Category: Influencing Policy

Improving science practice and impact for all

Influencing Policy

Socialising the Genome

DATE: 14/03/16
By Anna Middleton

gnome_01177How easy is it to strike up a conversation about genomics? Geno-what?

Does the average person on the street know enough about the issues to even care?  A project called Socialising the Genome has just been launched to explore how to turn genomics from an anti-social concept to a more social one. Animations were created from focus group discussions to help understand how people talk about genomics, and what they understand. These animations are now on the newly launched website www.genetube.org.

searchme_01263It’s not just science of genomics that can seem impenetrable. Just the name itself can take people in all kinds of odd directions. [Several focus group participants assumed there to be a ‘mistake’ in pronunciation: sounding the silent ‘G’ in Gnome. This takes us off into all sorts of interesting tangents about the options for ‘Gnome testing’!]

The first time people might experience genomic technology is when being tested as part of routine healthcare and something genetic or inherited is picked up. Given that genomics is now becoming a mainstream source of data within most disciplines in medicine, it is likely that all of us will have some sort of genomic test at some point in our lives.

dnazing_00843Some of us will care little for the science behind those tests – in much the same way many of us know little of the engine under the bonnet of our car. However, the impact of a genomic test result may be relevant, not only to you, but also your family (this makes it quite different from other sorts of medical tests that give individual health results). Such a test may also reveal information that is quite unexpected as many different medical conditions are tested in one go.

What hooks can be used to convey the concepts, make it personal, help it resonate?
What sort of framings – narratives, metaphors, mantras and memes – can we use to socialise an otherwise dense topic that even the specialists find difficult to navigate?
As a genetic counsellor, these are questions that I’ve been thinking about my whole career.

reasonstobecheerful_00130Reaching people with this, is a challenge; the science needs a conversation boost, it needs to feel meaningful, relevant and not least of all, it needs to be memorable so that the content can be relayed to relatives. After all, genetic information is not only important to individuals but also potentially those nearest and dearest too – it really is a social concept.

In the ‘Socialising the Genome project’ we are thinking carefully about what people already understand about genomics – even if they think they know nothing – and we have built on this to create a series of animations that can help to start a conversation about genomics with patients using the NHS.

searchme_00001The project is particularly exciting due to the novel partnership we have set up between social science (me) and the creative advertising world (Julian Borra Global Creative Strategist and Founder of Thin Air Factory and ex Saatchi and Saatchi Group Creative Director). Julian and I are using our collective skills to see if we can create a ‘populist, scalable conversation’. I provide the material; he provides the razzamatazz.

I have done a series of Focus Groups to explore what various groups of ‘public’ understand and believe already about genes, DNA, genetics and genomics. The insights gained from these have been given a creative makeover and turned into 6 animations. These animations will be evaluated via a set of questions to assess likeability, interest and whether the concepts inspire people to want to share them in some way.

glitch_00494The reason I feel particularly excited to be working directly with Julian is that he has a strong track record of delivering advertising messages that reach millions of people (know of the Churchill Insurance nodding dog? How about Richard Branson’s #VOOMPitch to Rich? Both of these are Julian’s handiwork).

We don’t yet know what messages about genomics resonate with people nor what information they feel they need to know and this is what Julian and I have been puzzling over in considerable detail for the last year. We have created a new partnership that aims to combine our collective skills. Together we plan to discover new messages to deliver information about genomics – messages that connect people to the science, messages that they want to share, and messages that help them when discovering genomics for the first time in the NHS.

dnazing_01427In that way we hope to rub some of the more anti-social corners off the deeper science conversations – and bring them to the dinner, café, chippy and brasserie table, so we can all benefit from having them and sharing them.

The animations can be found at www.genetube.org. Have a look, see what you think, leave us your views. We need to know if they are any good or not; and if not, then that’s useful to know too. We need to find out how to make genomics an everyday conversation for people currently unconnected to it and this is just a first step at finding out how to do this.

Anna Middleton
Anna is a Principal Staff Scientist (social science, ethics, genetic counselling), at the Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge

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Influencing Policy

“Being a scientist is fantastic”

01 July 2015
By Saher Ahmed

The Sanger Institute Fellowship, designed to support scientists who have taken a career break, has been renamed the Janet Thornton Fellowship in honour of Professor Dame Janet Thornton. Credit: EMBL-EBI

The Sanger Institute Fellowship, designed to support scientists who have taken a career break, has been renamed the Janet Thornton Fellowship in honour of Professor Dame Janet Thornton. Credit: EMBL-EBI

“Protein structures are like the atomistic view of life and they are beautiful. They have all the beauty of trees and flowers,” says Professor Dame Janet Thornton, Director of the EMBL European Bioinformatics Institute (EMBL-EBI), pointing out of her office window at the impressive greenery of the Wellcome Genome Campus. “Understanding the molecular basis of life, there can’t be anything better,” she continues. “You look at the trees and you think, they’ve got the same proteins as we’ve got. The fact that we’ve all got DNA is just amazing, isn’t it?”

