I've opted in to Australia's version of the biobank knowing that it's inevitable that it will be leaked some day, I think the data is so valuable in perpetuity that it's worth it. I remember Ben Goldacre has been working on how to make data more accessible in a safer way to (in part) avoid this very thing, but I haven't heard much of it since [0]
I like their idea of an audit log of analysis runs -- beyond transparency, I'm sure it'll help future researchers know how much iteration is needed to work with the messiness of medical records...
I'm also amused (in a good way) by the fact that SAS isn't supported as an analysis platform...
> It has given 20,000 researchers around the world access under strict agreements that prohibit sharing data further.
To me it seems rather naive to have done that.
After all, you can't un-leak medical data. So even if the "strict agreement" included huge punishments, there's no getting the toothpaste back in the tube.
If you want to ensure compliance before a leak happens you have to (ugh) audit their compliance. And that isn't something that scales to 20,000 researchers.
> The following steps require the ukbunpack and ukbconv utilities from the UK Biobank website. The file decrypt_all.sh will run through the following steps on one of the on-prem servers.
> Once the data is downloaded, it needs to be "ukbunpacked" which decrypts it, and then converts it to a file format of choice. Both ukbunpack and ukbconv are available from the UK Biobank's website. The decryption has to happen on a linux system if you download the linux tools, e.g. the Broad's on-prem servers. Note that you need plenty of space to decrypt/unpack, and the programs may fail silently if disk space runs out during the middle.
Good catch! The data is everywhere, re-uploaded every week.
I am aware of ~30 repositories that UK Biobank has asked GitHub to delete, and can still be found elsewhere online. They know the site, they have managed to delete data from that site before, and yet the files are still there.
It's exceptionally difficult to avoid the data being de-anonymised.
If an 'anonymised' medical record says the person was born 6th September 1969, received treatment for a broken arm on 1 April 2004, and received a course of treatment in 2009 after catching the clap on holiday in Thailand - that's enough bits of information to uniquely identify me.
And medical researchers are usually very big on 'fully informed consent' so they can't gloss over that reality, hide it in fine print or obsfucate it with flowerly language. They usually have to make sure the participants really understand what they're agreeing to.
It might still work out fine, of course - 95% of people's medical histories don't contain anything particularly embarrassing, so you might be able to get plenty of participants anyway.
In my experience with health data, the dates are usually offset by a random but constant amount for each person (e.g. id 12345 will have all their dates shifted by +5 weeks) to avoid identification by dates.
Unfortunately the sequence of treatments and locations are usually enough to identify someone, especially if it's a rarer condition.
You mean giving anyone access to the data? Or open sourcing the code? If the latter, I think that's a generally a good practice. Security through obscurity is never good for public infrastructure. In this case, UK Biobank has now switched to a remote access platform (not particularly secure, as the data was found for sale on Alibaba today), but contracting it to DNAnexus and Amazon. Private companies have no incentives to open source data, unless mandated to do so.
In the EU, there is a bigger interest in building scalable but also secure platforms for health data. Hopefully good innovation will come from there.
'Anonymisation' schemes are a little like encryption, in that they just get monotonically weaker over time as people work out attacks. But the attacks tend to be much worse. I work in academic open data publishing, and the netflix prize (https://arxiv.org/abs/cs/0610105) hangs over our heads.
But what this illustrates to me is that researchers are just really careless, despite everything we make them agree to in data transfer agreements. It seems absurd to have little cubicles like this https://safepodnetwork.ac.uk/ (think Mission Impossible 1) but I do despair.
The people who agreed to contribute their biodata did not consent to that.
If you want such a project you need to have a new project with a different agreement. I doubt you could get as many volunteers to freely give away such intimate data to anyone who wants though
That's a very important point. The people who opt out first are typically not a random fraction of the population, and this makes it much harder to make any analyses with the resulting datasets: it gets very hard to know if your analyses are representative of the population, or not.
This is why it was such a big deal when that researcher at Cleveland State misappropriated UKBB data for a race-science study with Emil Kirkegaard. After he was fired, people on Twitter were all like "this is just suppression of science", but the reality is that what they did, contravening UKBB rules, constituted potentially an existential threat to the whole program.
Hard to do. The same people with the collection and tracking infrastructure required are infinitely sue-able so you need legal protection if anything goes wrong.
From the perspective of someone who's worked with (biostatisticians who touch) Medicaid and Medicare billing data...
It looks like they've identified the institutions, at least... but aren't identifying it to the public for now. Are there going to be consequences? Are they going to be identified and sanctioned beyond "having their access suspended?"
In the US, HHS wouldn't hestitate to name, shame, and impose a sanction with corrective action plans. Not knowing much about how things work across the pond, I'm sure CMS PII gets used more often in research without these leaks left and right.
That's the least of it: https://www.bbc.co.uk/news/articles/cpvxgl3n138o
All 500,000 participants for sale on Alibaba...
And official response: https://www.ukbiobank.ac.uk/news/a-message-to-our-participan...
I've opted in to Australia's version of the biobank knowing that it's inevitable that it will be leaked some day, I think the data is so valuable in perpetuity that it's worth it. I remember Ben Goldacre has been working on how to make data more accessible in a safer way to (in part) avoid this very thing, but I haven't heard much of it since [0]
[0] https://www.bennett.ox.ac.uk/blog/2025/02/opensafely-in-brie...
