Digital DNA: Connecting Patients and Research – An Interview with Patrick Short, Sano Genetics
The Digital DNA series explores the role of large-scale genetic testing in science, industry and society. We aim to understand both the benefits and risks of this emerging technology and see what the future may hold.
In our third interview of the Digital DNA series we talked to Dr. Patrick Short, CEO of Sano Genetics. He describes how Sano Genetics is partnering with researchers and patient groups to promote research into rare genetic diseases.
FLG: Can You Introduce Sano Genetics?
PS: Sano Genetics is a genetic testing and research company based in Cambridge UK. We were founded in 2017 by myself, Will Jones and Charlotte Guzzo as we were all doing our PhDs at the University of Cambridge and the Wellcome Sanger Institute.
We came together to start the company to solve two problems; the first patient based, and the second research based. We felt that for patients, direct-to-consumer genetic testing can be full of misinformation and there is often a lack of transparency about how data is used. Researchers still struggle to access enough genomic and health data from patients, particularly for rare disorders.
We decided to build a platform that solved these two problems by allowing people to build personal genomic and health data profiles that they have full control over, and to connect with universities, pharma, and biotech researchers on the platform to learn more and advance science.
We work with researchers to help them recruit for clinical trials and get access to data for their pre-clinical drug discovery research. Although we do produce our own DNA testing kits, our business model is based around enabling research and not tied to selling kits. Participants can also get access to free sequencing through some of the research projects.
FLG: How Do Customers get Involved in Genetic Research?
PS: The platform is completely free for participants and they can upload data they already have, from sites like 23andMe or AncestryDNA for instance. If customers have a condition that qualifies them for one of our paid research projects then they can get opportunities to have free genotyping or clinical sequencing for free. We are currently running studies in rare disorders such as Muscular Dystrophy and Phelan McDermid Syndrome, as well as more common traits and disorders such as psoriatic arthritis, stomach ulcers, and autism.
Whenever patients participate in trials they are reimbursed for their time and access to their data. We are interested in this idea, that a lot of other companies are also going after, around a data economy; how can genomics companies give people fair compensation when their data may be used in for-profit research. Some companies offer people shares in the company, some pay them directly – for now, we are aiming to offer people free DNA sequencing and analysis in exchange for their participation in research. One of the big challenges that we see with the model of paying people directly is combating fraud – this is challenging when many of our studies are entirely online. This field is going to change a lot over the next couple of years and we hope to help shape it.
FLG: How Do you Work with Researchers and Patient Groups?
PS: We only work with researchers that have ethical approval for their proposed studies. The researchers must be open to interacting with patients. This includes giving patients information about the research, following up with them and in most cases returning sequencing data and results of the research to them.
We aim to support research that is really going to benefit participants. Even if the benefit is not immediate, as it may be in a clinical trial, there has to be a clear long-term benefit, whether it be improving diagnosis or understanding why some people do not respond to treatments while others do, or why patients with the same rare condition have very different symptoms, which is the focus of several of our studies.
We’ve focused so far on rare and chronic genetic diseases because these are areas where we know there are a lot of important problems to help solve. My PhD research was in rare neurodevelopmental disorders and getting a diagnosis for these diseases is still challenging, even with whole exome and whole genome sequencing making a huge impact. Treatments are now beginning to emerge for some rare disorders, but as they are expensive we have to figure out ways to track whether the therapies are working and how to get the cost of drug development down.
The stage that we are at now is a matchmaking process between finding researchers that are really interested in this new model of patient-centric research and patient groups that are interested in genomics for their research programmes, or to better support their members. The patient groups we work with have deep networks with access to engaged patients, and we have expertise around genomics and the research side. This way we can work together to make breakthroughs possible.
For researchers getting access to these patients is really challenging. Patients want to participate in research, as they want to see progress, and we thought there was an opportunity to help by bringing patients closer to the process. They have expertise and can help researchers understand more about their condition.
FLG: Can You Explain how Sano Genetics can Enable Genome Wide Association Studies (GWAS)?
PS: For GWAS studies you have two groups of people who have different traits or conditions, or a quantitative trait like height. For example, you may have people who have psoriasis and people who don’t. You then look for patterns in the DNA that are different between the two groups. At a particular position you might see that the people who have psoriasis are twice as likely to have a T base at that position than those who don’t have psoriasis.