The desire to unravel protein structure, function and evolution has been the driving force behind Janet’s visionary scientific career. However, science isn’t Janet’s only passion. For nearly 15 years, she worked part time while raising her two children; a choice that’s certainly not the norm in scientific circles and can be perceived as a barrier to career progress.

Janet insists that she never considered that her decision might be detrimental to her career. “I just didn’t think about it. I was worried about managing a pretty busy, complicated but very enjoyable life. I thought about the science and I thought about my family, my children and my friends at home and I really loved having those two sides of my life,” she explains.

Janet has been a leading supporter of the Wellcome Genome Campus’ Sex in Science initiative, which aims to redress the gender imbalance in scientific careers and drive policy and practice change. While women graduates outnumber men in the Biological Sciences, with women making up 58 per cent of the cohort, only 25 per cent of professors are women. Janet’s story is an inspiration and as such, she is lending her name to the Janet Thornton Fellowship, a fund set up by the Sanger Institute to support scientists, whether female or male, who have taken a year out of their career for any reason.

Why is it so hard for women to progress their scientific career and climb the ladder? Janet believes it is down to the perception that science is cut-throat and that taking time out to have a child will put you behind the competition. “Although I honestly don’t think the science is any more competitive now than it used to be, I think it’s perceived to be more competitive,” explains Janet. “There’s a lot more discussion about it being competitive. There’s a lot more hype about what your CV is like, how many publications you’ve got – all of these things that actually, in some ways, detract from the science that you’re doing.”

Janet’s advice is to stop worrying about other researchers and to focus on the science. Above all, Janet is certain that it’s possible to take time out for family and to work part time and still succeed in your chosen field. She says, “You need to be focussed, you need to work hard always, and you need to be flexible. There’s give and take; sometimes you need to be at work and sometimes you need to be at home. Don’t worry too much about what everybody else is doing.”

Everyone has a life outside of work, Janet explains – not just mothers and not just women – and sometimes that life has to take priority. But she adds that the most important thing is to make the most of what is on offer. “It’s about taking opportunities when they are there, being open, sharing and doing your bit for the scientific community.”

Opportunities like the Janet Thornton Fellowship are being created to change preconceptions about how scientists should work and what it takes to reach the top. Janet is a strong believer that a good scientist should be able to progress, whatever barriers stand in their way. “You never know what’s going to be thrown at you from all sorts of different directions but you can focus on living for the moment, both in science and in your personal life. It’s easy to say but it’s quite difficult to do.”

At EMBL-EBI, Janet is working to enable more researchers to follow her carpe diem approach to life in research and, crucially, to encourage more women and men who have commitments outside of work to continue pursuing their passion for discovery.

This year, Janet is stepping down from her role as Director and will begin working part time once more. “You come to work and you have the pleasure of going to lectures and seeing the most fantastic things and you think, ‘wow, I never realised it worked like that’. To be part of that, even if it’s only a little part is amazing. Well, being a scientist is fantastic, really.”

Saher Ahmed is coordinator of the Sex in Science initiative at the Wellcome Genome Campus.

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It's all about reproducibility
Influencing Policy

It’s all about reproducibility

27 May 2015
By Natasha Karp

The Animal Research: Reporting of in Vivo Experiments (ARRIVE) guidelines lay out the reporting requirements to ensure all the information is available to allow reproducible research

The Animal Research: Reporting of in Vivo Experiments (ARRIVE) guidelines lay out the reporting requirements to ensure all the information is available to allow reproducible research

Research has shown that experiments involving animals are frequently not reported with sufficient detail to allow results to be reproduced [1]. We have an ethical responsibility to maximise the value returned from a study involving animals and ensure that the data are collected and presented in a way that maximises reproducibility.

This reproducibility issue identified with published papers lead to the Animal Research: Reporting of in Vivo Experiments (ARRIVE) guidelines [2], which lay out the reporting requirements to ensure all the information is available to allow reproducible research.

The International Mouse Phenotyping Consortium is a world-wide project to understand how genes function in the body by systematically recording the characteristics (phenotypes) of mice in which an individual gene has been switched off. These are known as knockout mice. The ultimate goal is to relate gene function to human disease.

It is a large scale project, with all mathematical and image data published in a public database [3]. The dataset grows daily, and currently includes data from 734,284 experiments. We have taken the ARRIVE guidelines and applied them to our large international database [4]. Applying these guidelines led to two sets of challenges.

