If you have worked in a startup before, you will be very familiar with words like 'traction', 'KPI', 'OKR' and of course the reason for this blog post 'Business Metrics'. If you haven't worked for a startup or heard of these words before, then allow me to part on you some knowledge I have gained! :)

The reason these words are used so often in Repositive is because as a startup, we need to grow fast. It is burned into my mind that most older and more established companies look to achieve milestones in 6 months to 1 year. However, we are trying to achieve similar growth in as little as 3 months. Very fast and rapid growth, the sort of growth you hear about in the news and that makes investors very excited. Like any other startup - it's grow fast, or die trying! So these goals and metrics are used to demonstrate growth and also evaluate the success of activities which impact growth.

Why have goals?

It is very simple really. If you want to evaluate the impact of anything, you 1) need to have a goal, 2) an idea how to achieve it, 3) a plan for measuring it, 4) measurements of outcomes and evaluations".

It's a very scientific approach in my opinion. Without drawing a line in the sand somewhere, or creating a goal first, it is very difficult to see what impact you are having. This may seem very obvious to everyone and anyone who has a KPI and maintains metrics of some sort. But as a startup, you don't have these metrics at the start. Repositive is attempting something never before tried, so how can you create a goal when you have no idea what is realistic? This is one of the first challenges I faced when starting to create and track business metrics. What to track, why and how?

My main goal at present is simply user growth. Repositive is a freemium model and community-driven. Without a community input, Repositive cannot realise its mission of open data sharing and more efficient discovery of data. Being free means that anyone can contribute to a resource which can benefit the whole community.

At first I simply tracked new users. I kept a record weekly and I tracked the progression of new users and basked in glory when the numbers increased with each month. After I had 6 months worth of data, I began making projections or forecasts of what numbers we may achieve in 6 months to 1 year. However, this was still not a goal. I struggled to create one at first and understand what is realistic. It felt like a big deal at the time. With support from management and mentors at SeedCamp, I began to understand that the number was almost arbitrary. There was no way anyone could really know. I was worried that going to high would reflect badly on me when I did not achieve it. However, I soon began to realise that it was not the point of the goal. Reaching the goal would be awesome, but the most valuable thing to understand is why you did or did not reach that goal. A failure is not a failure if you learn. After this realisation, I began feeling comfortable giving myself almost crazy metrics, the best possible case scenario, or as our Chairman Steve Gledden explains it: BHAG (Big Hairy Audacious Goal).

How to track the untrackable?

User growth is easy. As long as you know when someone signs up, you can measure growth. You can create projections, set weekly growth rates and measure progress. But what about retention? Users are great, but every software company wants and needs users who come back again, and again, and again. This is retention. How do you measure a retained user? Is it someone who comes back monthly? Weekly? Do they just search? Do they create content? Do they access content? As you can see it becomes quite tricky. However, much like user growth, the first thing to do is to draw a line in the sand. You just say this is the definition of a retained user, and we are aiming for 20%.

What about visibility and reputation? Well, reputation has the NPS score. In short, how likely are your users to refer your services to someone else? This can be biased but it's often known as the most used metric for this purposes. You can also ask for feedback with surveys, you can see how people reference you online, offline. The hardest I find to track though is visibility. You can track how many views your site gets or how many retweets you get, the impressions you take from the global pie... But how can you tell if that was because of X or Y campaign? The best way I have found so far is giving unique links to a lot of campaigns and activities. Giving unique links helps me separate traffic from source and then see what these people do. How engaged are they? Did they signup and start using our platform? Did they spend long on our websites? Using Google Analytics I can see their journey.

How can you use Business Metrics?

I would say to get the most of business metrics, you first need to collect them in both convergent and divergent forms. Let me explain. Your business metric is user growth, you have a 2.6% growth rate week 1 and then 5.2% the following week. This metric is converged. Its the total, but to really make the most of this metric you need to diverage and split the data up. You can track growth rate in each channel and then if you are giving unique links you can see which channel or campaigns within them are bringing more users than others. If you are tracking web visits you can see which aquisition sources are highest, what campaigns did these relate to?

Perhaps you have more retained users. Where did they come from? From a particular source or channel? Are they a particular demographic? Is there an connection? What new features are impacting this?

Have you exhausted a channel? Does one show more promise? This is closely related to my previous blog post on traction.

Why keep this total metric? If there is such value in in the details? Well, it takes a long time to communicate every metric in detail, but overarching metrics are easy to see and understand. This is the metric you tell your team weekly. This the one the investors are interested in... "what's your weekly growth rate?"

Growing Metrics

The important take home I would like to leave is that metrics change. You start tracking user growth monthly, then you change to weekly. You set a goal of 2,000 users in 3 months at 4.5% week on week growth, then a longer goal of 20,000 in 18 months at 4.2% week. First, you define retention as someone who comes monthly, then you change so it does not count the first visit, then you change and its no longer just visiting that defines retention but activity and engagement does.

Metrics are meant to evolve. You get better at it. Things become more defined. It's OK for them to change and you change with them. In fact, I would say, if your metrics are not changing you aren't doing them properly or taking insight from them!

What metrics I collect and how

• Weekly User Growth - SalesForce
• User Forecasting - Signup Survey / SalesForce
• Retention - GoSquared
• NPS Score - Feedback Survey
• Surveys for Business Intel - Typeform
• Referrals - Signup Survey
• User Aquisition Sources - SignUp Survey
• Web Traffic - Google Analytics
• Cost per Aquisition for User - Online PPC tools like Twitter, Google AdWords + known costs for other channels

I am not expert in Excel spreadsheets or Salesforce dashboards. So far, a lot of what I do is manual. However with a supportive team, and lucky for me a senior Salesforce administrator as a husband, I will be able to automate these metrics. I will use the power of software to give me live data on my metrics and use the SalesForce dashboard to show it in a meaningful and easily digestible way.

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Traction: Are four bullseye's better than one?

Welcome to my podcast series 1 on Fundamentals of Precision Medicine. In this second podcast I talk about some of the challenges around the application of genomic technologies to the clinic and Precision Medicine.

This is the second of a podcast series on Precision Medicine whose objectives are as follows:

1) To help you learn the critical developments shaping the future of diagnostics, drug development and personalised treatments.

2) To allow you to discover in one single podcast series the challenges affecting clinical and industry key opinion leaders while delving into the ethical, social and legal implications of personal genomes.

3) To advance your knowledge of Artificial Intelligence, Big Data and High throughput technologies applied to Precision Medicine.

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Podcast Series 1: Fundamentals of Precision Medicine

A good and a bad example for how to share data from a high profile publication

I am glad to witness and participate via Repositive in the great initiatives that the UK government is embarked upon. The latest of these initiatives comes with great excitement through Dame Sally Davies, NHS's Chief Medical Officer.

In her latest Chief Medical Officer's summary, to be strictly embargoed until 00.01 on Tuesday July 4th 2017, she presents a new set of recommendations that will drive forward NHS's ambitious plans to extend genomics to the wider UK population.

This latest development is a clear green light into the implementation of the 'genome economy' in the UK.

Since early projects involving family sequencing for patients of rare disorders, tremendous efforts have been spent on developing UK regional hospitals to cope with the implementation and delivery of genome-based diagnostics and treatments. Now these recommendations from Dame Davies will have a palpable impact not just on rare diseases and cancer. She recommends:

1. The establishment of a National Genomics Board, ensuring appropriate delivery of genome technologies for patients, research and industry, joined by the accompanying regulation to strike a balance between patient data consents for research and the exploitation of this data.

