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Q&A: Genomes Unzipped's Luke Jostins on Building a 'Personalized' Genome Browser for Non-Scientists


This week, a group of thirteen scientists, researchers, and legal experts made their genomic data publicly available with the goal of educating the public about what goes into deciding whether to have a genomic scan done, what one can learn from such tests, and how it may or may not impact healthcare decisions.

The members of the project, called Genomes Unzipped, posted data from their 23andMe scans online with the aim of fostering open discussion and analysis of the ethical, legal, and scientific issues surrounding personal genomics.

Along with the data, the group released a version of the open source JBrowse genome browser that it customized to make the information accessible to non-scientists. Eventually, Genomes Unzipped plans to open up the browser's features, making it simpler to use so that interested members of the public can upload their own data and customize the browser for their own use.

"There are a large number of genome browsers for the scientist, but I've yet to come across one that is useful for the lay person," said Luke Jostins, a postgraduate student researching the genetic basis of complex autoimmune diseases at Kings College in the UK, and a Genomes Unzipped member.

Currently the browser displays genotype data with information about SNPs linked to disease predisposition and drug response. However, in the future, the group plans to include information from different types of tests, including whole-genome sequences.

PGx Reporter spoke to Jostins this week about how the group plans to customize the genome browser to make it more usable for the public, as well as the ethical and legal issues Genomes Unzipped members had to consider before deciding to go public with their data and the group's plans to educate the public about personal genomics.

The following is an edited transcript of the interview.

Can you tell me about the browser? How have you modified it to fit your purposes?

The browser is based on JBrowse, the successor to the popular GBrowse, on which the HapMap project was based. We've modified it to include a custom track, in terms of our own genome data. In general, genome browsers display static information in terms of annotation. And we've tried to modify it to try to think about how to display our own personal information. We've been concentrating on how to make the interface very simple, so individuals can browse around genes, or regions, or SNPs, and how to access that information for particular individuals.

We've had a lot of help from people like Mitch Skinner [a JBrowse developer at the University of California, Berkeley], who have given us a lot of ideas and information on how to use this. There is still a lot more stuff we want to do with the browser, a lot more customizing in terms of visualizing our data and in the future, also visualizing other people's data.

You said that current genome browsers are static, but what other kinds of things do they lack that you're trying to improve for the lay person?

Maybe 'what [browsers] lack' isn't the right way to put it. Genome browsers have always been a brilliant way of displaying information and making information easy to get to, especially for non-specialists. Once upon a time, information was stored in the form of flat files or databases, and genome browsers have done a lot to give us detailed information that's easily accessible.

But current genome browsers are aimed at scientists, and a lot of the time, they tend to drift toward the bioinformatics end of science. There are things like the UCSC Browser that are extremely detailed and have a lot of useful information for researchers and scientists of all stripes. But that very complexity and utility can make it difficult for people who are coming straight to the subject. That's what I mean in terms of [genome browsers] being overly complex.

In terms of it being static, there are genome browsers like UCSC that allow you to put your own information on and put custom tracks on, but it's almost always complicated and difficult to implement. Specialists find this easy, but for lay people, and interested members of the public, it's very hard for them to visualize their own data on existing browsers.

So, we've been focusing on visualizing our data in a very simple way through the browser. But of course the next stage is to figure out how others can visualize their own information.

So members of Genomes Unzipped added their 23andMe data to this custom browser?

Yes, for the moment, the browser is built on 23andMe. But it will not be exclusively that; there will be other genotype data that will be entered into the browser in due course.

Do 23andMe customers have access to a genome browser through the company?

Not a genome browser, no. 23andMe has put a lot of effort into visualizing [genomic] information, but almost all the information they [show] is focused around phenotypes or around variants. So, you can look at variants associated with cystic fibrosis or variants associated with age-related macular degeneration. If you want to get to a particular gene, or a region, or the genome, the 23andMe interface is somewhat unwieldy. It's more closely designed for use by lay people, but still it's not a genome browser. It's not easy to go from gene to gene, look at chromosomes, look at transcripts, get a simple and intuitive idea of a part of a genome. It's not what they're trying to do.

What needs to happen with the browser before you extend it from Genomes Unzipped member to other interested people outside the collaboration?