The first problem centred on understanding each other and explaining exactly how experiments were implemented at each contributing institute. The fact that the project is international and multilingual wasn’t the only barrier to clear communication; a common issue in science is that we describe things in a multitude of ways and we use the same words to means different things. As an example, the phrase “control mouse” was thought to have no ambiguity but in fact there are four different interpretations.

The second set of challenges was specific to a database of this scale and arose from capturing the data, organising it and presenting it back to a user. This problem is on-going. As the database and tools implemented grow, we have to continue to test our interface and ensure the data are accessible.

Setting this target has been challenging, but worth the journey. We can already see benefits; the process has highlighted good practice across our phenotyping centres and has provided the transparency necessary for scientists around the world to fairly evaluate data that will assist in genetic research.

Natasha Karp is a senior biostatistician who supports the International Mouse Phenotyping Consortium.

References

  1. Kilkenny C, Parsons N, Kadyszewski E, Festing MF, Cuthill IC, et al. (2009) Survey of the quality of experimental design, statistical analysis and reporting of research using animals. PLoS One 4: e7824. DOI: 10.1371/journal.pone.0007824
  2. Kilkenny C, Browne WJ, Cuthill IC, Emerson M, Altman DG (2010) Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. PLoS Biol 8: e1000412. DOI:10.4103/0976-500X.72351
  3. International Mouse Phenotyping Consortium website http://www.mousephenotype.org/
  4. Karp, N  et al (2015) Applying the ARRIVE guidelines to an in vivo database.  PLOS Biology 3: e1002151. DOI: 10.1371/journal.pbio.1002151

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Herds of zebra and impala gathering on Masai Mara plain. Credit: Roomtorun
Influencing Policy

Being part of the herd saves lives

13 April 2015
By Rebecca Gladstone

Barbara Bellingham, Wellcome Images

Vaccinating the population saves lives.
Credit: Barbara Bellingham, Wellcome Images

Streptococcus pneumoniae AKA the pneumococcus is a notorious bacteria that can cause countless types of infections from rapidly fatal meningitis and septicaemia, to pneumonia and common ear infections. The pneumococcus is in fact the leading cause of child death worldwide killing up to 1,000,000 children each year.

A number of new pneumococcal vaccines have been licensed to protect children against pneumococcal infections, which are now being introduced around the world. However, the full potential of these life-saving vaccines could be wasted if we fail to vaccinate enough people.

What’s getting up your nose?

Pneumococci can be found harmlessly living in the noses of around 30 per cent of healthy kids in the UK without causing an infection. This colonisation is not completely benign, though, as it is a way of hitchhiking through the population from person to person, resulting in new infections in the most at risk.

Crucially, a pneumococcal vaccine not only protects the individual against infection by readying the immune system but also prevents colonisation of their noses and subsequent spread of the pneumococcus through the healthy population.

Vaccination needs you and your kids

The reduction in spread between vaccinated individuals also means that infections in unvaccinated individuals can happen less often. This phenomenon is called herd protection.

There is a major caveat, though; enough children need to be vaccinated so that there are not enough unvaccinated individuals to continue spreading between. This is like removing enough stepping-stones from a stream crossing to leave the pneumococcus stranded.

Herd protection works for a number of infectious diseases where the bacteria or virus spreads between people, like measles and polio. With herd protection the minority are protected by the majority. The critical fact is that not everyone can be vaccinated for legitimate medical reasons and these people need to be shielded by having the population around them vaccinated.

Babies under a few months old can get pneumococcal infections like meningitis with devastating consequences yet are too young to be vaccinated, so herd protection is their strongest defence. Additionally, since a pneumococcal vaccine has been given routinely to children in the UK, another group of people vulnerable to pneumococcal infections such as pneumonia have benefited: the elderly. By vaccinating enough children we can protect their grandparents and elders too.

Unfortunately, unvaccinated individuals are not distributed evenly in populations. If the pneumococcus gets to a community where vaccination is low, the bacteria can be harboured in the unvaccinated cluster, moving from person to person like a fugitive searching for its next susceptible victim. The key is that although an unvaccinated child might not get sick themselves, they can pass it to others who could succumb to pneumococcal infection.

An international fugitive

The pneumococcus respects no political borders and is found all around the world. Lower income countries often have higher rates of colonisation and infection and can least afford the vaccines. Herd protection plays a key role here as it reduces the number of vaccines they need to purchase; just enough to block its spread.

Pneumococcal vaccination is complicated further by the >90 different types that exist. We can only vaccinate against a few of them: the most infectious and those most resistant to antibiotics. As we stop the types targeted by the vaccine from circulating and causing infections some of the remaining types partially take their place.

