients and controls, and measured protein concentrations with Somalogic 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact New bio-markers of psychiatric disorders 
 
Title MAP2PD 
Description We have collected blood samples of patients with neurological disorders, and measured protein concentrations with Somalogic technology 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact We are creating bio-markers with these data samples 
 
Description Alan Turing Institute 
Organisation Alan Turing Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution We provide advice to Alan Turing Institute on machine learning methods applied to psychiatric disorders. We collaborate in their talk series regarding natural language processing methods in mental health reserach.
Collaborator Contribution They provide advice and further funds for us to apply machine learning methods to data collected with digital apps from patients.
Impact Further collaborations with members of the network of the Alan Turing Institute. Some of our publications presented in this report.
Start Year 2019
 
Description DPUK 
Organisation MRC Dementias Platform UK
Country United Kingdom 
Sector Academic/University 
PI Contribution We have provided our blood biomarkers datasets to DPUK, in order for them to make such data available to other researchers internationally. We have further selected, managed and analysed blood samples provided by DPUK in order to create new biomarkers of psychiatric disorders.
Collaborator Contribution DPUK has provided a significant part of the blood samples used by Somalogic to measure protein concentrations. Somalogic then submitted this data back to us in order for us to build new biomarkers of psychiatric and neurological disorders.
Impact We have built several blood based biomarkers with the samples obtained through this collaboration. Several of the publications are a direct consequence of this work.
Start Year 2019
 
Description Department for Children, Adults and Health (S. Gloucestershire County Council) and Oxford MRC Pathfinder colleagues 
Organisation South Gloucestershire Council
Country United Kingdom 
Sector Public 
PI Contribution We provided expertise in making the best use of their survey data for research purposes, and also guiding policy.
Collaborator Contribution The council provided us access to their survey data to include in an analysis of our Oxfordshire data.
Impact A platform for this data is being set up on UKSeRP infrastructure.
Start Year 2019
 
Description Foster and Brown Research Ltd and MRC Oxford Pathfinder Colleagues 
Organisation Foster and Brown Research
Country United Kingdom 
Sector Private 
PI Contribution We gave them £65,000 (alongside the Oxfordshire County Council's £10,000).
Collaborator Contribution They collected online pupil survey data including recruitment, technical support, data cleaning, liaison with schools, training sessions and reporting.
Impact Outputs include - 4500 pupils' data. We're expecting another 15000 in 2020/21. Data are made accessible to participating schools and the local authority via an online data tool.
Start Year 2018
 
Description Fraunhofer Society 
Organisation Fraunhofer Society
Department Fraunhofer Institute for Algorithms and Scientific Computing
Country Germany 
Sector Public 
PI Contribution We have provided blood biomarker datasets to the Franhofer SCAI institute through our joint Virtual Brain Cloud program.
Collaborator Contribution Thanks to their accumulated experience on this area, SCAI has thoroughly curated the datasets that we have provided, to a level of quality that we would have been unable to achieve.
Impact Several publications in preparation are a direct consequence on this collaboration. Also a consequence of this collaboration is significant additional funding that we have obtained from the European commission in a joint proposal between Oxford and SCAI. They have further connected us with a significant network of collaborators across European, who closely share our same research interests.
Start Year 2018
 
Description Generation Scotland - University of Edinburgh 
Organisation Generation Scotland
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution We have selected and managed the blood samples provided to us by Generation Scotland. Somalogic has measured the concentration of 5000 proteins in these samples, which we have then analysed to created biomarkers of psychiatric and neurological disorders.
Collaborator Contribution The University of Edinburgh, through their Generation Scotland program, has provided a significant part of the blood samples used in our collaboration with Somalogic
Impact A good part of the samples profiled by Somalogic are coming from this collaboration with Generation Scotland. Several of the publications that resulted from our MRC Pathfinder program used these samples as their core dataset.
Start Year 2019
 
Description Generation Scotland - University of Edinburgh 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution We have selected and managed the blood samples provided to us by Generation Scotland. Somalogic has measured the concentration of 5000 proteins in these samples, which we have then analysed to created biomarkers of psychiatric and neurological disorders.
Collaborator Contribution The University of Edinburgh, through their Generation Scotland program, has provided a significant part of the blood samples used in our collaboration with Somalogic
Impact A good part of the samples profiled by Somalogic are coming from this collaboration with Generation Scotland. Several of the publications that resulted from our MRC Pathfinder program used these samples as their core dataset.
Start Year 2019
 
