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Covid-19 vaccines and treatments: we must have raw data, now

bmj.com

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Re: Covid-19 vaccines and treatments: we must have raw data, now

#181

Post by rvnx »

eminence32 wrote: post #168
invokestatic wrote: post #156

Earlier quoted context omitted.

Under the safe-harbor deidentification guide you posted, all dates must be removed except for the year. If this was done on a clinical trial dataset, the data would be useless. Specifically for the COVID vaccine trial, the “statistic” used is the number of days between when the patient enters the study and when they get COVID. This is called TTE or time-to-event and underpins the entire study design. You need the exa…

Focusing on the date aspect for a minute: is it possible to adjust the data (before the deidentification process) and convert relevant absolute dates into durations? For example, is it possible (and is it useful) to adjust the data so that it says something like "patient abc123 entered the study in 2021 and 83 days after receiving a vaccine they showed started to show symptoms. Symptoms ended 3 days later"

This would be great :)

Re: Covid-19 vaccines and treatments: we must have raw data, now

#182

Post by rvnx »

MauranKilom wrote: post #176
rvnx wrote: post #107

Earlier quoted context omitted.

It looks like you are trying to drift the intent and scope of the dataset disclosure. For example, having the list of symptoms, medications and even (just an imaginary example) pulmonary X-Ray or also on the chest having an open dataset of MRI pictures with the age of the patient, history of diseases would considerably help and there is no way you can link it back unless you know the history of the patient already (b…

> having an open dataset of MRI pictures with the age of the patient, history of diseases would considerably help and there is no way you can link it back Facial recognition works perfectly fine on MRI face renders. You speak awfully confidently about a problem you seem to have very little experience in. As with cryptography: Anyone can come up with suggestion that they themselves can't find an attack against.

True, true, pictures are even one level higher in terms of difficulty to anonymise right (and that's not even what they are asking, here it's about structured text records).

FYI, high-res face MRI are just pictures of the face. So yes, if you share the picture of the face of someone, they may find your identity back, but it's not specific to MRI.

Dealing with any medical record that contains pictures of patient you should take additional steps to prevent identification, and face is the most sensitive part of the body as it can be most likely identified.

If tomorrow there are publicly available anonymised close-up pictures of cardiac MRI, it'd be extremely challenging to map them to their real owner with a 100% certainty but the discoveries it could lead to are very exciting (and the same with skin cancer pictures for example, or suspiciouses moles)

Re: Covid-19 vaccines and treatments: we must have raw data, now

#183

Post by throwawaygh »

rvnx wrote: post #128
throwawaygh wrote: post #104

Earlier quoted context omitted.

> Re-identify based on what ? The fact that you poo-poo this question is telling. Preventing re-identification attacks is incredibly subtle and sometimes impossible. Removing "city and date of birth" is nowhere near sufficient. > this raw data is already available, but under a loose NDA for commercial partners and researchers... Yes. It's available to people who have their real identities tied to their access and can…

It looks like from what you are saying that it's an incommensurable effort to anonymize reasonably the dataset (the majority of the risks can be hedge by bucketing, and then there can be subtle deanonymization edge cases but they don't scale). It reminds me the FDA saying they can't release the COVID-19 documents because reviewing 44'000 documents would take 50 years. It didn't take 50 years to produce them... Yes th…

Presumable FDAs analysis assumed current staffing levels. Going to go out on a limb and assume they’ve got a LOT more people involved in creating docs than in deidentifying docs.

And, yes, I think public data on this sort of stuff is important and should be properly resourced.

I think:

Step 1. ASK PERMISSION before changing the way data is handled.

Step 2. Share full datasets more generously, but still gated by use and handling agreements. This probably means a private citizens without ethics research training and a supporting it dept can’t get a copy and peruse it on their personal laptop, but also that a truly enormous number of researchers would be able to access the data.

The gold standard of a CSV in a public s3 bucket shouldn’t be the enemy of good enough.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#184

Post by dragonwriter »

fsociety999 wrote: post #177
dragonwriter wrote: post #166

Earlier quoted context omitted.

> It absolutely is part of an ongoing clinical trial regardless us if it is authorized for emergency use. It is for the people enrolled in an actual clinical trial. It's not for people outside of the clinical trial using it under either the EUA or the subsequent full authorization. > How many people who were given the vaccine were told that it is part of an ongoing clinical trial, 100% of those for whom that was true…

I understand that, my point is that as part of the EUA, patients are required by law to receive information about the treatment. See section e-1-A-ii here: https://www.law.cornell.edu/uscode/text/21/360bbb-3 (ii)Appropriate conditions designed to ensure that individuals to whom the product is administered are informed— (I)that the Secretary has authorized the emergency use of the product; (II)of the significant known…

> So I am saying, what percentage of people who got the shot actually received this information?