For complex conditions like depression and autism you can find hundreds of associations. With GWAS studies, the challenge is replicating the results. We are working with quite a few researchers that come with this problem where perhaps they’ve done a GWAS in a group of patients that they’ve recruited and they’ve found something and want to replicate it. They approach us because we have an engaged community of people who’ve already uploaded data on the site and we have our own sequencing kits we can very easily send out to a wide group. Patients can opt in to give their data to the researchers to enable them to build a replication cohort in 4-6 weeks instead of having to recruit a new cohort from scratch.
FLG: How do You Help Patients Interpret their Genetic Test Results?
PS: I did a lot of science communication work during my PhD and I feel like it’s never done full justice – It’s something we never think about until it’s too late. We should be engaging people way before the research is finished as it’s such an important thing to get right.
We’re focused right now on providing customer access to only the highest quality science that people can get something out of, in the form of free access to reports and new research from top universities that are free or jargon. We have a lot of interesting trait reports that tell people fun stuff such as why some people have freckles, how our bodies process caffeine and alcohol, or how genetics influences our taste preferences.
As the company grows, we want to move into more medically relevant interpretations. However, the reality is for the vast majority of disorders it’s really challenging to give someone accurate and actionable pieces of information from their genetic data. In the future we hope to provide this, but we need to ensure that the support network is there, so if you tell patients they have a genetic condition then they have a genetic counsellor or a clinician to speak to. For this reason, we are very focused right now on connecting people to high quality research in personalised medicine.
FLG: Can You Talk about the DNA Testing Kit you are Launching?
PS: We are launching our own DNA testing kit at the end of summer 2019. We decided to launch these tests because currently we don’t have enough research projects to pay for tests for everyone, but there are people who message us every day who say ‘I don’t qualify for a research project, but I’m really interested in contributing in some way, can I pay for a test?’ Often, it’s people who are early adopters or enthusiasts of the technology and they want to get involved themselves to see what they can learn from their own data.
The test doesn’t promise a diagnosis or to give away any medical information but allows people to participate in research they want to support. We also provide access to trait-based reports that are designed to help people understand the research, not just make a prediction. A core part of our platform is that customers have a dashboard that gives them full control over who has their data at any time.
FLG: Can You Explain the Difference Between Genotyping, Exome Sequencing and Whole Genome Sequencing?
PS: We have six billion bases in our genome and genotyping looks at a pre-chosen set of around half a million of these. Even though statistical techniques such as imputation can be used to fill in the blanks, you do miss rare genetic variants and the majority of genetic variants that humans carry are rare. Whole genome sequencing, which is the most expensive, reads nearly 100% of the DNA. Exome sequencing is similar to whole genome sequencing, except you capture approximately only the 2% of the DNA that contains all the coding regions.
I have a soft spot for whole genome sequencing because my PhD looked at non-coding variants in rare developmental disorders, and whole genome sequencing provides more data to analyse non-coding regions. Future research projects are going to change our understanding of rare diseases by demonstrating what proportion of diagnosis we are missing while we are only looking at the coding regions of DNA.
Each sequencing type has their applications. Genotyping is the least expensive but cannot reliably identify rare variants. Genotyping is really very good for ancestry, population studies and pharmacogenetics which all rely on the analysis of common variants. We are working on a few projects in the pharmacogenetics sphere right now, which is about identifying people that might have safety issues with medications or required different doses based on their genetics.
For rare disorders, exome or whole genome sequencing are essential to ensure accuracy and full coverage of the potential disease-causing genetic variants.
FLG: Anything Else?
PS: A key part of Sano Genetics is partnering with patient groups and organisations. I’d just like to place a call out to any chronic or rare disease groups that are looking to get involved with genomics as part of their strategy. We can bring expertise in genome sequencing and analysis as well as access to pharma and biotech partners to help pay for sequencing, and to use the data to develop new therapeutics. If there’s anyone out there that falls in this category, then we’d love to get in touch. Please feel free to email firstname.lastname@example.org.
Our Digital DNA series will continue with more interviews and articles exploring the benefits, risks and potential of genetic testing. If you or your company would like to contribute to the Digital DNA series, please email email@example.com
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