Inside my genome

Or: Craig Venter and I1

I spat into a tube this morning:

This is to participate in a study called “Inside your genome” that is run by the good folks at the Wellcome Trust Sanger Institute. The study offers 1000 people working here on the Genome Campus to be voluntarily genotyped at a set of ~100-150 known variants, showing results for around 30 traits. Among some other things, this study is set up to explore people’s attitudes, views, opinions and awareness of personal genomics (using genetic technology) to learn about how their own genome sequence relates to their traits.

I like this simple description of what’s going on:

Every cell in your body has a complete set of instructions, known as the genetic code, that tell the body how to make your cells and their components, and to direct how these interact. This set of instructions is encoded in your genome. You could think of the genome as a recipe book that carries all of the instructions necessary to make a human being. Sometimes, variation in the genome between individuals can result in the presence of certain traits, some of which may be related to your health.

The traits included in this study – as voted for by study participants – are entirely “benign”:

  • Ancestry (Worldwide, Neanderthal and population markers)
  • Cholesterol
  • Eye colour
  • Smell perception
  • Taste perception
  • Blood glucose
  • Muscle performance
  • Blood pressure
  • Body mass index (BMI)
  • Blood type
  • Nicotine addiction susceptibility
  • Caffeine consumption
  • Fat distribution
  • Lactose intolerance
  • Norovirus resistance
  • Male pattern baldness

Most of this doesn’t sound very exciting. After all, I already know the colour of my eyes (green), my hair colour (dark blonde… well, increasingly grey), I know (from experience!) in which areas my body fat is most likely to be stored, and I am pretty sure I am not at risk of developing male-pattern baldness. I am, however, a tiny bit excited about the prospect of finding out exactly how “Neanderthal” I am – I do have all four of my wisdom teeth and they are fully functional… I’ve always wondered whether that may be any indication?

Even judging only by the number of times this was mentioned in the information paperwork, among the biggest concerns of the researchers seems to be:

  • Study participants asking researchers about specifics concerning their genome/results (which will NOT be possible)
  • Feedback of any “incidental” findings (i.e. things not included on the list above) to study participants (which will NOT take place)

The reasons for this (I am guessing) might be:

  • Practical issues involved in storing and (re-)analysing the data
  • Keeping data identifiable (i.e. possible to link with the individual study participant, which in this study is explicitly NOT the case)
  • and, probably the reason for the previous point, ethics involved in feeding back findings to the participants (probably along the lines of the issues described recently in an article in Nature).

But to be honest, and as much as I understand that this is not feasible, I was/am almost a bit disappointed that the study will not look at factors that may indicate detrimental health effects. For example, I would have liked to know exactly how likely I will be to get arthritis, as one of my close family members has it. Then again: arthritis is not life-threatening, and it’s probably sufficient if I just mentally prepare myself for the eventuality (plus try and keep my joints healthy by eating the “right” foods and exercising). It might be quite different if I was confronted with a finding that indicates I might die rather a bit sooner than I had hoped.

One of the aims of the study is to “give [participants] the opportunity to personally think through the technical and ethical considerations that surround personal genomics”. But I wonder whether looking at “harmless” traits contributes in any way towards finding out the real attitudes, since the big issues seem to me to only arise once the findings are not “harmless”. One colleague joked, predictably, that if traits relating to a detrimental effect on health had been included in the study, “the next thing would be that you’d find yourself being struck off the health insurance” – and I bet this or a similar thought is the first that pops into the head of anyone who thinks about genotyping, especially in the context of personalised medicine.. and despite its huge potential to help patients by targeting treatments. If not, let me know in the comments.

Just this morning it seemed like the participation in the study would be modest, judging by the number of sampling kits that were left over. However, with just 1.5 hours to spare before the deadline, there was an update that the kits have all gone now. A mad, last-minute rush – have people just made up their minds (or were they just too lazy to do it earlier, like me)?

How do you feel about genotyping – if you really think about it?



1. The study is completely voluntary, confidential, etc., and only looks at a veryvery limited set of traits, so it really is not quite like having your entire genome sequenced and published openly like Craig Venter’s… but since the consistency of his earwax was mentioned in the introduction to the keynote talk I heard him give a bit over a week ago at ESOF 2012 in Dublin, the subtitle seemed somehow appropriate.