2. The Human Phenotype Ontology should be used as a phenotype standard.

3. Guides for clinicians on how to initiate genetic testing for those who need it should be provided.

4. Access to genetic assessment to patients outside of rare diseases and cancer such as early onset obesity will be available.
   
   

What excites me most about this development is the potential these recommendations will bring, providing a baseline for the orchestration of government, research agencies, hospitals, regulation and the patient community. It is in this regard where, in my opinion, initiatives like Genomics England have excelled, becoming a referent to other national health service structures.

This kind of announcement is to my knowledge the first one where a government is committing to the widespread adoption of genome-based medicine universally for all patients. I will expect many other governments to follow suit. Good news indeed for researchers, academia, industry and any other genomics stakeholder based in the UK.

Did this interest you? Follow Manuel on twitter or his Personal Genomics Zone blog to stay connected.

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Getting Google to Find Human Genome Datasets

A good and a bad example for how to share data from a high profile publication

Special thanks to Edoardo Giacopuzzi, a post-doc working on NGS and data analysis for the Genetic and Genomics Analysis Platform at UniBS *, for writing this guest blog post.

The data are out there! How Repositive can help you find and access human genomic data.

I’m part of a small Italian research group working on genetic basis of psychiatric diseases and we have a couple of bench-top sequencers to support small NGS based projects for our Institution. However, since the introduction of genomic technologies, the real business in studying genetic basis of diseases has became GWAS/WES of thousands samples, an effort well beyond our resources.

I have a magnet above my desk citing E. Rutherford to remind me which is the winning approach for us: “We haven’t got the money, so we’ve got to think!”.
Indeed, we soon realized that we can’t afford discovery experiments competing with large consortia, but we may be able to think out-of-the-box and find new ways to aggregate genomic data to investigate specific biological mechanisms.

Luckily for us, and for researchers overall, the genomic field is quite open to data sharing and publication of raw data is often mandatory for papers involving NGS. As result, huge amount of data has accumulated during the years in data repository like SRA archive, ENA, GEO and there is almost no platform, method or phenotype that doesn’t have some data ready for you to grab.

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I was quite excited to attend ESHG 2017 conference, looking for new smart ideas and possible collaborations to produce good science at low budget.

During a coffee break, I was walking through company stands hoping that other attendees have left some pastries. Found one and refilled with sugar, I thinked back to talks of the day on complex diseases and multi omics integration and start wondering if we may apply these approaches to our study of regulatory landscape in Schizophrenia. I proposed this idea to collaborators wondering if we can put together a pilot study. We concluded that we may need some additional data and decided to try to explore repositories once I’ve came back home. So where to go to close the day? I looked at my program for evening corporate satellites and saw Repositive.io meeting “Find the most suitable genomic data repository for your needs”.

This sound exactly what we need, a way for effective and rapid search of genomic information! So I decided to stop by their stand to take a first look and talk about their service. After a short chat with their friendly staff and a brief overview of their web portal, I signed for the T-shirt lottery and their evening meeting. From the beginning, Repositive emerged as a friendly and open-minded group of people who believes in the power of data sharing and community effort to boost genomic science.

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The evening talk was a fun and informative overview by Repositive leader Manuel Corpas, which underlined the main feature of their search engine and the community-based approach they implemented to improve datasets information. Using also some fun real-world examples, Corpas illustrated their different look to genomic data. With an incredible amount of data rapidly accumulating, they understood that genomic field could take advantage of indexing and searching approaches previously applied for the world wide web data. Indeed, data are useless if you can't find them and effective search engines would improve sharing and avoid wasting resources on replicated efforts. Moreover, this would fit perfectly in genomic field allowing small research group (like us) to develop their ideas leveraging on large community based efforts, maximizing the scientific value of each dataset.

What’s Repositive?

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So what’s Repositive? And what can it do for me? As Corpas summarized during his talk: Repositive want to be the booking.com of genomic data. In my opinion, Repositive web service is a bit of Google search engine, a bit of booking.com and a bit of Wikipedia. The idea is to provide a centralized search engine where all genomic data repositories are indexed and can be searched by specific queries and filters. Each dataset is provided with description and attached meta-data (like platform, approach, sample source…). A second aspect is the Wikipedia like features of Repositive, where registered users can contribute to datasets by providing additional details and meta-data. Datasets can also be shared and watched to keep track of updates and changes and users can comment datasets like hotels on booking.com. Finally, users can register their own datasets or request for new repositories to be added, as well.

Since the amount of available data in genomics is rapidly growing and datasets are spread across several repositories, Repositive search engine has the potential to make data retrieval simple, quick and effective. The platform is now in its infancy, but it already include data from 43 repositories and a user-friendly web portal. Provided filters allow to restrict searches based on data accessibility, experimental approaches and source repository. The community based features has great potential to improve dataset description, but they impact depends largely on how much Repositive will be able to spread across scientific community.

Open questions and possible improvements

To provide an effective data search engine is essential to extract relevant information and made them searchable / filterable. To reach this challenge they have to face with the non-standardized ways of representing meta-data and manual revision should be need to actually provide all these information. This seems an enormous manual work to deal with… As Corpas underlined, part of the success of Repositive will depend on how many researchers decide to use and contribute in the platform. A large support by scientific community will indeed enrich meta-data and give Repositive influence to ask repositories for standardized representations.

By now, datasets are represented singularly by sample and not aggregated by project and available filters are still limited. By myself, I often want to be able to search for an entire project, like RNA-seq in a specific disease with case and controls, rather than by single sample data. Moreover, a filter on number of samples and platform used (i.e. hi-seq, bead-array, ion…) are needed to better define useful data.

They are also thinking about some kind of centralized management for data access request and automation of data access, so that for both open and some managed access data, Repositive will became a search, click, download platform. This will really make the difference!

My personal experience with Repositive

By myself, I’m quite a fan of data and knowledge sharing, since it can really speed up research, avoiding redundant efforts and allowing for quick and effective hypothesis testing.

Taking advantage of the increasing amount of accessible genomics data, we gradually shifted from production to analysis, trying to integrate our small scale experiments with big data produced from others to improve our hypothesis and investigate those aspects that was not addressed by the original authors. In this process, we soon discovered that even if data are out there, they are far from simple to catch! Indeed, they are spread across multiple repositories and several ones are not so easily searchable. Moreover, several data are under restricted access that requires complicated administrative procedures.

As soon as I got back to the lab after ESHG17, I gave a try to Repositive to find out if it could help me retrieve useful data. My first experiment was an easy one: search for additional genomic data on NA12878 reference sample that I could use to develop variant filtering algorithms. Using Repositive, I found about 40 WES and 1600 WGS, all open access and spanning different platforms. Good! A lot of material to work on. The second experiment was to find some WGS and transcriptome data for major depressive disorder. Here, the task was a little more difficult, since I want to retrieve case/control studies and, as I mentioned above, the present Repositive interface list samples one by one and not aggregated project data. However, I discovered CONVERGE data are available for download (around 11k low-coverage WGS and variant calls), as well as some interesting gene expression data from GEO repository. I’ve also noted that data from NIMH genetic repository are missing...I will request to have them added!

