5 ms·

There's no drift, OP stated this clearly in the original post when he wrote: "I strongly believe there is enough information to re-identify patients" If you we

There's no drift, OP stated this clearly in the original post when he wrote: "I strongly believe there is enough information to re-identify patients" If you were to have access to my MRIs you could almost certainly identify me based on physical characteristics which can be seen in my MRI data which would correlate with data found on social media where I've sometimes generally discussed my medical conditions without going into specifics. There are MRIs for conditions I haven't discussed, in addition to the identifying ones I have. There are a lot of people with fairly unique medical conditions and body situations (eg: missing a limb, surgical implants). The gap between "I got hurt in this way" and "here's the MRI scans of my body in detail along with other lab notes and other unrelated and possibly extremely embarrassing conditions" is huge

rvnx 5y ago
Fair enough, what do you propose to give access to people who want to help ?
- throwawaygh 5y ago
  A strict data use agreement signed by a real person with tangible assets and reputation at stake, outlining the acceptable and unacceptable uses of the data and well as appropriate data handling rules. Until/unless patients agree otherwise. I.e., the status quo.
- jacquesm 5y ago
  Go to work in the field.
- bshipp 5y ago
  Anonymizing datasets is time consuming and would take resources away from the FDA to implement, instead of doing it themselves. I have no doubt people want to help but the only way they really could would be to sign a contract with someone who is allowed to share that data internally, and operate in a embargoed situation (such as on-premise) under an NDA. Otherwise it's sort of like my 10-year-old wanting to help me replace an engine in a car. It's important to let him do it so he can learn but it's likely going to take me much longer to on-board him and get him up to speed than if I did it myself.
  - rvnx 5y ago
    I think Pfizer got 50B+ USD in revenue in 2021, maybe they can find a little bit of change somewhere to hire specialists to prepare the data cleanly and release it ?
    - deleted 5y ago
      [deleted]
    - snowwrestler 5y ago
      A dataset that Pfizer spends a ton of money redacting before releasing might not address concerns that Pfizer could be hiding something.
nextos 5y ago
This is already a solved problem. I have deposited datasets with full transcriptome data, which you can use to infer most of the genome in a straightforward manner, from clinical trials. In that case, you simply use off-the-shelf tools to anonymize datasets by flipping lots of SNPs. Additionally, raw data is made accessible only through an ethics committee. Summary counts from transcriptomes are publicly available, though. There are equivalent practices for other biomarkers. I must say The British Biomedical Journal (BMJ) is really spearheading all transparency efforts. They have been publishing lots of inconvenient truths for many years. For example, they reported some fairly serious conflicts of interest where professors from Oxford are getting huge "consulting" fees from pharma. And they pretty much publish any reasonable letter to the editor. Nature, Science and Cell, on the other hand, are heavily biased.
- throwawaygh 5y ago
  > This is already a solved problem... raw data is made accessible only through an ethics committee. Summary counts from transcriptomes are publicly available, though. Right. 1. I'm not sure you understand the extreme position being taken by rvnx in this thread. 2. Presumably the patients agreed that their transcriptome data could be shared in this way, and you didn't change your data handling post-facto without their consent.
  - nextos 5y ago
    Of course patients need to agree. It's actually even simpler. When you recruit patients into a study they sign an agreement that is broad and usually includes data sharing terms. Properly anonymized, of course. Said agreements have previously gone through ethics committees which tend to be extremely strict. They are rarely changed afterwards, since this requires agreement of patients, which is impractical to obtain in all but tiny studies. The only exception I can think of is Scandinavia. They have national registries where all census information, plus electronic health records, is available to researchers by default, unless you explicitly opt out. Their philosophy is that this is a negligible reduction in privacy, in exchange for medical progress. I must note said records are not publicly open, you need to apply for access. As a consequence, Sweden and Denmark have some of the best epidemiological research in the world and they've been able to spot pretty odd correlations (e.g. ibuprofen and male infertility).

rvnx 5y ago

Fair enough, what do you propose to give access to people who want to help ?

throwawaygh 5y ago
A strict data use agreement signed by a real person with tangible assets and reputation at stake, outlining the acceptable and unacceptable uses of the data and well as appropriate data handling rules. Until/unless patients agree otherwise. I.e., the status quo.
jacquesm 5y ago
Go to work in the field.
bshipp 5y ago
Anonymizing datasets is time consuming and would take resources away from the FDA to implement, instead of doing it themselves. I have no doubt people want to help but the only way they really could would be to sign a contract with someone who is allowed to share that data internally, and operate in a embargoed situation (such as on-premise) under an NDA. Otherwise it's sort of like my 10-year-old wanting to help me replace an engine in a car. It's important to let him do it so he can learn but it's likely going to take me much longer to on-board him and get him up to speed than if I did it myself.
- rvnx 5y ago
  I think Pfizer got 50B+ USD in revenue in 2021, maybe they can find a little bit of change somewhere to hire specialists to prepare the data cleanly and release it ?
  - deleted 5y ago
    [deleted]
  - snowwrestler 5y ago
    A dataset that Pfizer spends a ton of money redacting before releasing might not address concerns that Pfizer could be hiding something.

nextos 5y ago

This is already a solved problem. I have deposited datasets with full transcriptome data, which you can use to infer most of the genome in a straightforward manner, from clinical trials. In that case, you simply use off-the-shelf tools to anonymize datasets by flipping lots of SNPs. Additionally, raw data is made accessible only through an ethics committee. Summary counts from transcriptomes are publicly available, though. There are equivalent practices for other biomarkers. I must say The British Biomedical Journal (BMJ) is really spearheading all transparency efforts. They have been publishing lots of inconvenient truths for many years. For example, they reported some fairly serious conflicts of interest where professors from Oxford are getting huge "consulting" fees from pharma. And they pretty much publish any reasonable letter to the editor. Nature, Science and Cell, on the other hand, are heavily biased.

throwawaygh 5y ago
> This is already a solved problem... raw data is made accessible only through an ethics committee. Summary counts from transcriptomes are publicly available, though. Right. 1. I'm not sure you understand the extreme position being taken by rvnx in this thread. 2. Presumably the patients agreed that their transcriptome data could be shared in this way, and you didn't change your data handling post-facto without their consent.
- nextos 5y ago
  Of course patients need to agree. It's actually even simpler. When you recruit patients into a study they sign an agreement that is broad and usually includes data sharing terms. Properly anonymized, of course. Said agreements have previously gone through ethics committees which tend to be extremely strict. They are rarely changed afterwards, since this requires agreement of patients, which is impractical to obtain in all but tiny studies. The only exception I can think of is Scandinavia. They have national registries where all census information, plus electronic health records, is available to researchers by default, unless you explicitly opt out. Their philosophy is that this is a negligible reduction in privacy, in exchange for medical progress. I must note said records are not publicly open, you need to apply for access. As a consequence, Sweden and Denmark have some of the best epidemiological research in the world and they've been able to spot pretty odd correlations (e.g. ibuprofen and male infertility).