PhD opportunity

Applying Statistical and Deep-Learning Methods to the Joint Analysis of Pathology and Sequencing Data in Prostate Cancer

The project

 

There are many questions in Prostate Cancer that we can seek to address either through sequencing or imaging (e.g. tumour classification, prognosis, inference about the micro-environment). There are questions about sub-cellular localization that can be answered directly for small numbers of molecules via imaging approaches or inferred for large numbers of molecules from sequencing data. Further, it was recently shown that characteristics of the genome such as whole-genome duplication as well as focal mutations can be inferred from pathology images with the application of deep learning (https://www.biorxiv.org/content/biorxiv/early/2019/10/25/813543.full.pdf). While it seems likely that a portion of the RNA profile of a tumour could be similarly predicted from the pathology images. Considering data from the Cancer Research UK-funded Prostate Cancer ICGC Group, and the PanProstate Cancer Group, this project will look jointly to analyse pathology and sequencing data, both to understand better those data, but also to find the best estimates of characteristics that can be estimated from both.

Primary supervision will be provided by Prof Andy Lynch with secondary supervision from Dr Peter Caie, both within the School of Medicine. Prof Lynch is also a member of the School of Mathematics and Statistics, while Dr Caie is a platform lead at the Sir James Mackenzie Institute for Early Diagnosis, and the successful student, while based in the School of Medicine, will have interactions with these as well.

Andy Lynch was a PI on the phase of the Cancer Research UK-funded Prostate Cancer ICGC project that generated RNA- and Methylation sequencing data from 200 men with prostate cancer. These data joined the rich whole-genome sequencing and clinical data generated for the same men in phase I of the project. He is now involved in several analysis groups of the PanProstate Cancer Group project (http://panprostate.org/), an international effort to combine data from over 2000 prostate cancers, which is part-funding this project.

Dr Peter Caie is the PI of the Innovate UK-funded iCAIRD project in St Andrews (https://icaird.com/about/eco-systems/). The iCAIRD project involves analysing thousands of pathology images through computer vision algorithms, developed in house, in order to perform automated and accurate diagnostics for gynaecological pathology. iCAIRD involves clinical and industry partners collaborating with our academic teams to ensure high impact of the research. Dr Caie’s other funded projects involve the analysis of the complicated cellular interactions and associated protein expressions within the tumour microenvironment, through automated image analysis, that may inform on disease aggression.

 

Entry requirements

Candidates should have a numerate background preferably with a master’s-level degree giving them expertise and experience in applied statistics or machine/deep learning.

 

Funding Notes

This is a 3 year funded PhD studentship comprising of tuition fees (Home/EU) and stipend at current research council rates.

 

Start date

September 2020 to January 2021, Negotiable.

 

How to apply

In the first instance, applicants should submit a CV and covering letter to Andy Lynch andy.lynch@st-andrews.ac.uk  and Peter Caie pdc5@st-andrews.ac.uk

 

Closing date

Open until the position is filled

 

For further details on the project or informal enquiries please contact Andy Lynch andy.lynch@st-andrews.ac.uk  or Peter Caie pdc5@st-andrews.ac.uk

 

 

Associate Lecturer in Medical Ethics

We are seeking to appoint an Associate Lecturer in Medical Ethics to deliver a mix of online and face to face teaching for the BSc and ScotGEM programmes. The postholder will work closely with the BSc (Hons) and ScotGEM Course Directors to enhance curriculum, deliver lectures, teaching and assessment; and to support the schools wish to inspire the next generation of medical graduates.
The post is fixed term for 2 years for 11 hours per week.
Requests for additional information and informal enquiries may be directed to Dr Anita Laidlaw (ahl1@st-andrews.ac.uk) or Dr Alun Hughes (ah200@st-andrews.ac.uk)
The University is committed to equality for all, demonstrated through our working on diversity awards (ECU Athena SWAN/Race Charters; Carer Positive; LGBT Charter; and Stonewall).  More details can be found at http://www.st-andrews.ac.uk/hr/edi/diversityawards/.
This role does not meet the minimum requirements set by the UKVI to enable sponsorship of migrant workers.  Further information can be found at https://www.st-andrews.ac.uk/staff/policy/immigration/.
Closing Date: 13 July 2020                                                                     
 
Interview Date: 30 July 2020     
Please quote ref: AO5549DD                              
Full details of the post can be found on the University’s vacancies page

Feel the beat: implanted microlasers scan heart from inside

Leading an interdisciplinary team of scientists, Dr Samantha Pitt of the School of Medicine and Dr Marcel Schubert and Professor Malte Gather of the School of Physics at the University of St Andrews, embedded tiny lasers into individual heart cells, and by analysing the light these lasers produce they monitored the contractions of the heart muscle.