Looking around their blog, I also found suggestions and walk-throughs for data access in managed systems that can help newbies in their first time application at dbGaP or similar platforms.

Based on my first quick experience, Repositive can be extremely useful for our analysis projects making data retrieval easier. However, some improvements (project based and platform based filters for example) are surely needed to allow effective retrieving of useful data.

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Happy sharing to everybody!

*To keep up with the great work Edoardo is doing, see: 1. Genetic and Genomics Analysis Platform @ UniBS, 2. NGS-Brescia blog

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ESHG 2017 Presentation: Finding & Accessing Human Genomic Data

A good and a bad example for how to share data from a high profile publication

Final Results from 'Tools and methods in genomic data analysis'

Friday, 7th July 2017 | 19:00 - 21:30

2nd DNAdigest guest talk from Amy Tang, EBI: data sharing & open science

Repositive are delighted to announce we will be sponsoring DNADigest.org’s upcoming guest talk from Amy Tang, EBI: data sharing & open science!

Some of you may remember that Amy recently wrote a guest blog post for us on ArrayExpress. She will continue to share her experience in curating ArrayExpress submissions, discussing the challenges we face at the crossroad of submissions, data sharing, publishing and open science.

We will be happily sponsoring the event with free pizza!

Venue: The Red Bull (Upstairs)

Barton Rd, Newnham, CB3 9JZ, Cambridge, UK

Event registration (free)

Title: Data sharing and reproducibility --- musings of a data archive's gatekeeper

Abstract: Research reproducibility has been a buzz word in recent years. Some mainstream media (e.g. BBC, Forbes, Guardian) have introduced the issue to the public, which helps to raise its awareness, but most of the discussions outside of the Open Data community remain at the level of dissecting the problem, or offering solutions which mitigate but not tackle the root causes. In this talk, I will share my experience from interacting with depositors of ~4000 data sets at ArrayExpress as well as my discussions with several journal publishers, on what I perceive as the major challenges in tackling poor reproducibility of research. As I bid farewell to EMBL-EBI this summer, I will also reflect on the measures we've implemented in ArrayExpress to address some of the issues, and what more can be done as a community.

Bio: Originally trained as a mouse developmental geneticist, Amy is the curation and training lead for ArrayExpress and Expression Atlas databases. She leads the ArrayExpress data submission service for functional genomics data (e.g. expression arrays, RNA-seq, ChIP-seq), drives the user-centric development of submission tool Annotare, and delivers training on best practices of sharing biological data. Before joining EMBL-EBI, Amy was a senior bioinformatician in the Ensembl GeneBuild team, curating gene models for key model organisms such as mouse and rat. She holds a PhD in mouse epigenetics (2006) and a MSc in Bioinformatics and Systems Biology (2008), both from Imperial College London.

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ArrayExpress at EMBL-EBI - quality first!

Welcome to my podcast series 1 on Fundamentals of Precision Medicine. Here I introduce the concept of Precision Medicine, its history and how it differs from ‘conventional’ imprecision medicine.

This will be the first of a podcast series on Precision Medicine whose objectives will be as follows:

1) To help you learn the critical developments shaping the future of diagnostics, drug development and personalised treatments.

2) To allow you to discover in one single podcast series the challenges affecting clinical and industry key opinion leaders while delving into the ethical, social and legal implications of personal genomes.

3) To advance your knowledge of Artificial Intelligence, Big Data and High throughput technologies applied to Precision Medicine.

Did this interest you? Follow Manuel on twitter or his Personal Genomics Zone blog to stay connected.

Related Blog Posts

Getting Google to Find Human Genome Datasets

A good and a bad example for how to share data from a high profile publication

The 50th ESHG Conference took place in Copenhagen (the same place where it started in 1967) and gathered around 3,000 researchers from all over the world. Four super intense days (27-30 May) were filled with lectures, workshops, poster sessions, exhibitions and a real Danish party!

Attending the event was our Scientific Liaison Nadia (left), Scientific Lead Manuel, or our CEO Fiona Nielsen (right):

Exhibit

We had a poster and a stand featured in the exhibit area. We had a great location and size for our booth, and a lovely colour carpet too! We shared super Repositive goodies and held a t-shirt contest. But best of all, we got to meet and talk with interesting people about how they can get involved in collaboration and data sharing. It was fantastic!

Workshop

Our Scientific Lead, Manuel Corpas, attended this event to hold a unique Satellite workshop on Finding & accessing human genomic data. You can view the workshop below:

Look out! Next we will release a "demo" workshop video of how to use Repositive.

Users!

Our Scientific Liaison, Nadia, said:

"Seeing old colleagues and friends and meeting new ones was definitely one of the greatest experiences at the event!"

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Is sharing always caring? On open genomic data sharing and why people do it.

A Genome Blogger Manifesto - Revisited.

In search of data to add to our Microbiome collection, we have recently attended several events where researchers mentioned the connection of gut microbiota with human health and disease. This has been particularly useful in understanding how a microbiota-friendly diet can play a significant role in managing syndromes and diseases.

Our marketing manager, Craig Smith, witnessed and described on our blog a case where diet was playing a significant role in managing autism.

Among many fantastic things that Craig is doing inside and outside of Repositive, he has been living with multiple food intolerances for more than 14 years. So, today we are talking to Craig about his own experience and views.

Q: I remember on the first day when you joined Repositive, you brought a fancy gluten-free lactose-free and something else-free cake and told us you were allergic to that stuff… So, how did it all start? How did you notice it? What did you feel?

A: I was around 18 years old and was working in a store room in Newmarket. I was quite energetic because I used to drink about two litres of coca-cola a day. I was addicted to coca-cola. I remember one day I took a sip of it and I just felt incredibly sick shortly after, and to be honest it never really went away. This intense feeling that I was going to be sick (but never was) lasted for about two weeks. I then went to my GP and they said there was an acid imbalance in my stomach and that’s what was making me feel sick. Obviously, they probed into my diet and obviously, I told them how much coca-cola I drank… I think it is pretty clear that drinking that much coca-cola is probably gonna do some nasty things to your stomach.

Q: For how long have you been drinking it?

A: I always used to drink coca-cola, but never that much. I got to the age where I started to earn money, became more self-sufficient and wasn’t relying on my parents for food. I was buying my own food from Iceland’s, the supermarket closest to my office. When I mean food I am referring to crisps, chocolate, soft drinks, microwave meals... all the bad things! I was on that diet for around two years before my IBS started. It was also a very stressful job, so I think part of it was stress and part of it was diet. Oh, and I was smoker too.

Q: Right. What did the doctor say?

A: At the beginning they said there was medication I could take that would help my stomach get better. They were supposed to give me a PPI (Omerprazol) but they made a mistake and gave me a tablet that made me produce even more stomach acid. I can't recall the name of the tablet, but I took it and I felt even worse. A lot worse. I went back to the GP, mentioned it to them, and it was then they realised that they had done the wrong thing. By that point I lost faith in tablets and medication, so I enquired into alternative ways to treat my IBS. I asked the doctors “What else can I do, because I don’t want to take tablets and go through that again?”. They said “Well, you could try controlling your IBS with your diet. You will need to keep a food diary to find out what food and drink would make you feel better and what would make you feel worse, but it could take years." And out of defiance, I did exactly that!