The pneumococcus is a moving target. For this reason we need to constantly monitor which types are causing infection or circulating in healthy individuals all around the world. This is why the Global Pneumococcal Sequencing project is sequencing the biggest ever collection of pneumococcal genomes from all over the world, trying to use genetics to understand changes in the pneumococcal population as it responds to the introduction of vaccines.

NB. I refer to herd protection here rather than herd immunity as technically in the case of the pneumococcal vaccine no active immunity is gained by the unvaccinated, instead the surrounding herd protects them.

Rebecca Gladstone is a Senior Bioinformatician in the Pathogen Genomics group at the Wellcome Trust Sanger Institute, where she is currently working on a global collection of 20,000 pneumococcal genomes to assess pneumococcal vaccine impact. Rebecca is interested in learning how to better share the research findings with the public. She Tweets as @becctococcus.

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Influencing Policy

From bench to bedside

18 March 2015
By Sarion Bowers

Stem cell technology has the potential to deliver new treatments. Credit: Genome Research Limited

Stem cell technology has the potential to deliver new treatments. Credit: Genome Research Limited

The transition from science to technology is not straightforward – great science is not enough to ensure success.

Some technologies, such as the internet, are so novel that they require new infrastructure to make them succeed. Other technologies take us to places we could never foresee: no-one predicted the invention of the selfie-stick when Martin Cooper at Motorola made the first ever mobile phone call.

So how does a new technology go from an experiment in the lab to becoming a life-changing innovation?

It is tempting to think that the steps to making a new technology are easy. Do some interesting science, fiddle around with it to make it useful, market it and lo and behold you have a successful innovative product. Alternatively, that societal need is all that’s required to drive innovation – as the saying goes necessity is the mother of all invention.

However, innovation is not always so simple. Brilliant ideas fail to make workable products or new products cannot overcome incumbent technologies. Sometimes people get so used to using a technology that they cannot or will not change the way they work; that’s when technology gets locked-in.

As I type this on my qwerty keyboard I’m living an example of that very technological lock-in. Despite the fact that I’m creating an entirely electronic document that will possibly never see a piece of paper I’m doing it on a typewriter keyboard. The neat analysis of which letters commonly go together when writing and then ensuring they were placed apart on the keyboard to avoid clashes was so brilliant that the solution has stuck even when the problem is long since gone away. The vast effort that would be required to move on from qwerty is so costly that we are locked-in with this historical relic.

Being the perfect solution to a problem is not the only way to become a successful technology. The Pap smear has long persisted despite being not particularly well suited to the task. Interpreting Pap smear test results is highly subjective and the knowledge required to do this interpretation is hard to transfer from one person to another. It is not easy to describe the changes in a cell that mean it may be cancerous and therefore it is not easy to write down and pass on. Worse still, it is not even clear which changes lead to cancer and which do not.

Learning to interpret Pap smears is time-consuming, difficult and requires experience. However, the relative ease of collecting the sample and the fact that the repetitive task of interpreting results can be done by technicians rather than doctors, who at the time the technology was first introduced were typically women and therefore paid less than men which reduced the cost, means the technology has stuck around for 60-odd years.

Only in the last five years or so has a workable alternative to the Pap smear begun to be introduced. The development of a new test has required the coming together of DNA amplification technologies developed in the 1980s, with the finding that cervical cancer is caused by the Human Papilloma Virus (HPV) and collaboration between industry hospitals, universities and government bodies. The test has to be cheaper, more effective and easier to use than the Pap smear and patients and doctors must be convinced of the validity of testing for HPV rather than looking at cellular changes. The battle between Pap and HPV is far from over and any woman reading this will testify that the speculum is still very much a part of screening for cervical cancer.

These examples show us that the relationship between science and technology is complex. The cost of abandoning an obsolete technology can be too high and the simplicity of a technology can overcome its inadequate nature.

Turning science into technology requires planning, careful thought and consideration and often a serious commitment from governments and other major institutions to push a technology through. This is a problem the Wellcome Trust Sanger Institute is familiar with.

Nearly 15 years on from the completion of the Human Genome Project, we can see how the science of genomics could become a transformative technology for healthcare, but in order to for the idea to become a reality the NHS must be able to take it on, the public must support its use and we must understand the ethical, legal and societal issues surrounding it. It also requires the government to understand the value of these technologies and the challenges faced when trying to introduce a radically different approach to the established organisational structures of the NHS.

The Sanger Institute has been working on these areas for a number of years, through projects such as DDD, research by Anna Middleton into ethics and genomics and through the creation of spin-out companies such as 14M Genomics and Congenica who are developing new technologies for the healthcare market.