There are the technological aspects, where we need think about how we can distribute this information. That's a technical problem that's probably not a very hard one to surmount. The bigger issues are legal and ethical. It took us a very long time to make full ethical appraisals of putting our own information online and we need to make sure we have covered the ethical implications of encouraging other people to do the same, and also the legal aspects of using this information, storing it, and sharing it with other people.

We are very committed to the idea that every individual should be able to and will get a lot of benefit from sharing their genomes publicly. But we want to make sure we're not doing anything rash there. The main obstacles for the moment are making sure we've fully thought through the legal and ethical ramifications.

What kind of legal and ethical requirements do you have to meet in order to enable people to upload their information and share it?

This can be complicated from the perspective that this is a transatlantic project. Most of our legal expertise in Genomes Unzipped is focused on the American side of things. A lot of our members have reported on privacy and ethical issues in the US.

In terms of the ethical boundaries, there are certain things to be overcome. Just in preparing for this project, we've noticed that individuals can learn information in their genomes before they have shared the data that has caused them to decide that they did not want to share their data publicly. We have to ensure that that realization doesn't happen after they have shared their genomes. We have to make sure that people are entirely prepared for the benefits and for the risks.

Can you give an example of when that's happened, maybe in your own experience?

In my own genome I was expecting to see very little. I have a family history pretty clear of disease. I learned that I had a number of minor but potentially significant findings: I'm a carrier of cystic fibrosis; I'm a dual heterozygote for hemachromatosis; I am homozygous for the major risk allele for age-related macular degeneration. When I learned these things, I wondered, 'Do you want to put these things out? Do I want people to know of all these potential risks and problems?'

In the end I decided that I did want to. As a sort of hypothetical example, there are variants such as the APOE variants that cause strong predisposition to early-onset Alzheimer's. It's possible that people don't want that known about themselves. We don't think that's a reason not to release your data. But it's a good reason to give strong thought to whether you want to release your data, weighed against the risks and benefits. And on our side, we want to make sure that we don't put people in a position where they [regret releasing their data].

Whenever people talk about their genome data publicly, the topic of insurance discrimination always comes up. Did you worry about that at all in sharing your data?

That's another topic that changes based on what country you're in. I reside in the UK, and I intend to live my entire life in the UK. We have a National Health Service that's not run for profit, and has no interest in denying me treatment to save money. From my own point of view, I've been very confident. However, many of our [members] are from Australia, and plan to go back there at some point, and the insurance system over there is more uncertain.

It was a reason to worry but also a reason to do this. These risks need to move from the hypothetical. We believe that these reasons are probably not going to materialize. There are strong political reasons for not discriminating against people on the basis of their genetics. There are people who strongly dislike that idea. In the US, with the Genetic Information Nondiscrimination Act, there have been a lot of moves to make sure [certain types of discrimination] aren't possible. We believe [insurance discrimination] will not be a large risk, because of the political climate.

But at the same time, if there are risks, we're well placed to deal with them. We have the contacts, the knowledge, to fight back against these problems. These risks are mitigated when you share your information publicly, in a support network, in a community of like-minded people. We can muster support in the instances of genetic discrimination. Bring attention to it, start a dialogue and fight things like genetic discrimination. One of the reasons we started Genomes Unzipped was to fight things such as this.

In terms of the educational goals of Genomes Unzipped, what are you doing beyond making your genomic data public?

There are two branches of that idea of education and outreach. We are going to be doing a lot of novel analysis of our genome. Don Conrad [of the Department of Human Genetics at the University of Chicago] in our group has been applying techniques for finding copy number variations in his own genome and to his family's genome. We're going to be writing about this kind of analysis and making tools public. We're going to be pushing for open release of data and open release of tools, and do open-source projects to allow individuals to easily and openly look at their own genome.

There is also education through example. We've all been wrestling with our own genomes and have been since we got them done. For example, after learning about the genetic conditions I talked about before, I went to talk to my general practitioner and he in turn referred me to a clinical geneticist. I'm going to be writing about that experience, and writing about things I learned from the clinical geneticist, and what other people can learn, and when they should and shouldn't consider seeing a specialist.

A lot of other people are making health and lifestyle changes based on their genome. By looking at these things and writing about them and analyzing them, we hope to be able to educate people on what their DNA data can and cannot tell them, and how it can and cannot guide their lives.

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