I kept a food diary quite religiously. I did it for a while and I kept trying, every time I fell ill, to look at what I’ve eaten shortly before but it was really difficult to trace the exact ingredient. So, after a few years of trying and not getting anywhere, I tried the opposite: I really limited my diet to not eating many things at all. Just things like rice, then maybe rice with butter and then eventually I would start introducing different things and that is when it became a bit easier.

Q: So, what did you figure out your intolerances were?

A: Gluten, lactose, caffeine. I say lactose but I only mean milk, cream, yogurt, soft cheeses. Hard cheeses are fine for some reason. I don’t quite understand it. If I eat mozzarella I will feel sick 10 minutes later. There is a brand of milk where they remove a protein that may cause allergies, I did try that milk but didn’t really see any amazing difference (other than the price!). So, I just decided not to use ordinary milk and use soya, almond and hazelnut milk instead.

I also noticed that it is not just food and diet but stress does make my IBS worse too! When I am stressed I hold it in my stomach. I get really tense in this area and I don’t think it helps. I laugh at work and say 'I am allergic to work' when referring to my allergies, but really, my body does not cope with prolonged stress. I have learned to let it go at the end of the day.

Weirdly, the doctors told me that alcohol wouldn’t help due to the acidity but I noticed that drinking a little red wine makes me feel better. If I feel ill, a glass of red wine can help me to get rid of the sick feeling in a few hours. But I’m not sure how much of that is because I feel de-stressed from drinking wine or whether it is something in the wine itself. Perhaps it's a placebo?

Q: What do you actually eat?

A: Interesting question! At the moment I eat very little carbohydrates. A few years ago I stopped eating gluten and bread and pasta and things like that unless it was a gluten free substitute. At the moment I eat soya yogurts in the morning, nuts, fruit, a lot of meat and vegetables. I substitute a lot of things, e.g. in a stir-fry instead of rice I will use spiralised courgette. I make my own rice from cauliflower. You grate it first then you fry it and it tastes similar to rice. I don’t necessarily do the carb thing for my stomach but for losing a little weight before my wedding, although I have noticed it does help because I think by cutting out carbs one also cuts out a lot of gluten.

I do eat rice or oats occasionally because I think it is not a good thing to completely go without anything... It’s like hayfever, after a while my body builds a tolerance and then I don’t feel the effects as severe. I think it's the same with food: if I didn’t have any carbs for a while then when I do eat them my body just goes crazy because it is not used to it.

Q: Do you know anything about the connection of gut microbiota to different diseases, including IBS, depression etc?

A: From interviewing Finley I know that he has a really strict diet and that this significantly affects his autism, so I can see that link now. I understand that there is good and bad bacteria in your stomach, and a balance of both is the best and an imbalance can cause problems, like IBS. I do not know of scientifically proven links between microbiota and depression, but believe me, at the height of my IBS, I felt depressed! It felt like it was taking over my life.

My nephew Finley outside Delisiously Ella's deli. Deliously Ella specialises in gluten and lactose free food

Q: Would you contribute your data to a research project? Why?

A: I definitely would, without a doubt. I still don’t really understand why I have this condition. To me, IBS is just a medical term to say you have stomach problems but without a specific cause. I would do it in the hope that it would tell me exactly why I have IBS, because I am sure I may be more strict on myself than what I need to be. I also know a lot of people who suffer from IBS, so I would do it because research might provide a solution for everyone. If there is something in our gut microbiota that we can change to stop IBS, well... it would be amazing!

Q: What exactly do you do at Repositive? Why did you choose to work here?

I am marketing manager; what I do is giving visibility to what we do at Repositive, why we do it and who we are.

In my family, all the members have different ailments; my aunt has panic attacks, my grandmother has migraines, my dad has hayfever and IBS, my mum has anxiety attacks... and I am the only one who seems to be blessed with all of them [laughs]. I guess, to a degree, I am here selfishly. I feel there is a lot wrong with me that I have to deal with myself and supporting science support patients is self-serving. But I think I do it more for people like my husband Samuel who has Tourette's Syndrome or my nephew Finley who has Asperger's. I do it for those who need it more, people whose daily lives are affected by conditions and diseases. I can manage my symptoms, and it doesn’t really interfere with my day to day life anymore, but for the people where it does interfere with their lives… I want to help them. I am not a scientist, so this is a way I can contribute and support.

Craig, Samuel and Finley being typical tourists in Brussels

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Microbiome Forum in Amsterdam: some glimpses

Moving to human microbiome data

As part of the Repositive team, I have recently attended the Microbiome forum in Amsterdam, that brought together academic, clinical and industrial researchers as well as business developers.

In her previous post, Charlotte has already explained why studying microbiome is becoming more and more popular. Based on the scientific program of the forum and recent publications¹, one can see that there are more and more areas where microbiota is found to play a crucial role.

My personal favourite

was the keynote lecture by Elena Verdu from the Division of Gastroenterology, McMaster University, Canada, about the role of intestinal microbiota in gluten metabolism and its implications for celiac disease.

Celiac disease is a common autoimmune condition occurring in genetically susceptible persons (but the presence of susceptibility genes is not sufficient to induce autoimmunity). It appears to be triggered by peptides - partially degraded fragments of gluten, which itself is a mix of proteins. Clinical studies have demonstrated alterations in the microbiota of celiac patients compared with healthy controls. It has been hypothesised that microbial factors modulate celiac risk in people with genetic predisposition. In Verdu's group, they studied gluten metabolism by opportunistic pathogens and commensal bacteria isolated from duodenum of people with and without celiac disease. Certain bacterial species metabolised gluten to immunogenic peptides (i.e. they could cause immune response in gluten sensitive organisms), whereas other species metabolised them further leading to non-immunogenic peptide products.

The works of Verdu's group demonstrate how exactly different small intestinal bacteria metabolise gluten and how the resulting peptides increase or reduce gluten immunogenicity.

Other topics

There were many other interesting examples of how microbiota is involved in different aspects of human life. For example, vaginal microbiota - maternal host interactions are important in pregnancy ²; microbiota clearly plays a role IBD and its extra-intestinal manifestations^{3 4}; cutaneous microbiome is involved in inflammatory skin diseases ⁵ and so on.

In some cases, analysing tissue microbiota (e.g. blood) allows to see correlations with different diseases and can be used in diagnostics for early detection. To learn more, please check the works of Benjamin Lelouvier from Vaiomer.

You can read more about what happened on Day 1 and Day 2 on the organiser's blog or join their open group on LinkedIn to stay up-to-date.

Conclusions

It occurred to me that people do not yet combine (or do it very seldom) sequencing data of bacteria (16S rRNA sequencing) with sequencing hosts, i.e. human genomic data that we at Repositive are most interested in. This happens mainly because of the higher costs of the latter and (!) the absence of clarity on which questions to ask? Since this is a new paradigm, no clear pathways exist yet, but we come across more and more scientists who would like to have the combination of human and bacterial genomic data. We are looking forward to the developments in this field and hope to add more data to our Microbiome data collection.

To access the Microbiome collection, please visit https://discover.repositive.io/collections

If you have any questions of suggestions please contact nadia@repositive.io

P.S. And this is how some of our "bugs" look like!