That's very different than what you said before, and all of them who got it under the EUA.

> Since the trials are ongoing

The trials being ongoing is immaterial, it's required when under an EUA, not when the intervention is one for which trials are ongoing, which are different things.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#185

Post by throwawaygh »

rvnx wrote: post #178
Tostino wrote: post #158

Earlier quoted context omitted.

It's that knowing that someone has a rare medical condition that someone willingly shared can be a signal to find out other things in their medical records that they may not have wanted to share with others they know.

Let's look in practice, as they exist: look at VAERS for example, it's in this exact situation (these are public records posted on a public and non-confidential HTTP server): https://vaers.hhs.gov/data/datasets.html This is the type of raw records we are talking about, and they carry useful information. Yes, maybe the dates could be anonymised better, if I know the age of someone, and I know when he got his vaccine p…

I can show you 10 code snippets that don’t contain sec vulns. Therefore, software security is easy.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#186

Post by rvnx »

bshipp wrote: post #148
rvnx wrote: post #136

Earlier quoted context omitted.

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

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…

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 ?

Re: Covid-19 vaccines and treatments: we must have raw data, now

#187

Post by guywhocodes »

fabian2k wrote: post #91
nsainsbury wrote: post #82

Earlier quoted context omitted.

Actually, I would argue we don't have good data from the use of the vaccines. Part of the reason is because all the mechanisms used for reporting things like side-effects, effectiveness, etc. have a litany of confounding variables which haven't been controlled for which could be far better corrected for/isolated with good studies. For example, when it comes to vaccine side-effects, I don't think there exists a true a…

But we actually don't need the VAERS data to examine if the vaccines are better than the alternative. We do need it to provide accurate labels for side effects, but that is all. We can simply look at infection, hospitalization and death in vaccinated and unvaccinated populations. If we properly match the populations, we can determine if the vaccine saves lives, and it turns out that they do save a lot of lives.

But we have a similar noise in COVID death and injury as we have incentivized hospitals to register everything and everyone as COVID related. And I believe we all know just about any PCR test can be made positive if you use enough cycles.

Sorry but I can't distrust VAERS and then trust the COVID injection complication data added by the same people but now with financial incentives.

Re: Covid-19 vaccines and treatments: we must have raw data, now

#188

Post by rvnx »

throwawaygh wrote: post #134
rvnx wrote: post #132

Earlier quoted context omitted.

Ok then next steps: Plan A: - sit and do nothing "it's impossible to release any data, too bad, we'll never know!" Plan B: - "we have a risk that a few % of ppl may be identified if we already know their medical history/details , it's impossible to release any data, too bad!" Plan C: - "we remove the biggest identifiers to make sure the majority of the people cannot be reasonably identified, this is going to take a f…

Why don't you include a step where you ask patients if they're ok with their medical history being put in a public s3 bucket ? I'm fully supportive of the right to pseudonymous speech, but it strikes me that you are in an awfully awkward position of speaking anonymously while demanding that you should have access a trove of patient history without signing any sort of data use agreement and without even the most basic…

Ok, why not, this is what I propose:

Asking the user:

"This record is going to be shared publicly, do you agree to share this information (without revealing your name and address) ?

> [...]

This information can help researchers, doctors and people interested into science to discover new information about drugs and diseases interaction."

Re: Covid-19 vaccines and treatments: we must have raw data, now

#189

Post by nextos »

throwawaygh wrote: post #163
nextos wrote: post #147

Earlier quoted context omitted.

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, t…

> 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…

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).

Re: Covid-19 vaccines and treatments: we must have raw data, now

#190

Post by trhway »

mberning wrote: post #24

It’s incredible how quickly pharmaceutical companies rehabbed their deservedly awful reputation by using the pandemic. Years from now, maybe decades, I’m sure we will find out there were very troubling results from the clinical trials that were swept under the rug.

The troubling result is that vaccines have been forced upon [majority] of the people to whom it has no public interest effect - the existing covid vaccines (except SinoVac for which there is no reliable data) don't reduce the spread nor affect hospitalization rate for most as the most have close to 0 chances of hospitalization to start with.

When it comes to spread the vaccines may be even making the situation worse as the infected vaccinated people spread virus at the same level as infected unvaccinated while having less symptoms for the vaccinated means higher chances of them walking around spreading it.

>there were very troubling results from the clinical trials that were swept under the rug

this is why the clinical trials aren't going to conclude until few years down the road as operating under EUA is basically get-out-of-jail-free card for the BigPharma here.

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