I like their idea of an audit log of analysis runs -- beyond transparency, I'm sure it'll help future researchers know how much iteration is needed to work with the messiness of medical records...
I'm also amused (in a good way) by the fact that SAS isn't supported as an analysis platform...
> It has given 20,000 researchers around the world access under strict agreements that prohibit sharing data further.
To me it seems rather naive to have done that.
After all, you can't un-leak medical data. So even if the "strict agreement" included huge punishments, there's no getting the toothpaste back in the tube.
If you want to ensure compliance before a leak happens you have to (ugh) audit their compliance. And that isn't something that scales to 20,000 researchers.
Too late to do anything about it now though :(
The irony is, they don’t even provide the data to the participants themselves.
Huh? I got my report over email. I think you have to ask for it.
Took me 5 minutes to find more: https://github.com/tanaylab/Mendelson_et_al_2023/blob/9c5a65... (Uses Date of Birth column).
And some information on how they were distributing it to researchers: https://github.com/broadinstitute/ml4h/blob/master/ingest/uk...
> The following steps require the ukbunpack and ukbconv utilities from the UK Biobank website. The file decrypt_all.sh will run through the following steps on one of the on-prem servers.
> Once the data is downloaded, it needs to be "ukbunpacked" which decrypts it, and then converts it to a file format of choice. Both ukbunpack and ukbconv are available from the UK Biobank's website. The decryption has to happen on a linux system if you download the linux tools, e.g. the Broad's on-prem servers. Note that you need plenty of space to decrypt/unpack, and the programs may fail silently if disk space runs out during the middle.
https://biobank.ctsu.ox.ac.uk/crystal/download.cgi
Good catch! The data is everywhere, re-uploaded every week.
I am aware of ~30 repositories that UK Biobank has asked GitHub to delete, and can still be found elsewhere online. They know the site, they have managed to delete data from that site before, and yet the files are still there.
What are the pros/cons of just open-sourcing everything for future bio bank projects?
It's exceptionally difficult to avoid the data being de-anonymised.
If an 'anonymised' medical record says the person was born 6th September 1969, received treatment for a broken arm on 1 April 2004, and received a course of treatment in 2009 after catching the clap on holiday in Thailand - that's enough bits of information to uniquely identify me.
And medical researchers are usually very big on 'fully informed consent' so they can't gloss over that reality, hide it in fine print or obsfucate it with flowerly language. They usually have to make sure the participants really understand what they're agreeing to.
It might still work out fine, of course - 95% of people's medical histories don't contain anything particularly embarrassing, so you might be able to get plenty of participants anyway.
In my experience with health data, the dates are usually offset by a random but constant amount for each person (e.g. id 12345 will have all their dates shifted by +5 weeks) to avoid identification by dates.
Unfortunately the sequence of treatments and locations are usually enough to identify someone, especially if it's a rarer condition.
You mean giving anyone access to the data? Or open sourcing the code? If the latter, I think that's a generally a good practice. Security through obscurity is never good for public infrastructure. In this case, UK Biobank has now switched to a remote access platform (not particularly secure, as the data was found for sale on Alibaba today), but contracting it to DNAnexus and Amazon. Private companies have no incentives to open source data, unless mandated to do so.
In the EU, there is a bigger interest in building scalable but also secure platforms for health data. Hopefully good innovation will come from there.
'Anonymisation' schemes are a little like encryption, in that they just get monotonically weaker over time as people work out attacks. But the attacks tend to be much worse. I work in academic open data publishing, and the netflix prize (https://arxiv.org/abs/cs/0610105) hangs over our heads.
But what this illustrates to me is that researchers are just really careless, despite everything we make them agree to in data transfer agreements. It seems absurd to have little cubicles like this https://safepodnetwork.ac.uk/ (think Mission Impossible 1) but I do despair.
The people who agreed to contribute their biodata did not consent to that.
If you want such a project you need to have a new project with a different agreement. I doubt you could get as many volunteers to freely give away such intimate data to anyone who wants though
One of the most important "con"'s is that without controls, fewer people will allow their data to be included in the data sets.
That's a very important point. The people who opt out first are typically not a random fraction of the population, and this makes it much harder to make any analyses with the resulting datasets: it gets very hard to know if your analyses are representative of the population, or not.
This is why it was such a big deal when that researcher at Cleveland State misappropriated UKBB data for a race-science study with Emil Kirkegaard. After he was fired, people on Twitter were all like "this is just suppression of science", but the reality is that what they did, contravening UKBB rules, constituted potentially an existential threat to the whole program.
Hard to do. The same people with the collection and tracking infrastructure required are infinitely sue-able so you need legal protection if anything goes wrong.
Really don't think this is any issue given the post we are commenting on...
From the perspective of someone who's worked with (biostatisticians who touch) Medicaid and Medicare billing data...
It looks like they've identified the institutions, at least... but aren't identifying it to the public for now. Are there going to be consequences? Are they going to be identified and sanctioned beyond "having their access suspended?"
In the US, HHS wouldn't hestitate to name, shame, and impose a sanction with corrective action plans. Not knowing much about how things work across the pond, I'm sure CMS PII gets used more often in research without these leaks left and right.