Low-temperature electron micrograph of a cluster of E. coli bacteria, magnified 10,000 times. Each individual bacterium is oblong shaped. By Photo by Eric Erbe, digital colorisation by Christopher Pooley, both of USDA, ARS, EMU. [Public domain], via Wikimedia Commons

References

Related Blog Posts

Moving to human microbiome data

New PGP Data Collection to Be Unveiled at ESHG

Cambridge, 26 May 2017 ... Repositive, the company that created the world’s largest portal for accessing human genomic research data, is expanding the range of data available with the launch of a Specialist Data Collection for the Personal Genome Project. The new PGP Collection will be formally unveiled at Repositive’s satellite symposium Finding and Accessing Human Genomic Data, which will be held at EHSG on the 28th May in Copenhagen.

The latest addition to Repositive’s Specialist Data Collections will see all of the data collected for the Personal Genome Project available in one place, combining data currently held in the US, UK, and Austria.

The Personal Genome Project is a study which aims to sequence and analyse the genomes and medical records of 100,000 volunteers globally. It contains large amounts of genomic data including whole genome sequencing, methylation analysis and RNA-Seq.

The new PGP Specialist Data Collection adds to Repositive’s series of community led data collections which include Autism, Microbiome, Personal Genomes, Population and Methylation data collections.

Manuel Corpas, Scientific Lead at Repositive, said:

“I am delighted to be able to launch this new data collection. I have long had a very strong personal interest in the Personal Genome Project, and making data collections such as this more widely findable, will be crucial to improving our access to key reference datasets for biomedical research.”

Fiona Nielsen, CEO of Repositive, added:

“The Repositive Specialist Data Collections are already proving to be of significant benefit to many researchers. By collecting hard to find data in one place, we can ensure that researchers are able to quickly and easily find the data they need. I am delighted to be working with PGP to ensure this data will be easily accessible as I believe it will be of significant value to our growing community of users.”

Last night on Twitter I saw a mention to an article in The Guardian entitled "Scientists identify 40 genes that she new light on biology of intelligence".

Cool, this sounds like my kind of thing. Luckily the article itself did contain a link to the original source, a Nature Genetics article entitled "Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence". So I went to the actual article to check it out. The abstract mentions that from these 78k+ individuals they came up with 336 SNPs implicating 22 genes, of which 11 are new findings. OK, the result a priori looks credible given the huge amount of individuals that were implicated in it. In addition, the named genes appear to be mainly expressed in the brain.

As I begin to read the introduction, it says that they combined genome-wide association study (GWAS) data from 13 cohorts. It then refers me to 'Online Methods', presumably directing me to where the data from which results originated is available.

The problem is that I am not subscribed to Nature Genetics and I am not able to check the online methods. Online methods are behind the paywall. Nature Genetics does kindly allow the reading of the paper via its application ReadCube but access to the online methods remains elusive. Other than making reference to the online methods, there is no clear indication of where the data is. I scrolled up and down the online open access bit of the article and the only indication of what data they are using appears in Supplementary Table 1, an excel spreadsheet where cohorts are indicated as codes. I find no links to public repositories from which these cohort codes could be retrieved from.

Next, I decide to search Google. I take the name of the first cohort 'CHIC:ALSPAC' in the spreadsheet and perform a search. Google points back to the article. However the exact text that Google matches is still behind the paywall. I cannot access it.

 
I cut then the bit of text that Google provides in its search results. Despite it has now made clearer that this cohort name is relevant for me to find the original datasets, I am unable to see whether there is any indication of any potential repository related to this dataset.

Next, I search Repositive. 'CHIC:ALSPAC' retrieves nothing. Searching for CHIC retrieves 11 results, all relate to 'Capture Hi-C experiments' but this does not seem that relevant.

Just to get to this point it has taken me almost an hour. I have another meeting and I have stop searching. I do not question that the authors have put somewhere the datasets from which the study is derived from. By reading the supplementary text and figures I find potential data sources, e.g., 'Manchester and Newcastle Longitudinal Studies of Cognitive Ageing Cohorts', 'Twins Early Development Study', etc. Despite this, there are no clear links as to how to even get access to the data.
 

In my opinion, this is not how data should be made available for any given published research. I would argue that articles need to clearly show the links to where the data is deposited, even if granted access need to be sought.

An example of good data accessibility? Here is one:

A study that shows a description about induced pluripotent stem (iPS) cells. It comes from an initiative called HipSci. I search Google using 'HipSci' as query. The top link in the Google search retrieves the project's website, which directly links to a page describing the data.

Not only it is clear to find about the data. There are instructions for how to access, find and download the data.

I then decide to search Repositive for 'HipSci' and this is what I get:

I am not sure whether this search result matches all of the actual data provided by the study, but in any case, it looks very comprehensive to me. I am impressed and pleased.

This is a good old #DATAEUREKA moment! Yay!


Did this interest you? Follow me on twitter or my Personal Genomics Zone blog to stay connected.

Special thanks to Tobias Haeusermann¹, (postdoctoral researcher at University of Zürich), and Bastian Greshake² (co-founder of OpenSNP.org) for collaborating to write this guest blog post.

View the new OpenSNP Data Source on our platform

In times of political turmoil, we tend to see discussions about the responsibility of science in academic circles. But unfortunately, something is rotten in the state of academia too. While the academic pursuit should, first and foremost, entail the cultural accumulation of knowledge and its transmission across generations and borders, the structures and strictures of science often tend to hinder rather than foster the sharing of knowledge. In their recent book “A Passion for Society: How We Think about Human Suffering”, sociologist Iain Wilkinson and medical anthropologist Arthur Kleinman openly address academia’s centuries-old dirty little secret: the barriers the ‘ideal’ dispassionate researchers erect around themselves is frequently selfish and self-serving. Oftentimes, Wilkinson and Kleinman write “what now passes as social science is in thrall to technocratic procedures and structures of career that leave it critically sterile, cynical and devoid of passion” (p. xi). They conclude that now might be the time to renegotiate the terms once again. As medical researcher John Tregoning lamented in his NATURE column not long ago, “researchers reap more rewards for publishing flashy papers than for doing solid work, and the two do not always align. Everyone ends up chasing trends and asking the same questions. Broad, multidisciplinary research might achieve more in terms of advancing science, but it is harder to publish and finance. We end up sticking to the narrow path towards prestigious papers and big grants at the expense of worthier endeavours”. Neil Hall, from the Centre for Genomic Research at the University of Liverpool has even proposed a ‘Kardashian index’, to measure of discrepant social media profile for scientists, or in other words, a way to expose academics who are famous just for being famous.

Data is becoming the world’s most valuable resource…

Along with the corporatization of higher education, data is also rapidly becoming the world’s most valuable economic resource. Over the past decade, IT companies have become the custodians of crucial technologies. They are ever more operating as gatekeepers, and as a result dominate critical data junctions. This even led the reliably business-friendly ‘Economist’ to write in one of their recent issues, that if governments don’t want a data economy dominated by a few giants, they will need to act soon“. All in all, it seems that the reluctance of academic institutions, scientists, and companies to share their knowledge openly and for free is not helping to stop the trend toward knowledge inequality.

In genomics, one example stems from data that is emerging from direct-to-consumer genetic testing (DTC-GT). Companies such as 23andMe, FamilyTreeDNA, and Ancestry.com now provide customers access to their genetic data for a comparatively affordable fee. And the industry is flourishing. Yet, genetic tests lead to crucial data and with that to new forms of power. Indeed, the proliferation of DTC testing raises pressing questions about whether commercial firms are gaining access to health data without the necessary accountability.