Now the Sanger Institute has joined a prospective new cross-Parliamentary group that will focus on implementation and the importance of effective delivery of health innovations for patients as a partner organisation. We believe that by working with politicians across all parties we can help ensure that exciting new sciences become societally valuable technologies for healthcare which can benefit all.

Sarion Bowers is the Research Policy Advisor at the Wellcome Trust Sanger Institute. She has a PhD in Biochemistry. Before joining the Institute she did postdoctoral fellowships in Leeds and Connecticut. She recently completed an MSc in Science and Technology Policy, in which she researched the adoption of genomics into the NHS.

References

  • Casper MJ and Clarke AE. (1998). Making the Pap Smear into the `Right Tool’ for the Job: Cervical Cancer Screening in the USA, circa 1940-95 Social Studies of ScienceDOI:10.1177/030631298028002003

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Credit: Wellcome Library, London
Influencing Policy

Patience is a virtue for tolerant bacteria

13 March 2015
By Kate Baker

Researchers produced three strains of <em>E. coli</em> bacteria tolerant to antibiotics. Credit: David Gregory and Debbie Marshall, Wellcome Images

Researchers produced three strains of E. coli bacteria tolerant to antibiotics.
Credit: David Gregory and Debbie Marshall, Wellcome Images

Treatment failure of antibiotics for bacterial infections represents a global public health crisis. The most well-known issue is antimicrobial resistance, which is identifiable by an elevation in the amount of antibiotic required to stop bacterial growth. Another problem that can result in antibiotic treatment failure is that of antibiotic tolerance.

Tolerant bacteria can survive exposure to elevated concentrations of antibiotics for a limited period of time, with no overall change to the concentration of antibiotics needed to stop the bacteria growing.

Antibiotic tolerance has been linked with treatment failure in those infected with Pseudomonas aeruginosa, a bacterium that often causes blood infections, pneumonia and other complications in hospital patients with weakened immune systems, and Candida albicans, a type of yeast that causes infections such as thrush. Although both the resistance and tolerance of these bacteria to antibiotics are important factors in treatment, the latter is much less studied.

To meet the challenge of safeguarding antibiotics as a therapeutic option, it is important to study antibiotic tolerance and the mechanisms that underpin it. Antibiotic tolerance has previously been linked to small subpopulations of dormant microbial cells, known as persisters, that are not active at the time of antibiotic exposure. However, a recent study identified a further evolutionary mechanism behind tolerance and used genomics to identify the genetic changes responsible.

In the study, researchers from The Hebrew University and the Broad Institute produced three strains of E. coli bacteria tolerant to antibiotics by cyclically exposing them to high concentrations of the beta-lactamase antibiotic ampicillin for periods of three, five and eight hours every 24 hours. After eight to ten cycles, the bacteria were tolerant to ampicillin, as well as an antibiotic from a different antibiotic class, the quinolone norfloxacin.

Researchers could tell that the bacteria were tolerant because the time it took to kill 99 per cent of the bacterial cells increased, whereas the effective concentration remained unchanged.

The altered time period was not associated with changes in cell-doubling time during exponential growth or an increased proportion of persister cells. Using a recently developed automated microscopy monitor (ScanLag1), the authors were able to attribute the enhanced survival to the increased amount of time it took for cells to begin to grow vigorously after exposure to antibiotics, the lag time.

Remarkably, the increase in lag-time was dependent on the length of time each strain was exposed to antibiotics, indicating that the tolerance was customised to the original selection pressure.

The authors named this mechanism tolerance-by-lag and went on to explore the genetic mechanisms behind the phenotype. Performing whole-genome sequencing of individual clones from each of the evolved strains, the authors identified eight new mutations in six genes.

By introducing the genetic changes they saw in the tolerant strains into the original strains, the researchers confirmed that mutations in three of the six genes conferred tolerance-by-lag. The systems of two of the genes (the antitoxin homolog vapB and tRNA-synthetase metG) have been previously associated with persisters but the authors also identified a further pathway involving the essential prs gene, which encodes ribose-phosphate diphosphokinase, an enzyme involved in forming genetic letter bases. In this way, the authors identified and confirmed the genetic changes responsible for tolerance-by-lag.

The clinical significance of tolerance-by-lag will undoubtedly be investigated in subsequent studies. In the interim however, we should consider that antibiotic tolerance goes largely undetected in routine clinical microbiological testing, and that tolerance-by-lag, would be readily identifiable.

As well as uncovering another potential basis for antibiotic treatment failure, this study highlights the benefits of using whole-genome sequencing of bacteria to investigate antibiotic tolerance and resistance within bacterial populations.