The paper “Monitoring contractility in cardiac tissue with cellular resolution using biointegrated microlasers” by Marcel Schubert, Lewis Woolfson, Isla R M Barnard, Amy M Dorward, Becky Casement, Andrew Morton, Gavin B Robertson, Paul L Appleton, Gareth B Miles, Carl S Tucker, Samantha J Pitt and Malte C Gather is published in Nature Photonics (June 15th 2020) and is available online.

Although the research is still in its early days, the present study proves that microlasers can act as versatile contractility sensors that can resolve fast dynamic processes inside individual live cells and whole hearts.

The University press release can be found here https://news.st-andrews.ac.uk/archive/feel-the-beat-implanted-microlasers-scan-heart-from-inside/

Unlocking the spread of Covid-19

Medical scientists at the University of St Andrews have joined forces with data scientists Blue Hat Associates to further medical research and understanding about the spread of Covid-19 within the community.

How Covid-19 spreads within the community and individual households remains uncertain as current data is based on people who receive medical care.

A Covid-19 tracker app allows people to share data on the members of their household including symptoms.

This research, one of three research projects awarded to St Andrews as part of the Scottish Government’s Covid-19 Rapid Research programme, aims to extract key information from households’ reports of Covid-19 and link these with medical records to get a better idea of the true number of people with the disease.

The project will look to see if people who stay at home with Covid-19 have different symptoms to those who need medical help or are admitted to hospital.

Using data being collected in the recently launched c19track.org website, this crowd-sourced data will help researchers understand the profile of the pandemic within households and within communities.

Key advantages of this tracking includes:

  • Capturing data and updates on an entire household or neighbourhood
  • Tracking the disease in children
  • Recording all symptoms of illness
  • Simple technology allowing those without smartphones to record their data

St Andrews Medical School intend to use the data to research the outcomes for patients recovering in a home setting against those who seek GP support.

The data collected will be made available to research institutions and those signing up will be able to see the profile of their local area. Those signing up are agreeing to share their anonymous data with other organisations, and can opt in to share personal data for St Andrews medical research.

Professor Colin McCowan from the School of Medicine at St Andrews said: “One of the big unanswered questions with Covid-19 is how many people actually have caught it. We know about the people who contact the NHS but not those who have stayed at home self-isolating.

“This work will help us identify that group of people and allow us to examine if there are differences between them and the people who have contacted the NHS. This will give us a more accurate picture of how many people have Covid-19 and also help in planning how best we look after them.”

Blue Hat founder, Tim Palmer, said: “As experts in data and analytics, we saw a lack of breadth in the data being collected, focussing on a narrow set of symptoms of those within a medical environment. We developed a crowd sourced data tracker in March to catch data from families who may only have minor symptoms and are delighted St Andrews will be using the data to aid the research.”


What is the purpose of the website?
In March a group of data scientists launched c19track.org. At this point no one knows exactly how many people have been infected with Covid-19. There are many people with the virus who are invisible in the official numbers or only have mild symptoms. Without testing it is hard to know, so the aim is to help record peoples’ symptoms to get a better snapshot of where the infections are and how many people really have the disease.

Who is Blue Hat?
Blue Hat is a team of data scientists who want to help, coming together to gather the missing information and provide it to the scientists who can help stop this virus. Blue Hat believes you can help by self-reporting online using this website, which will help understand more about the virus in our communities.

What is it trying to capture?
The website looks to build up a picture of the health for all members of a household, and for as many households in a geographic location as possible. This will provide crucial information and permit analysis at a postcode and local level of both the spread and current existence of the Covid-19 virus.

The data will help scientists to understand the profile of the disease at a local level, not a national or even county-wide level, but at a level which will be more relevant for each household, their local school and local community.

Is it any different to the others already out there?
Other symptom tracking apps are available, but Blue Hat’s website allows an entire household’s data to be captured on a simple web page allowing the scientists to track children and vulnerable people who could not fill in the forms for themselves. Occasional updates of this data are requested.

Unlike a number of apps which look to track a person’s Covid-19 symptoms in considerable detail, asking a significant number of specific health questions, the Blue Hat website approaches pandemic data gathering from the perspective of the community effect of the disease.

The aim is to build up a picture of the spread of the virus within households and within communities.  This is something personal app trackers do not do, and is something that Blue Hat believes is going to become crucial in understanding the spread of the pandemic, the real level of infection in a community, and the potential for any local relaxation of quarantine in due course.

How does this link to the NHS contract tracking app?
Blue Hat’s tracking works in an entirely different way and for a different purpose. The website is asking households to record contact information, creating a sample of a different cross section of the population without access to the latest technology.

What personal information will it hold?
The information collected by the website is simple, limited, and focused on the health of each member of a household in relation to Covid-19 symptoms. It includes:

  • email address to communicate
  • postcode to identify geographic location
  • names of people of household
  • health of each member of the household
  • IP address for data security management

Isn’t it becoming too late to capture this information?
It is clear that in a number of regions and communities there is a growing instance of suspected Covid cases, and tracking this information is going to be increasingly important.