An open data sharing approach to genomics

Against this background, an open data sharing approach to genomics feels like a breath of fresh air. Enter OpenSNP. Rather than allowing for companies to hoard the spoils of DTC-GT, some scientists and consumers have taken matters into their own hands. Initiated in 2011, the platform openSNP allows individuals to contribute diverse sets of DTC-GT results, along with phenotypic annotations about themselves. Specifically, users can share their results from micro-array based genotyping, which makes up the vast majority of all data sets. In addition, users can upload VCF (variant call format) files, which may include exomes and full genomes. Genomic and phenotypic data are subsequently openly available to anyone, without any limits or restrictions on the use of the data.

In spite of the platform’s radically open nature, the project has attracted more than 5,000 registered users to date, relying purely on social media and word of mouth for recruiting. Since September 2011, users have uploaded over 3,000 data sets and interest in using them for scientific studies and commentary continues grow.

Why people share

In our study, published this week in PLOS ONE, we set out to discover more about the motivations of users who had decided to share their genomic data on openSNP. It is the first attempt to describe open genomic data sharing activities that takes place without institutional oversight. Unsurprisingly, the geographical distribution of the respondents showed the USA as dominant. There was no significant gender divide, the age distribution was broad and there was no marked gender divide. Educational background was varied, with the median distribution towards a slightly more highly educated population. These characteristics differ from other research, which suggests that, as a rule, individuals purchasing DTC genetic and genomic test are highly educated, middle aged users

Above all, however, we found that health, even though prominent, was not the users primary or only motivation to be tested. Rather, it was ancestry that was most commonly mentioned. Regarding their motivations to openly share their data on openSNP, 86.05% indicated wanting to learn about themselves as relevant, followed by contributing to the advancement of medical research (80.30%), improving the predictability of genetic testing (76.02%) and considering it fun to explore genotype and phenotype data (75.51%). Instead of focusing exclusively on health-related aspects of genetic testing and data sharing, we therefore emphasize that it is important to consider all the benefits and risks that stretch beyond the health spectrum.

In his aforementioned nature column, John Tregoning is giving the following advice: “Don't wait on your senior colleagues, and definitely don't wait until you become one. Build a network of like-minded people. Identify something that doesn't work and fix it. It can be as small as a leaky tap or as big as peer review. Idealism can be catching“. OpenSNP is going in this direction and perhaps offers new paths to the cultural accumulation of knowledge and its transmission across generations and borders. Now please share this news, so that at least our Kardashian index goes up.

Tobias Haeusermann¹ is a postdoctoral researcher at the Health Ethics and Policy Lab of the University of Zürich and affiliated researcher at the Cambridge Department of Sociology.

Bastian Greshake² is one of the co-founders of openSNP.org and currently pursuing his PhD in applied bioinformatics at the Goethe University, Frankfurt am Main.

Symposium to discuss better ways to Find and Access Human Data.

Cambridge, 17 May 2017 ... Repositive, the company that created the world’s largest portal for accessing human genomic research data, is hosting a satellite symposium at ESHG, on the 28th May in Copenhagen.

The satellite symposium, Finding and Access Human Genomic Data, will cover all aspects of human genetics, from cutting edge research into the human genome and individual genetic or chromosomal conditions, right through to the practical issues of organising genetic services to deliver the benefits of this knowledge. The event will be hosted by Manuel Corpas, a leading genomic researcher and author of Perfect DNA.

Alongside the symposium, Repositive will also have an exhibition stand and a poster presentation. The Repositive poster (No. P16.35C) will be within Poster Section P16 – Omics/Bioinformatics and the exhibition stand (No. 732) can be found throughout the event in the Exhibitor Hall C.

Manuel Corpas, Scientific Lead for Repositive and Symposium Organiser, said:

“With the explosion in the amount of human genomic data now available, searching for the most appropriate data can often be a challenge. We hope that by demonstrating a range of techniques to help users better search for data, coupled with the Repositive platform, we can help our growing community of researchers to find the right data to power their research.”

After a successful two weeks' visit earlier this year, the Repositive team welcomes back Prof Rolando Rodriguez this week for a further two months.

Prof Rolando Rodriguez is leading the creation of Cuba’s national eHealth infrastructure - as a reference project for the WHO - for the integration of hospital, clinical and molecular information. Rolando has many years of experience in clinical data collection and data standards for clinical applications and is heading the eHealth Implementation Task Force for the Ministry of Public Health.

On 04 February, Rolando gave a talk where he described Cuba’s national eHealth Infrastructure and told us about his approaches to developing a nation-wide infrastructure for sharing clinical data.

In this interview, we summarise the most interesting points that were raised during our conversations in these two weeks that Rolando stayed with us.  

Could you please introduce yourself and talk a bit about your background and current activities? 

I graduated as a chemist from the University of Havana in 1989, then I stayed at the Protein Research Institute of the University of Osaka doing mass spectrometry of proteins and later on I started working at the EMBL in Heidelberg on protein engineering and rational drug design. At the same time, I was leading a group on molecular design and bioinformatics in Havana at the Centre for Genetic Engineering and Biotechnology. I am currently the Head of the Department of Computational Medicine at the National Institute of Nephrology and a Professor on the Faculty of Physics at the University of Havana, where I am also involved as one of the mentors with the Start-up Incubator. I have been visiting professor in several Universities and Institutes mostly in Europe and I am consultant for ITC systems design with some industrial groups.

I am currently leading the ISO TC215 standard implementation task force and the eHealth project at the Cuban Ministry of Public Health, setting and implementing the standards for a countrywide electronic medical record system and clinical data management protocols.

What are the most interesting facts you want us to know about Cuba? 

It is a beautiful and warm place with beautiful and warm people! Cuba is the largest and most populated island of the Caribbean, with almost 12 million inhabitants. Fairly known by making the best cigars in the world, also exports rum, sugar from sugar cane, coffee, cacao and nickel. Tourism industry is large due to Cuba being a very healthy and safe place and having a very mild climate all over the year.

Healthcare and education work very well in Cuba and are major cornerstones of our life. Healthcare is very well organised, and it is totally free. If you cannot get treatment in Cuba specific for your condition, you will be paid to go and get it abroad, but this happens only in very rare cases. More than 50% of the annual budget goes to education, social security and healthcare. Cuban doctors and healthcare professionals are present in 67 countries, giving care and teaching. Cuba has been the first to go to fight the last Ebola outbreak in Africa and in our Medical Universities we have almost 13,000 students from 127 countries.

What is the purpose of setting up eHealth system? 

As mentioned above, Cuba actually possesses one of the best healthcare systems in the world*, and transition to eHealth is the natural evolution of any healthcare system: if you want to provide better healthcare you need to move to eHealth.

You also do it to save a lot of money by avoiding the repetition of assays, some of which can be quite expensive, avoiding multiple prescriptions and doing in-house follow ups with mHealth (mobile Health) and a more developed community medicine were doctors can immediately share the current data of the patients. You can really do precision and preventive medicine this way and real-time epidemiology that is a dream of every healthcare system.

With the communication infrastructure that you will set up for eHealth, you can empower patients who could see their latest results online and interact with the doctors. You can also create social networks for patient communities and societies, where they are able to share data and to participate actively in searching for the solution of their health issues. To share data across the country via a nationwide computer cloud for a distributed public health system, turns out to be the most effective solution for all that. 