Kate Baker is a Postdoctoral Fellow in the Pathogen Genomics group at the Wellcome Trust Sanger Institute, working on the global molecular epidemiology of enteric pathogens and their antimicrobial resistance determinants

References

  • Lewis K (2010). Persister cells. Annual review of microbiologyDOI:10.1146/annurev.micro.112408.134306
  • Fridman O, et al (2014). Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations. NatureDOI:10.1038/nature13469
  • Levin-Reisman I, et al (2010). Automated imaging with ScanLag reveals previously undetectable bacterial growth phenotypes. Nature MethodsDOI:10.1038/nmeth.1485
  • Kaspy I, et al (2013). HipA-mediated antibiotic persistence via phosphorylation of the glutamyl-tRNA-synthetase. Nature CommunicationsDOI:10.1038/ncomms4001

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Influencing Policy

Can sharing your personal data protect your freedom?

28 January 2015
By Sarion Bowers

Professor Mike Stratton supporting the Data Saves Lives Campaign

Wellcome Trust Sanger Institute Director Professor Mike Stratton supporting the Data Saves Lives Campaign

We increasingly live in an age of big data, but does that equate to an Orwellian dystopia where “Big Brother is watching you”? Are privacy and data sharing directly in conflict, or can an organisation’s decision to share your personal data be compatible with protecting your freedom and choice?

The European Union is proposing a new Data Protection Regulation, which could curb data sharing in Europe, including for research purposes. Could legislation that is designed to protect individuals from unwanted use of their data actually undermine the wellbeing of the people it seeks to protect?

At the Wellcome Trust Sanger Institute big data is our bread and butter. In January 2014 we reached a major milestone having collected 1 petabyte (1 million gigabytes) of genomic data and we continue to collect about 1 terabyte (1 thousand gigabytes) each day.

The data that we collect is used around the world to improve knowledge of human and animal health. We pride ourselves on our expertise in sequencing and analysing genomes. Our research is overwhelmingly supported by charitable and public funds, so we believe it right and in the public interest that others benefit from the science we create by sharing our expertise, resources and the data we generate. Doing great science is of limited benefit if others cannot use it.

So, if sharing genomic data is in the public interest where does that leave our participants’ privacy? Our human data is generated from volunteers who donate samples. Whether they are apparently healthy people or people with specific illnesses, they appreciate the fact that their data are beneficial to society. For many participants, they do not simply donate for an individual project, but instead expect and want us to share the data we derive from their donation freely with other researchers.

Our participants recognise that it is not possible to predict the future uses for their data but they still consent to and want their data shared for research purposes. This is typically done in a coded anonymised form that prevents researchers from knowing individuals’ identities.

Alongside consent, the Sanger Institute also operates a managed system whereby researchers must apply to access data. An application to access data is never judged on the merits of the science or whether it competes with our own research, but simply on whether the applicants are seeking to use data for legitimate and ethical research purposes.

As we have the consent of our participants to share data, it is not unreasonable to ask why we have managed access. Consent is a fundamental and critical cornerstone of research, the importance of which cannot be underestimated, but believing that consent completely protects participants from having their privacy breached is, perhaps, a mistake.

Every day people give commercial organisations consent to use their data when they sign up for their services and yet often feel their privacy has been invaded if an organisation uses their data in a way they did not expect. This was exemplified in the backlash that accompanied publication of the experiment Facebook carried out on its users. Every user had given consent but many still felt that Facebook had breached their privacy.

At the Sanger Institute, we believe that guarding data from misuse stands alongside consent as the best means to guarantee we protect our participants’ privacy.

Given that consent is rightly enshrined in research and permeates our society, it is understandable that the European Parliament put consent at the heart of their proposed Data Protection Regulations, which will include health-related and genetic data. Under the proposals, individuals need to provide purpose-limited consent for their personal data to be used and they must re-consent on a case-by-case basis for their personal data to be shared.

On the face of it this sounds reasonable, but, in reality, vital research that is legal and ethical would not be possible because of the difficulties of re-consenting thousands of participants each time their data were shared for new research.

We believe that these Regulations will make research at the Sanger Institute and worldwide extremely difficult in a way that would be detrimental to research and healthcare, but critically they also undermine the autonomy of research participants throughout Europe. We should all have the right to say how our data is used.

For these reasons the Sanger Institute has chosen to support the Data Saves Lives Campaign, which aims to persuade the EU to recognise the importance of sharing data for research and to revise its restrictions on research. The Sanger Institute is committed to protecting the privacy of our participants, without whom our work would not be possible.

Over the coming months we will campaign to be allowed to do the research that we believe is so important to patients and beneficial for wider society and in the process we will be campaigning for our participants’ autonomy and their right to self-determination.

