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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

#161

Post by enkid »

mchusma wrote: post #157
invokestatic wrote: post #59

I’m a software consultant for Pharma companies and have worked on projects that used the same kind of study design as the Pfizer COVID vaccine (Kaplan-Meier). “Raw data” is submitted to the FDA in the CDISC format. This format contains a lot of pretty sensitive medical information, including which diseases a patient has, their medical history, what drugs they take, etc. This is supposed to be anonymized, but if the p…

I think the level of effort we make as a society on medical privacy is backwards. All health information should be public except in extreme circumstances. Right now, it's almost impossible to get datasets on health data. Imagine if 100% of everyone's data was digitized. The amount of health innovation, lives saved, cures found, is likely to be incredibly large. All the costs that go into trying to comply with HIPPA,…

You don't see any potential misuse if having people's STD results publicly available? (To use an extreme case)

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

#162

Post by fxtentacle »

mchusma wrote: post #157
invokestatic wrote: post #59

I’m a software consultant for Pharma companies and have worked on projects that used the same kind of study design as the Pfizer COVID vaccine (Kaplan-Meier). “Raw data” is submitted to the FDA in the CDISC format. This format contains a lot of pretty sensitive medical information, including which diseases a patient has, their medical history, what drugs they take, etc. This is supposed to be anonymized, but if the p…

I think the level of effort we make as a society on medical privacy is backwards. All health information should be public except in extreme circumstances. Right now, it's almost impossible to get datasets on health data. Imagine if 100% of everyone's data was digitized. The amount of health innovation, lives saved, cures found, is likely to be incredibly large. All the costs that go into trying to comply with HIPPA,…

With black box AI, any legislation on data use is impossible to enforce. So limiting access to the data might be the only way.

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

#163

Post by throwawaygh »

nextos wrote: post #147
throwaway09223 wrote: post #129

Earlier quoted context omitted.

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 g…

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 consent.

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

#164

Post by mchusma »

throwawaygh wrote: post #94
rvnx wrote: post #86

Earlier quoted context omitted.

And ? Where is the bad thing to open a dataset of comorbidities and related / suspected effect of vaccines / medications ?

What is your full name and address? Age? Weight? Height? Eye color? Blood pressure? What STDs do you have, if any? How often and how much do you drink? Smoke? Any history of drug use? Mental disorders? What about your family? Where is the bad thing in you posting this information here right now? Actually, that's not even analogous. A better analogy would be you post all this info under a pseudonym -- e.g., "rvnx" or…

I'll just note that I have no problem with all this information being public for health research. I'd take privacy hits all day long in return for better cures, health, and longevity.

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

#165

Post by bsder »

One thing I haven't seen is the "raw data" people being willing to pay for their own government certified consultants to anonymize the data.

I presume this would actually be the solution if the "raw data" people were making good faith requests.

Is there any reason why this wouldn't be viable?

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

#166

Post by dragonwriter »

fsociety999 wrote: post #39
dragonwriter wrote: post #16

Earlier quoted context omitted.

> Also, how can Pfizer claim that their "study" ends in 2023? Because it does. https://beta.clinicaltrials.gov/study/NCT04848584 > Several hundred million people have already received their vaccine, unaware that it's part of a study Because it's not. Use under the EUA and subsequent approval is separate from and in parallel with continuing studies.

> Because it's not That is misleading at best. It absolutely is part of an ongoing clinical trial regardless us if it is authorized for emergency use. How many people who were given the vaccine were told that it is part of an ongoing clinical trial, authorized for emergency use, and the data from the trial won’t be available for years? I suspect a very small percent.

> 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. Which is a very small percentage of the population who has received it.

> authorized for emergency use

100% of those for whom that was true, who aren't the same people.

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

#167

Post by cogman10 »

jjulius wrote: post #137
cogman10 wrote: post #131

Earlier quoted context omitted.

Frankly, putting up my name with my medical history has far less to do with having the two linked and far more to do with "I'd rather not have a future employer have an easy link to my social media information". Oh genetic disorders, you didn't ask about that earlier. My family is a carrier for cystic fibrosis. Is that something that's supposed to be super terrible to share? I'm not the GP, but frankly I think it's a…

>... my name with my medical history... > My family... >... I'm far more worried about that advertising profile than I am about the "what if's" of my medical data... Again - yours . It's great that you're fine with your data being public, but as is evidenced by the way certain posts in this comment chain are being down/upvoted, clearly many other people share the opposite view and would prefer their data remain priva…

Other nations have more open laws about sharing medical data than the US. (I believe Iceland? Greenland? One of those island nations has genetic ancestry data for all citizens).

AFAIK, the world hasn't ended and they aren't living in a dystopia because their medical information is so well documented. On the contrary it has served to stop the spread of genetic disorders and aid in medical research.

Certainly I personally don't have these hangups about privacy. I think it's weird that society has created them. Pre-HIPAA that wasn't the case and it wasn't exactly seen as major breaches of privacy for doctors/nurses to talk relatively openly about diseases their patients had. The sanctimony of medical data is a recent development practically unique to the US.

I'm not advocating that we broadcast to everyone details of every medical checkup. I am, however, saying that we shouldn't have nearly the level of restrictions we have around sharing medical information, particularly between medical institutions doing research.

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

#168

Post by eminence32 »

invokestatic wrote: post #156
nradov wrote: post #141

Earlier quoted context omitted.

What is the specific basis for your belief that patient re-identification is possible? The federal government has provided clear guidance on de-identification which should eliminate that as a serious concern. https://www.hhs.gov/hipaa/for-professionals/privacy/special-...

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"

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

#169

Post by brianmcc »

fabian2k wrote: post #23
brianmcc wrote: post #12

I remember writing the following about the AstraZeneca vaccine in Nov 2020 when concerns were raised with it. Two things can be both be true: - the vaccine is safe and effective - parts of approach in running studies weren't as good as they should have been Seems to perhaps apply here too.

Why not? Any mistake or design flaw in the trials reduces their value, it doesn't completely eliminate it. The mistake in the AZ trial is something I consider extremely embarassing and stupid (assuming the published information about it is correct). It's the kind of mistake nobody that actually works in a lab should make, and I really question the competency of the people involved here. But in the end this meant that…

Yep I agree, that's my point!

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

#170

Post by sjtindell »

mchusma wrote: post #164
throwawaygh wrote: post #94

Earlier quoted context omitted.

What is your full name and address? Age? Weight? Height? Eye color? Blood pressure? What STDs do you have, if any? How often and how much do you drink? Smoke? Any history of drug use? Mental disorders? What about your family? Where is the bad thing in you posting this information here right now? Actually, that's not even analogous. A better analogy would be you post all this info under a pseudonym -- e.g., "rvnx" or…

I'll just note that I have no problem with all this information being public for health research. I'd take privacy hits all day long in return for better cures, health, and longevity.

Just curious, do you have anything particularly embarrassing to share? Easy to say when everyone on Tinder can’t Google your name and get “alcoholic with herpes”. I would also be open to share if there was tangible benefit today because I’m healthy. But in the future who knows.
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