About steffi suhr

Once upon a time, I was an enthusiastic and hopeful biological oceanographer who did a bunch of work in the Antarctic. I was alternately wearing labcoats or extreme weather clothing and hard hats, but have long since swapped survival suits for dress suits and do science management, currently as the BioMedBridges project manager at the European Bioinformatics Institute. I still like to use my brain. I'm a German serial expat, currently - again - living in the UK.
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25 Responses to Inside my genome

  1. Y’know, just yesterday I was musing on Twitter about doing 23andMe, which offers something similar but with more health-related genes included. I’d love to know what’s in my genome, but the medical history of both sides of my family suggests that there might be things I’d rather not know… e.g. susceptibility to conditions you can’t do much to prevent. I’d do the scheme you mentioned in a heartbeat though!

    As you know from private correspondence, I’m getting really interested into the ethics of genome sequencing, from a clinical (mostly cancer research) point of view.

    This comment should really be at least two blog posts 🙂

  2. steffi suhr says:

    Write those posts, Cath, please! I for one would be interested also in seeing the “process” of thinking about the ethics involved. For example, not so many years ago I might have been squeamish about doing this, but now I didn’t think twice – even though possible pitfalls (of personal genomics) are becoming clearer (to me).

  3. steffi suhr says:

    One more: you mention for example that there are things you’d rather not know (same here). What if it was compulsory to have your genome sequenced? (Or if there was e.g. the possibility of getting lower-cost healthcare? I realise these aren’t new questions and they’ve probably been discussed elsewhere at length – I’d be grateful if anyone reading this could post some (sensible) links here.

  4. Frank says:

    You are right it has been discussed before going back many years. Search for ELSI (Ethical, Legal Social Issues) and you will get a ton of references. Here are a couple of more recent items.

    Something from the AMA: Genome sequencing to add new twist to doctor-patient talks.

    A report from the Nuffield Council on Bioethics: Personalised healthcare.

    Also worth poking around on the ESRC Genomics Network.

  5. steffi suhr says:

    Thanks Frank, I’ll have a read. The current very rapid developments make the issue more pressing though, don’t they? And I wonder how many people have happily ignored personal genomics and any implications this may have for their lives.

    I keep meaning to link to Erika’s prize-winning Sci-Fi story on this from quite a while back!

  6. steffi suhr says:

    Still trying to explain where some of my thoughts are coming from: I just put together my first storify of my notes from the “true cost of personalised medicine” session at ESOF 2012.

  7. amy says:

    Hi, Steffi! Here’s my main worry about handing over the DNA (and I’ve no doubt we’ll all be corralled into it at some point not too far off): People are more than a little nuts, and cook up none-too-bright theories, and then believe the (occasionally lunatic) theories to be fact, and this becomes the basis of policy. You don’t have to go all the way to Kubrick to see how badly that can work out. I find that people engaged in research remain relentlessly hopeful about human nature and trust that only lovely things will be done with the information. I’m less optimistic.

    That’s it. It’s just a very large it.

    Did you hear, by the way, about the man arrested in Oregon for being too complaint with TSA? They’d taken him off in a corner and had him take off his shoes, and socks, and etc., and at a certain point he got so annoyed with them he just stripped bareass in front of the whole airport and said, “See?!” Arrested for indecent exposure, but, as I heard it on NPR, in Oregon you can’t be convicted of indecent exposure unless the object is to titillate.

    In every airport in the land you have to take of your shoes, be scanned nekkid, and explain your shampoo on demand. If this isn’t reason enough why we’re not sufficiently responsible to handle large quantities of human genomic information, I don’t know what is.

    • steffi suhr says:

      Hi Amy! First off, I understand where you are coming from. The same aguments could be – and are of course being – made about nuclear energy, genetically modified organisms, etc. I understand the concerns, and I do not personally in any way have a see-the-world-through-pink-lenses view of science and scientists, nor do I think science is or is going to be the answer to everything.

      BUT: over the centuries, science has provided the knowledge that led to some pretty amazing and many very useful technologies. There were and are a number of not so brilliant ideas, to be sure. But overall the balance isn’t bad, and in my more hopeful moments I want to think that we may increasingly be going in the right direction with respect to – for lack of a better word – keeping science under control and maximising benefits (e.g. recent developments with open access, citizen science, etc. and the power of the interwebz in general). Hence I am hopeful that we may find a sensible way to deal with personal genomics and personalised medicine.