Description Johnson and Johnson 
Organisation Johnson & Johnson
Department Janssen Pharmaceuticals
Country United States 
Sector Private 
PI Contribution We are analysing the cardiovascular and immune component of psychiatric disorders with additional funds provided by Johnson and Johnson (J&J), which is a common area of scientific interest to our laboratory and to J&J.
Collaborator Contribution J&J has provided significant funds to completely support the research on this common area of interest.
Impact Several of the publications of our MRC Pathfinder program are a direct consequence of this collaboration. Future collaboration with J&J in planning stage are a direct consequence of this shared work with J&J.
Start Year 2018
 
Description NIHR Clinical Research Network 
Organisation National Institute for Health Research
Department NIHR Clinical Research Network West Midlands
Country United Kingdom 
Sector Academic/University 
PI Contribution MRC Pathfinder colleagues have designed a study to assess the role of physical health on response to treatment for depression.
Collaborator Contribution NIHR CRN are providing infrastructure support in developing the protocol and preparing the trials for the study. Biotekna are providing hardware to use in this study, to assess the physical health of patients.
Impact This collaboration has helped to strengthen our relationship with health professionals and industry.
Start Year 2019
 
Description NIHR's Applied Research Collaboration (ARC) and MRC Oxford Pathfinder colleague 
Organisation National Institute for Health Research
Department NIHR CLAHRC East of England
Country United Kingdom 
Sector Public 
PI Contribution We are working together in next iteration of the survey and research and dissemination plan: Schools Mental Health Implementation Workstream, Mental Health across the Lifespan Theme, along with ARC.
Collaborator Contribution They funded the salary of one of our lead researchers and guidance.
Impact We are working together in next iteration of the survey and research and dissemination plan: Schools Mental Health Implementation Workstream, Mental Health across the Lifespan Theme, along with ARC.
Start Year 2019
 
Description Ono Pharma 
Organisation Ono Pharmaceutical
Country Japan 
Sector Private 
PI Contribution We have been developing new Artificial Intelligence (AI) and Neural Networks (NN) methods to analyse genomics datasets. These new algorithms have a sensitivity unmatched by any current genomics technique. Ono Pharmaceutical is then applying these algorithms to psychiatric disorders of common interest to us and Ono.
Collaborator Contribution Ono Pharma has provided significant funds to completely fund this work.
Impact Several publications in preparation are a direct consequence of this collaboration. New algorithms to analyse genomic data have been developed.
Start Year 2018
 
Description RED January & MIND exercise intervention 
Organisation Mind Association
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution This is a new collaboration between the RED January organisation, Mind, the mental health charity and the University of Oxford. We wanted to test the efficacy of the month-long 'intervention' to encourage people to exercise to benefit their mental health. A post-doc (Catherine Wheatley) adapted the before and after questionnaires in collaboration with Mind, and conducted structured interviews with >30 participants.
Collaborator Contribution Mind collects and hosts the questionnaire data which is collected from individuals who respond to RED January marketing material. We entered into a data sharing arrangement with Mind so that we can analyse the data.
Impact Data collection just completed - outputs pending
Start Year 2019
 
Description Somalogic 
Organisation SomaLogic
Country United States 
Sector Private 
PI Contribution Somalogic (https://somalogic.com/) is our main partner in our bio-markers research. They specialise on measuring protein concentration in blood samples, with a state-of-the-art platform able to obtain the concentration of 5000 proteins simultaneously. This is the service that they provide to us. The collaboration is very active and on-going.
Collaborator Contribution Our partners select and prepare the blood samples of our research participants. Somalogic then process these samples to measure protein concentration, which they then submit back to us. We use these measurements to predict patient prognosis.
Impact - Thanks to this collaboration, we have obtained the protein concentration of approximately 1200 patients and controls. We have then used these measurements to predict patient diagnosis in advance to the presentation of any behavioural symptoms. Several of the publications of our MRC Pathfinder program are a result of these samples. Future publications will still emerge from these samples - Through this collaboration we are currently processing an additional 2000 samples of psychiatric patients and controls. Once Somalogic provides to us their measurements, this dataset will be the largest proteomic cohort word-wide for some of the diseases under scrutiny. Significant publications are expected to emerge from this dataset.
Start Year 2018
 
Description University of Manchester - NLP 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution We have collaborated with Prof Goran Nenadic and his team (University of Manchester) on the Natural Language Processing (NLP) work of our MRC Pathfinder program.
Collaborator Contribution Prof Nenadic has provided advice and supervision to our NLP work.
Impact Several of the publications of our MRC program are a direct consequence of this collaboration. As a consequence of this collaboration, we have further obtained £60,000 in funding from EPSRC's New Mind program.
Start Year 2018
 
Title Machine learning genomics 
Description New machine learning methods able to improve the sensitivity with which we can analyse genomics data from psychiatric disorders. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2019 
Impact MSc students projects and publications 
 
Title New Mind NLP library 
Description In collaboration with the University of Manchester and Deep Cognito (Manchester), we have developed a Java library to extract medical information from text as recorded in Electronic Health Records. 
Type Of Technology New/Improved Technique/Technology 
Year Produced 2019 
Impact Some of our publications are a result of this software. Our research team and collaborators in the UK-CRIS network are using this software. 
 