When and how did you start the transition to eHealth? Did you start from scratch or were there examples to follow? 

As I said above, the transition to eHealth is a natural development of any healthcare system, it is needed for the improvement. In the current world of IT and Big Data, the healthcare systems are very well defined as some of the largest data providers. Some people may think that in countries like ours, where IT has been applied for hospital management for a while, we have most of the clinical data stored and sorted out. In fact, we are only storing a minute amount of the clinical data that we collect every day!

With respect to starting from scratch and following examples... There has always been a science of distributing data, so there is no reinventing a wheel here. We took the best approaches from data distribution and processing and applied it to our system. Canada, for example, did the same, and in fact we will have very similar system implementations. 

We did not start the eHealth project from scratch, because since computers were introduced in our country, clinicians did extensively use them and the Ministry of Public Health has always been a pioneer on the use of computers and information technology in Cuba.

The Healthcare System Computer Network, Infomed, was founded almost 25 years ago and is the largest private network in Cuba not only on coverage but also on the number of users and content availability, mainly from two very large resources, the Virtual Library on Healthcare and the Virtual University of Medicine.

Infomed also provides free hosting for all the Healthcare Facilities, free e-mail services to almost all healthcare professionals and Internet access at home for all doctors, and it will be extended to all professionals in the field progressively. Last year, the Ministry of Public Health provided 82,000 laptops to be sold to all medical doctors at a minimum fee and is planning to continue this year with the dentistry doctors and later on with all healthcare professionals.

What types of data you collect now and plan to collect in the future? Will you also collect genomic data? Any data sharing plans? 

In the long run, we will gather everything that can be gathered, i.e. all data generated from your stay in the hospital. Right now we are still prototyping, so it depends on any given hospital where we test the collection of data. 

As far as genomic data is concerned, we have a very interesting genetic admixture in the population of Cuba. Collecting genomic information is something we would like to do but only after eHealth is up and running to some extent, because using genomics without clinical data infrastructure would be meaningless.

Genomics is about the genotype, clinical data is mainly about the phenotype: the expression of the genes and the regulation machinery in a given habitat and development condition subjected to societal pressure. Humans are bio-psycho-social beings and we are very unique. To be able to use genetic data to the full extent we would need to be able to relate it to the clinical behaviour of each individual, if we can do that we can start grouping populations in a very different way we do now and we could hopefully start preventing diseases rather than curing them.

For us there is no rush on sequencing whole genomes now; we have a very good program of genetic counselling, we do genetic tests for newborns for the most important genetic conditions and we maintain a database with all twins. We need to start the collection of clinical data first, and then based on diseases we can slowly start sequencing people. By that time it will also be much cheaper than today! I also believe that if we have clinical data organised we will have a better chance of getting grants to sequence individuals. Having a very consistent eHealth programme is essential. 

What are the biggest challenges in setting up eHealth? 

Everything is a challenge! Not only for us in Cuba, where we have our own particular challenges having a "first world" healthcare system in a "third world" country, but for any country eHealth is challenging: it is all about development and change.

It involves changing the whole society and infrastructure, it will change the workflows of the healthcare system making it more efficient and easy for doctors and transparent for patients enabling and empowering the whole society. It is about people and about change management.

A big challenge that also takes much time is collecting opinions and suggestions from all stakeholders to achieve a coherent vision of what and how needs to be done.

One of the most important things to remember during this process is remembering that we are all patients. We strive to make everybody look at things from a patient's perspective, by asking them:

• What would you like to have when you arrive ill to a hospital or bring a relative for medical care?
• How would you like to be treated?
• What would be a logical workflow to take care of you in the fastest and better way?
• Which data would you like to access and how?
• What is being done wrong right now?"

What help us make our choice of development via eHealth unique and viable is the monolithic structure of Cuban healthcare system and the commitment of our leaders, you must be providing the best possible healthcare for our people as guaranteed by our Constitution.

We also take care of sharing our experience with other countries and we are collaborating with the eHealth groups on the WHO and PAHO, exchanging vital information and experiences as our eHealth project could be used as a reference, especially for the developing world.

We aim to have one of the best eHealth services on the world, matching indeed our public healthcare system stature and so guaranteeing its further development.

Prof Rolando Rodriguez joins the Repositive team again from now until the 30th of June, to assist in our strategic roadmap and expand our networks and market offerings. We see much value in working with him, and we expect to share more news in the future of his time and work with us.

*Note from the Editor: we are not talking about any ratings here; to learn more about Cuban healthcare you are invited to read this article

I was quite humbled by the popularity of my last data collection blog post Asperger's from an Asperger's mind. Not only did this post add variety to the Repositive blog, but by interviewing my nephew, I got a much better understanding of what Asperger's is, and what it is like for someone who has it.

I've known for quite some time that our April data collection would be Breast Cancer. I have long been inspired by a very good friend of mine (and ex-colleague), who beat breast cancer. I did not know her during her diagnosis or treatment, but it was her courage and outlook on life after having cancer, which inspired me.

I was very lucky that she gave me permission to interview her for our blog, but it should be noted she is rather camera shy. So I am afraid, this blog won't have quite as many pictures as my last one.

The "WTF is that" moment

It was quite surreal interviewing my friend Donna. Firstly, because our humours are perfectly aligned, it's almost impossible for us to keep a straight face when we catch up. But secondly, because we decided to meet at a new 4 star hotel near Cambridge station, the backdrop to our slightly humorous but serious interview was a luxurious floral patterned wall with an army of waiters in red velvet jackets. Like I said, it was very surreal. Before we even got to my interview questions, Donna proclaimed that it was exactly 10 years ago that she had cancer. It certainly called for an overpriced cocktail.

I found it incredible that Donna remembers exactly when she found the lump...

It was a Sunday morning. I got out of bed, and usually I never look at myself, but today I did and I saw a 2 inch lump. My initial reaction was "WTF is that!"

Donna said she knew, deep down, that it was cancer. Now, we all jump to the worse conclusions - I have done it on numerous occasions, so I understand that she did. Sometimes, we worry for nothing, but on this occasion it lead to Donna seeking immediate medical attention... and good job she did! It was a fast-growing tumour and fortunately Donna had discovered it at the early stages.

From "0" to "cancer" in 2 weeks

The time from finding the lump, to getting her biopsy, was only 5 days apart. I can only imagine how unprepared she must have felt. Donna said that two days after finding the lump she made an appointment to see a nurse. She vividly remembers that the nurse took one look and said: "I'll make you an appointment at Addenbrookes" [Hospital in Cambridge]. This was the moment Donna realised her worst fears were real.

Two days later, Donna was in Addenbrookes having her biopsy. She simply stated "it was not a nice experience". One week later, she received her official diagnosis - Grade 3 Cancer. Her partner at the time Mark "fell off his chair in shock", but Donna herself was not shocked at the diagnosis. Donna remembers clearly the day she received this news... it was 5th April and she even remembers her doctor was a "little Indian man".

Chemo, mastectomy, radiotherapy, reconstruction - her doctor told her everything that may happen after giving her the initial diagnosis. Donna admitted it was a lot to take in. I was not surprised. Part of me feels relieved that the medical system reacted so quickly. With such a fast-growing cancer, a short snippet of time can literally save your life. But on the other hand, I feel like rushing Donna through all this information straight away wasn't really taking into consideration her emotional wellbeing. It certainly didn't seem like there was much emotional support during this time.