      Having said all that, and as I tried to say in the post, I am still trying to find out what *exactly* my own attitude is when it actually comes to my own, very personal information – I’m basically trying to do my homework, and maybe participating in this project is part of that.

      • steffi suhr says:

        Just for some more context: I just re-discovered this article that I had bookmarked a little while ago – it argues rather enthusiastically for making genomic data availabe, plus mentioning some important projects and linking to background.

  8. Eva says:

    I don’t really want to know everything that’s lurking in my genes. There’s something on my mother’s side of the family that for the past couple of generations has caused loss of eyesight at old age. It was probably there before then, but people just never reached the age where it kicks in…(I think it’s retinitis pigmentosa, but not even 100% sure because I just don’t want to think about it too much. Could be a variation thereof.) One of my aunts knows she has the mutation, and is now pretty much waiting for it to kick in. My mom doesn’t want to know whether or not she has the mutation, so even if I change my mind and want to check MY genes, I *can’t*, because if I *do* have the mutation, I’ll know that my mom does, too! I don’t want to be responsible for unearthing that knowledge if she doesn’t want to know…
    There will likely be a treatment in my lifetime, but there isn’t yet, so there’s not much point in knowing what will happen to me in 40-50 years.

    And for any other possible disease the same holds true: either there’s a cure and I’ll be fine, or there isn’t and I just don’t want to know. I don’t want anything looming over me for the rest of my life.

  9. steffi suhr says:

    So Eva – would it be fair to say that (other than “gimmicky” harmless stuff) we’re not comfortable with knowing the *health* implications of our entire genetic makeup? But that the situation is different if personalised medicine comes in once the patient is already sick: e.g. to see which drugs/treatment would be most effective (see my storify from ESOF: with personalised treatment, patients can apparently avoid getting nasty chemotherapy in some cases etc.).

    So, in summary: stay away from my genome unless/until I get sick (even if it means you could avoid getting sick in the first place?).

    But what happens then with “incidental findings”: say you’re at the hospital for something and there’s testing to see what drug will help you – and in the process it’s discovered that there’s something else going on that’s quite serious. And let’s say on top that there may be something that can be done *then*, i.e. before you’re sick, and that it would be too late once you *are* sick. What then? (I realise these are incredibly construed “what if..” scenarios!).

  10. That’s fun. There are all kinds of these personal-genome/genetics things cropping up (the Ontario Science Centre here in Toronto has a “spit for science” initiative, for example). As a fun aside, the company that makes the most popular “spit kits” for DNA prep, DNA Genotek, is located not four hours from here (if you drive fast) in Ottawa.

    Interesting discussion regarding the ethics – people get very wound up about “whole genome” approaches and all the potential for incidental findings, but this is really not new at all. Genome-wide genotyping has been around for 10 years or more, and even in the bad old days of the 1980’s it was more than possible to find out potentially harmful incidental findings in even single-gene (or single-polymorphism) studies. I uncovered a case of non-paternity in one family my PhD lab was studying (it was irrelevant to the medical status of the patient and family members involved, and no, we didn’t report it). The chance of finding something potentially harmful in whole-genome data is much higher of course, but the underlying ethical questions are essentially the same, IMHO.

    On the other hand – things do depend a bit on who you are. Craig Venter was firmly in middle age and had been healthy his whole life, so it’s not surprising that there was little of medical note in his genome sequence. The approach might need to be different for, say, a teenager.

    • steffi suhr says:

      Oh, I forgot something else I wanted to ask concerning that “non-paternity” incident, Richard: did it make you, as the researcher who discovered this, feel uncomfortable to have found this (regardless whether it had any implications) – you knew something very personal the study participants weren’t or may not have been aware of?

      • I confess it didn’t worry me at all, but I was less sympathetic then than I am now. I think any uncomfortableness was overwhelmed with the idea that it was better to leave the situation “as is” and not tell them (which I basically couldn’t have done anyway, as I recall).

        If it had been medically important… well, let’s just say I’m selfish in being glad it wasn’t.

  11. steffi suhr says:

    It probably hasn’t come out clearly before, but of course I have been/am aware that there has long been a general discussion on ethics invovled in “genomics” in the widest sense (even though I am clearly not as familiar with the details – yet – as someone who’s career has been linked to this topic all this time). But am I the only one who has just recently started to really think through what this means for me personally???