It is likely that there will be great benefit for researchers, for purposes such as immunisation, to have accurate information and this can only be collected at the time a community is experiencing the pandemic. Surveys undertaken after the event are likely to be of limited use or have sufficient detail to be able to make critical judgements from.

Will my neighbours be able to see if I have had Covid-19 through the website?
Data will not be shared at a level where it will be possible to identify an individual household. Data will be anonymised and reporting is done on groups of households. The size of the area disclosed to a registered user will depend on the uptake in the area, but will not permit any sole households to be identified within a postcode.

How do I know my details will be safe?
The website has been properly registered with the information commissioners and will operate within all the regulations of the UK/EU in terms of data protection and GDPR. All information will remain within the EU and held securely on a globally recognised cloud platform.

Only aggregated and anonymised data will be shared – no personal information will be shared unless specifically requested and then only for the purposes of medical research. The underlying data will be made available free of charge to academic researchers working to understand the virus and helping to prevent future outbreaks.

Who has developed the website?
The c19track website has been developed by a group of experts in high security data systems who are used to working in government and banking technology software. The software team working on c19track are all affiliated with Blue Hat Associates, a London-based software development business.

What will St Andrews do with the information?
Subject to approval from the individuals, St Andrews will combine the tracker data sourced in the community with NHS medical data.

Is anyone going to make money from the Covid-19 data?
No, the purpose of the website is to help medical researchers and academics better understand the spread of Covid-19, and for contributors to see the profile of their local area. The data is being made available to these groups for free, and individual data will only ever be shared for medical purposes and only if explicit consent has been given.

Issued by the University of St Andrews Communications Office.

 

Unlocking the spread of Covid-19

 

Teaching Excellence Awards 2020

Dr Lysa Owen was one of the recipients of five Teaching Excellence Awards which were made for outstanding contributions to learning and teaching across the University. Lysa’s nomination mentioned her exceptional work in the development and delivery of inspirational teaching as part of the innovative Clinical Interactions Course (CLIC) component of the ScotGEM programme.  In particular, her hands-on approach and enthusiasm demonstrated by how students immerse and engage themselves in their learning experience.

 

The full list of winners can be found on the University website, congratulations to all nominees and award winners.

Students Association Annual Teaching Awards

The Students Association held their annual teaching awards in virtual format this year, and we were delighted to see so many members of Medicine nominated by students this academic year:

David Harrison – Nominated for Best Teacher

Predrag Bjelogrlic – Nominated for Teaching Innovation

Gozde Ozakinci – Nominated for Best Project/Dissertation Supervisor

Gary Barclay – Nominated for Commitment by a Member of Professional Services Stafff

 

We are also delighted that Nathan Titterton recieved the Proctor’s Award for his outstanding contribution to the experience of all students within the School of Medicine.

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Funding awarded from the CSO for research into Covid-19

Researchers from the School of Medicine have been awarded funding from the Government’s Chief Scientist Office following their funding call for for Scottish-led rapid research in Covid-19.

 

Dr Ruth Bowness will lead Multiscale mathematical model to simulate Covid-19 infection, and Prof Colin McCowan has been awarded funding for the project Identifying community Covid-19 cases and exploring differences with patients diagnosed in healthcare settings.  Additionally, Dr Anita Laidlaw and Dr Jo Cecil will be working with Dr Kim Walker from the University of Aberdeen on the project ‘To develop evidence-based interventions to support doctors’ well-being and promote resilience during COVID-19 related transitions (and beyond)’ and Dr Gozde Ozakinci will be working on the project ‘Protecting population physical & mental health during the coronavirus pandemic: A representative national weekly survey to understand changes’ with Prof Diana Dixon also from the University of Aberdeen.

 

Full details of all the funding awarded can be found on the CSO website

Covid-19 – Ask the experts

During April and May 2020, ‘three ask the expert’ sessions were held for staff to answer their queries on Covid-19. These were introduced by Prof Stephen Gethins. The panel included Prof Stephen Gillespie and Dr Devesh Dhasmana from the division of Infection and Global Health in the School of Medicine and Janey Watt from Environmental Health and Safety Services

Dr Dhasmana

 
Dr Dhasmana responded to queries around treatments for the virus, and why the NHS isn’t using treatments being used elsewhere. Professor Gillespie addressed questions on lockdown and how long it will last and compared the various coronaviruses, specifically Covid-19 with SARS and MERS. Janey Watt addressed anxieties around PPE, and in particular face masks, how the University is keeping essential staff safe, and what Occupational Health offers to support mental wellbeing.

Professor Gillespie

 
The panel also shared information on what asthmatics need to know to protect themselves and fielded live questions on obesity as a high risk factor for Covid-19; the risks to staff members who have to administer emergency first aid; how long the virus lives on surfaces and what you need to do to eliminate it; and why the UK has one of the highest reported death rates.

 

Source: In the Loop, Issue 391