Title True Colours platform 
Description True Colours is a web application that allows patients and participants to self monitor their mood and associated metrics (e.g. sleep, life events, activity etc). It has been in use for >10 years and the Pathfinder grant has enabled its continued development and maintenance. 
Type Of Technology Webtool/Application 
Year Produced 2019 
Impact True Colours has been used by >36000 patients/participants as part of research studies, trials and clinical service. There have been >50 publications arising from its use and a paper was published this year describing the impact (Goodday et al, 2019 - see publication list). 
URL https://oxfordhealth.truecolours.nhs.uk/www/en/
 
Company Name Akrivia Health (Cristal Health) 
Description With over 440 billion datapoints, agreements with 12 NHS trusts, and more than 3 million patient records, Akrivia has the largest and richest mental health dataset to accelerate research for better treatments and care. 
Year Established 2019 
Impact The company is making Electronic Health Records (EHRs) accessible for research purposes. A thorough data access process has been established for this aim, with close supervision from patients and NHS trusts.
Website https://akriviahealth.com/
 
Description : Feedback of findings of Oxfordshire Online Pupil Survey to school mental health leads as part of Oxford Health NHSFT outreach event to Trailblazer schools. 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact As described above
Year(s) Of Engagement Activity 2020
 
Description CAMHS evaluation Dissemination event 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Dissemination activity informing attendees of results of evaluation of CAMHS including some key data from the survey that was conducted as partof pathfinder
Year(s) Of Engagement Activity 2019
 
Description Chair at NICE meeting to discuss guidelines for depression 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Chaired a meeting to discuss the NICE guidelines for treating depression.
Year(s) Of Engagement Activity 2019
 
Description Chaired a session on 'MRC Pathfinder Session 2' at MQ Mental Health Conference in Edinburgh, Scotland (September 2019) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact John chaired a session on the Edinburgh, KCL and other Pathfinder award presentations at the MQ Mental Health Conference in Edinburgh, Scotland (September 2019). He took the place of Prof Andrew McIntosh at very short notice. The purpose was to increase awareness of one's own work and network with other Pathfinder award winners. The impact was gaining new insight into other Pathfinder projects' and new strategies for developing a platform.
Year(s) Of Engagement Activity 2019
URL https://www.mqmentalhealth.org/articles/data-science-meeting-2019-agenda
 
Description Presentation of survey results. Youth in Mind conference. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Third sector organisations
Results and Impact Presentation of research plan with keynote presentation to delegates from children's services across all sectors in Oxfordshire
Year(s) Of Engagement Activity 2019
URL https://www.oxfordshiremind.org.uk/youth-in-mind-conference/
 
Description Presentation to schools and parents at "Young Resilient Minds" event 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Presentation of preliminary pupil survey results to local schools, service providers, third sector and parents at "Resilient Young Minds" event organised at Bladon Primary School.
After the presentation, I (Karen Mansfield) gave a short interview to local news.
Year(s) Of Engagement Activity 2019
URL https://www.youtube.com/watch?v=vK_cFOky22c
 
Description Public seminar for Department of Education 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This is made into a podcast and presentation of findings from survey has been included
Year(s) Of Engagement Activity 2020
 
Description School governor meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Talk to school governors including results of pathfinder survey
Year(s) Of Engagement Activity 2019
 
Description School meeting with governors and pastoral team leads 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact In depth examination of survey findings of relevance to the school
Year(s) Of Engagement Activity 2019
 
Description Supported Karen Mansfield (Postdoc) Presentation on Pathfinder at MhDEL workshop (Mental Health Data Ethics Leadership - Ethics and Governance in Data Linkage Workshop) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Karen Mansfield (Postdoc) presented her talk on opportunities and challenges for linking adolescent mental health data in the UK - the purpose was to get feedback from others working in the area and beyond to understand the issues from multiple perspectives, including HRA and funders. Outcome - we got useful feedback and contacts to move this work forward in collaboration with other researchers across the UK.
Year(s) Of Engagement Activity 2019
 
Description Thames Valley Strategic Health meeting 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Discussion with key practitioner with regards to the long term plans for childrens services
Year(s) Of Engagement Activity 2020
 
Description child Psychiatry Regional Meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presentation of pathfinder results to Child Psychiatrists
Year(s) Of Engagement Activity 2019