    Eva got me thinking again concerning what it means for the patient’s/study participant’s family when a discovery is made. There was a quesiton in the study survey along the lines of “would you tell your friends/family/spouse/children”. I enthusiastically ticked “yes” on everything, but now I’m not so sure anymore – as Eva says, what if my family members don’t want to know what they’re at risk for? But could I NOT tell them if something was up with me (similarly to telling them if I found out that I am seriously/terminally ill and not keep that to myself?).

    • The trickier question is whether your friends/family/spouse/children would want to know. Some genome sequencing initiatives have I believe explored consenting direct relatives separately, which makes sense to me. A thornier issue is that if something pathogenic is found in your genome, we can’t tell without testing a blood relative whether they carry it as well. But the simple act of finding it in you, and you telling them, puts them in a situation that they may not have asked for (i.e. anxiety at learning that they might be at risk of whatever it is, and then the decision process of whether to be tested or not).

      Much of this could be seen as kind of irrelevant though, as it is not that different from you going for, say, a mammogram, and coming back from the clinic with a positive result for breast cancer (knock on wood; this is just a thought question). Whether or not you tell friends/family/spouse/children about that is pretty much exactly the same question as whether you would tell them about something in your genome – with the important difference that the mammogram is specifically looking for one disease, whereas the genome sequencing is a catch-all (or more accurately, a “catch some, kind of”).

  12. Frank says:

    I confess I am not really thinking about its implications for me. Both my parents are dead, I have no children. I am moderately healthy, but need to lose a little weight. I dont want to learn that there is an x% risk of this and a y% risk of that.

    I am much more interested in the issues more generally, and how it will change our thinking about health and disease in future. I think genetic counselling will be a growth industry. It will be a challenge for counsellors to explain “what does it mean for me” when they have to explain half a textbook’s worth of molecular genomics.

    Another organisation you might want to explore is the Genetic Alliance (UK).

    • steffi suhr says:

      Thanks, Frank!
      Yes, the things you mention caught my eye among the recommendations and conclusions from the Nuffield Council on Bioethics report you provided the link to above as well. They go as far as saying: “Doctors should receive training on giving advice to patients about commercial genetic profiling services”, which seems entirely sensible – but I wonder how this would work in practice. At some level, you’d have to teach every single GP about genomics, wouldn’t you?

      • Something we have given a lot of thought to. It might make sense in the context of an MD-PhD program, say, but for basic MD training… well, here, the med students get about two weeks of genetics in their second year, I think. That’s not enough… and it’s hard to make the argument they should get more, when they’re also overwhelmed with pathology and anatomy and all the rest of the things they need to know.

  13. Amara Graps says:

    Steffi: I have 23andMe subscriptions for both my daughter and I. It was the best thing I’ve ever done, after having a baby and earning my PhD. 🙂 I am so enthusiastic about the concept and the information that I have from them, that I could easily write a full page on the topic. Are you interested in a long monologue? Or I can stop here, with my simple opinion: ‘I think it’s great.’. Amara

    • steffi suhr says:

      I would actually absolutely love to hear your full opinion, Amara! Just as long as you declare any conflict of interest in case you get paid by them 🙂

  14. Frank says:

    Just seen that the Presidential Commission for the Study of Bioethical Issues is also thinking about these things. Quick extract from their blog:

    “The Commission’s recommendations,” said Dr. Amy Gutmann, Commission Chair and President of the University of Pennsylvania, “clump into two big categories, one is consent to whole genome sequencing and to the possible findings and how they will be treated, and the other is oversight.”

    One question that was explored in depth was, as Commission member John Arras, Ph.D., of the University of Virginia, put it, “the impending merger between clinical practice and research,” and how that would impact informed consent.

    Commission member Raju Kucherlapati, Ph.D., from the Harvard Medical School Department of Genetics, said, “Genetic testing for research purposes involves extensive informed consent forms signed by individuals, while the process of consent for clinical testing is not as extensive a process.”

    • steffi suhr says:

      Thank you, Frank – the pending tie-in of research and treatment is one of the reasons why I feel the urge to make up my own mind, given my current job! The BioMedBridges project has been funded by the Commission to put the technical tools in place for this type of work, but also includes the development of detailed briefs on data security and ethics (with the latter driving the former: ethical considerations driving data security needs).

      I definitely have another post coming up on this.