Sarion Bowers is the Research Policy Advisor at the Wellcome Trust Sanger Institute. She has a PhD in Biochemistry. Before joining the Institute she did postdoctoral fellowships in Leeds and Connecticut. She recently completed an MSc in Science and Technology Policy, in which she researched the adoption of genomics into the NHS.

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Influencing Policy

Getting to know you

17 December 2014
By Anna Middleton

People want data but do not expect researchers to deliver results if this compromised their research. Credit: DOI: 10.1016/S0140-6736(14)62119-X

People want data but do not expect researchers to deliver results if this compromised their research. Credit: DOI: 10.1016/S0140-6736(14)62119-X

Our genomes contain information that controls every aspect of our biology. A very small, but ever-growing, fraction of this can be decoded by scientists and can tell us what’s going wrong or what’s likely to go wrong in the future. As we understand more and as the cost of sequencing falls, the likelihood of patients encountering genetic sequencing in the process of their treatment increases. Because of this, the public needs to have a say in how this very personal data is used.

In 2010, when the Deciphering Developmental Disorders project began screening patient genomes, we began talking to scientists, clinicians and patient families to uncover potential ethical issues. It was always our intention that the genetic data relevant to the patient’s developmental disorder would be shared with patient families as this, the diagnosis they had often waited years for, was the driving force of the whole project. What though, of the rest of the genome? In those billions of letters of genetic code that don’t tell us about the patient’s specific disorder there may lurk genetic variants that can drive tumour development or increase susceptibility to other diseases.

We made the decision for this research to report back only pertinent findings. But was that the right decision? To find out, we had to ask all the relevant stakeholders for their views; a challenging task when you consider that we wanted to know people’s opinion on very new and complex scientific methods.

We created an online survey that contained 10 short films to describe the ethical issues raised by sequencing technologies. The survey went viral and we had just under 7,000 responses from 75 different countries. It has since been translated into Danish and Spanish by other research groups to be used with different poputlations. The response we received from the public, health professionals and scientists round the world was clear: most thought that important health implications discovered accidentally in the process of answering a research question should be reported to the participant.

However, what was also clear was that participants did not expect researchers to deliver such results if by doing so this compromised the ability to conduct their research. This indicates a very common sense approach – people want data. But they don’t believe it should be delivered to them at all costs. A more detailed breakdown of the survey results can be found here.

Engaging with the public, health professionals and scientists about how genetics is likely to shape healthcare and asking everyone to play a part in these major decisions is incredibly important. As research develops and the capabilities of genomic sequencing increase, we will need to continue this conversation.

Anna Middleton is a social scientist and registered genetic counsellor researching ethics and genomics at the Wellcome Trust Sanger Institute.

References

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Credit: Kate Whitley, Wellcome Images
Influencing Policy

Understanding the impact of genomic data

12 December 2014 – updated on 12 February 2015
By Anna Middleton


The genomic era is upon us. From the Government’s pledge to sequence 100,000 genomes to the launch of 23andMe, a private company that can offer personal genotyping for £125, having bits of your genome sequenced has become a very accessible option. Millions of us will be able to receive information encoded in the three billion chemical bases that offer instructions for everything we are and everything we will be. The big question now is, what do we want to know?

Genetic testing, where we look at a small section of DNA known to be linked to a specific condition, is already widely used by the NHS for diagnosis of illness with a genetic basis. This can be an emotional moment in a patient’s life for many reasons. With genetic conditions, there is a family context to consider; patients may have lived-experience of seeing a family member suffer through the same condition and often patients are worried about passing on conditions to their children.

In clinical genetics, results of genetic tests are communicated by clinical geneticists and genetic counsellors and both are available to talk to a patient through the implications of the findings and provide information to be shared with their family members.

Currently there are just under 300 genetic counsellors working in the UK, where thousands of genetic tests are being carried out in clinics each year. The number of tests will only increase as we understand more of what our DNA has to tell us about disease and as the cost of sequencing continues to fall. There’s a clear need to increase the number of genetic counsellors and to train a workforce of doctors and nurses who will increasingly encounter genetic data.

Genetic counsellors talk patients through implications of findings and advise them on how to share findings with family. Credit: Anthea Sieveking , Wellcome Images

Genetic counsellors talk patients through implications of findings and advise them on how to share findings with family. Credit: Anthea Sieveking , Wellcome Images

There’s another crucial shift that’s needed: a move from genetic counselling to genomic counselling. The difference is one of scale. The amount of information contained in our genome is potentially enormous and the number of exome and genome sequences being done outside clinical genetics is on the increase. The resource of data (the exome/genome) can be mined in an almost infinite manner of ways to yield useful clinical answers – the question is….what is it actually helpful to know and share? The other issue relates to accessing the technology – virtually every area of medicine now is able to integrate genomics into patient management – oncology, paediatrics, obstetrics, dermatology and so conversations involving genomic data will be happening across a whole health service – other questions are…..how to communicate genomics effectively? How can mainstream medical services care for a whole family (usually the domain of clinical genetics services)?