The ups and downs of treatments

Chemo treatment shrunk the tumor considerably and Donna was able to have a lumpectomy instead of a mastectomy. Doctors then discovered that Donna's cancer was hormone related and estrogen lead. Then came 6 weeks of radiotherapy and Herceptin injections. Donna recalled that these injections were the worst bit because many of her veins collapsed, and the doctors had to resort to "sticking it in [her] ankle".

Then came 5 years of Tamoxifen, which had horrible side effects. Tamoxifen made Donna feel "awful, fussy and have hot flushes", but it stopped her ovaries from working as a necessary measure to prevent further cancer developing.

Donna decided to have her ovaries removed, but on the day of her operation, just moments before going into surgery, Donna changed her mind momentarily. In a moment of terror, she even recalled attempting to leave the building in her surgery gown. But in the end, she collected herself and decided go through with the surgery. I can only imagine what it would be like to go through such a procedure and operation. I have only had two stitches in my life - both in one toe!

Amazing care by mistake

As we continued to chat about her treatments and care, Donna surprised me by saying that she felt like she got amazing care, but that a lot of information she received was by mistake. By this, she explained it was more "being in the right place at the right time" and hearing information, than being told intentionally at a precise time. Now, I understand that this happened 10 years ago, but I would have thought there would have been more support before, during, and after treatment, and all the information a patient was told would have been purposeful and well-thought through.

There is also the consideration that withholding information to a more appropriate time may have been better than telling every patient everything at once. For the doctors and nurses, everything makes sense and follows a procedure, however this is not the same for the patient. Donna admitted; " I wanted to bury my head in the sand".

As well, whilst the doctors told her this abundance of information, they did not tell her about any of the side-effects of her treatments. Perhaps there isn't a right or wrong way of dealing with the treatment of cancer. However, I would think it would be better to explain things in words that a patient would understand, give them enough detail to feel settled but not be overwhelmed, and certainly tell them what may happen next and the potential side-effects. To me it sounds like Donna was informed about the technical procedures almost straight away, ultimately overwhelming her, but then neglected to tell her about any side effects of her treatment.

The faded memory of a clinical trial

The story above was naturally what information Donna recalled when reliving her cancer diagnosis and treatment from start to end. This was the point that I began to explain what Repositive did and why. Soon after explaining the value of genomic data, you could see a fresh memory resurface, and it was actually her daughter sat next to us who pointed it out first. Donna had took part in a clinical trial. She was actually the second person in the country to take part in this particular one.

The trial basically consisted of taking a different combination of drugs in a particular sequence. Donna would need to record how she felt at several time intervals. The trial was known to her as a "neotango trial". I asked Donna why she took part in it.

I took part in the trial to help future generations. I could die, so what did I have to lose?

Obviously, I explained the value of clinical data such as this, and that of genomic data. This triggered another memory from Donna: her doctors asked her if they could keep a sample of her biopsy for research purposes. Again, Donna agreed.

Donna consistently motioned that clinical trials and consenting to tumor samples being used for research, for her, was logical. She seemed confused as to why someone would not share this information. I explained that some people are concerned over privacy or that they could be identified by their data. This didn't concern Donna at all. In fact, it seemed nothing in comparison to the value of the data itself.

Like mother, like daughter?

Having Donna's daughter Alyce in the room lead to a very unexpected conversation. After her mother's diagnosis, Alyce was also encouraged to get checked, however, although it was explained that the type of cancer Donna had was NOT hereditary. Ironically, at the same time, Alyce worked for a company who ran an incentive for women to get their DNA sequenced, especially those with a family history of cancer. So Alyce took the chance. She apparently had the same mutation as Donna, but was told there was "nothing to fear". Something I sense she is still dubious about.

This prompted a conversation about receiving genetic results. There seemed to be a difference in opinion between Alyce and Donna. Alyce seemed a little more apprehensive to know her results, whereas Donna motioned she would want to know. It is an interesting paradox. Would you rather a) not get tested and live the rest of your life unburdened that you may have a genetic risk of cancer or b) find out if you carry a mutation so you have the chance to prepare mentally and seek early medical intervention? It is a very personal question. What the three of us did agree though, is that getting such feedback or results from genetic tests should be adaptable.

Donna and Alyce both pointed out that they had little access to knowledge about genomics. It's the second time I have seen the opportunity for this knowledge to make an impact on a patient, and yet they had no idea about it.

The "F$%K IT" moment

If you recall my opening sentence regarding this interview, I said I thought of interviewing Donna for this blog post because she inspired me. How Donna refers to her diagnosis and treatment and how she dealt with having breast cancer is amazing. Her outlook was so bright, considering how bleak her options were. I really wanted to understand how she did it!

F$%K IT! Stay positive and try to live a normal life.

That was Donna's advice. Donna told me she only had (an incredible) two days off during one year of treatment! From all the side effects of treatment both emotionally and physically, and even having her son James running off after hearing the news, she only took two sick days. It was a classic example of the Great British motto... rolling up your sleeves and just getting on with it. Donna recalled that so many people at Addenbrookes who were getting the same or similar treatment were "crushed" from their diagnosis and subsequent treatments. She kept busy though and didn't allow cancer to define her or take over her life.

Advice from Donna

• Follow your "gut instinct". Don't ignore signs and make sure you seek professional advice if you find a lump. Catching cancer early can make all the difference.
• Explore options - these days there are better treatments, better awareness, and better support. Explore what's involved and take an active interest in what is happening to you.
• Speak to someone who has been through it - meeting someone who gone through treatments and has "made it through to the other side" is a real inspiration. Hope can be powerfully emotive and can help you deal with the stress of getting cancer.
• BE POSITIVE!

The thoughts of the interviewer

Much like in my Asperger's post, I was again surprised by the limited understanding Donna and Alice had about genomic research. This comes from two people who work for biotech companies that deal with DNA data. And one even had her genome sequenced. There really needs to be more visibility and education surrounding the role of genomics in medicine and diagnosis. This should not just be for patients either, but especially DNA test consumers and also the general public as a whole.

(By the way, our Scientific Lead Manuel Corpas addresses these issues in detail in his novel "Perfect DNA" available from amazon).

Precision medicine is the theory that a person can be treated as a person, not as the disease. This would mean you have treatment specific for you. In my opinion, it is clearly the future of medicine. However, I also think we should approach emotional support in the same way, and specific for the person. Some people want to know everything straight away. That is what would be best for them. Others need time to process and want to be kept up to date as their treatment progresses. Others do not want to know genetic results at all. It is a personal decision, and I think the healthcare system could be more mindful over the power of knowledge on a patient and their family.

The healthcare system is like a machine. It has different protocols and processes. Once diagnosed, there is a wealth of experience and knowledge around you developed to give you the best possible care. However, the first step is with you. Make sure you do regular checks and if you find a suspicious lump seek professional medical advice. There can be a clear path for you, but you need to step onto the path first.

The "positive-thinking gene"

At the end of the interview, Donna proclaimed that being so optimistic was not a reflection of how amazing she is. She continued playing it down, saying it was "in her genes" and that she had a "positive-thinking gene". Thats an interesting point, I think. Perhaps she's right.

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Asperger’s from an Asperger’s mind