Existing genetic counselling models used in clinical genetics will be a strong starting point for thinking through how to translate genomics into mainstream medicine. But capacity and training will be an issue. Explaining genomic results requires knowledge of bioinformatics, sequencing, data interpretation and visualisation as well as ethical, legal and social issues. It may be that genomic counselling becomes a distinct profession, or that genetic counsellors take a central role in training health practitioners in the technical and empathic skills required.

How this need will be filled remains to be seen but what is certain is that health services and genetic counsellors need to begin this discussion now to prepare for a future that is very close at hand.

Anna Middleton is a social scientist and registered genetic counsellor researching ethics and genomics at the Wellcome Trust Sanger Institute.

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Influencing Policy

Open season in science

03 November 2014
By Sarion Bowers

Open-access online journals have transformed science publishing. Credit: Shutterstock, Jocic

Open-access online journals have transformed science publishing. Credit: Shutterstock, Jocic

The past decade has seen a fundamental change in science culture and the way scientists operate.

The fear of being scooped and a strong sense of competition traditionally led to researchers carefully guarding their data and resources, sharing only with trusted and known collaborators, before they published their research in journals that people had to pay to view. Now, times are changing and a new paradigm of openness is coming into play.

The idea that everyone, including non-scientists should be able to access the fruits of research has been around for a long time but it has really taken hold in the past few years with the development of open-access journals, which cover their publication costs and profits by asking authors to pay to publish rather than charging readers. This model of publishing has become popular and, according to the Directory of Open Access Journals, there are now more than 10,000 open-access journals offering more than 1.7 million articles, from social anthropology to quantum physics.

However, the ethos of openness has extended far beyond the creation of a new publishing model and researchers increasingly are sharing their data sets and their resources and are even creating data and resources with the primary goal of sharing them as widely as possible; both to benefit the greatest number of people and to engage the public in their research. This open-access attitude to data was a founding principle of the Wellcome Trust Sanger Institute, as it raced to sequence the human genome and to ensure that data was open to all.

Increasingly, researchers are discussing their work on social media and in the process they are opening up a dialogue with the public. The view that science is best protected by secrecy and by shielding it from a public, who must be told what is good for them, is being replaced with the idea that science is strongest when it works for society and is guided by societal input.

Perhaps the most striking example of this change is in the discussions about animals in research; an area that has traditionally been explored very cautiously. Secrecy was considered necessary to protect both research and the people who worked with animals. Now however, universities and research institutes, including the Sanger Institute, are keen to have the public see their animal work and judge this work for themselves.

Although there is much to be celebrated in the opening up of science, there are pitfalls. Traditionally, we expect journals to select the best papers based solely on peer review, so a conflict arises when a journal is at once responsible for ensuring rigorous peer-review of articles and at the same time making their profit from authors paying to have their articles published. It has been argued that this conflict risks undermining the peer-review process and causing a reduction in standards.

In addition, openly sharing data may encroach on individuals’ rights to privacy. Here at the Sanger Institute we deal with genomic data and as our understanding of the human genome improves, the risks associated with openly sharing genomic data increase. A balance has had to be struck between the principles of openness and the need to protect the individuals who donate samples to a study. As a result, the majority of human sequencing data at the Sanger Institute is not entirely open but instead is in a managed database that researchers can access if they have the necessary approvals and permissions.

The move towards openness is now being driven by the organisations that fund research in science, the social sciences and the arts and humanities across the UK. The Wellcome Trust is at the forefront of these changes and as a result there are a number of policies in place at the Sanger Institute that are designed to ensure all data generated is shared as speedily as possible, with strict timelines in place for deposition of sequencing data in the various databases.

Furthermore, researchers funded by the Wellcome Trust, including all those at Sanger Institute, are required to publish in journals that are either entirely open access or allow deposition of the article in an open-access database within six months of publication, and authors are expected to put the relevant identifiers in these papers that will allow other researchers to access their data.

The change in scientific culture towards openness is a recognition that the public are interested in research and discerning in their support of it. Science thrives when supported by the public; allowing the public and researchers to access work produced by Sanger Institute will help its researchers continue to provide the best science that is most beneficial to society.

Sarion Bowers is the Research Policy Advisor at the Wellcome Trust Sanger Institute. She has a PhD in Biochemistry. Before joining the Institute she did postdoctoral fellowships in Leeds and Connecticut. She recently completed an MSc in Science and Technology Policy, in which she researched the adoption of genomics into the NHS.

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