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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

#141

Post by nradov »

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…

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-...

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

#142

Post by NicoJuicy »

throwawaygh wrote: post #116
jjulius wrote: post #110

Earlier quoted context omitted.

>So tell me, what harm have I done to myself by sharing this information? You're comfortable sharing it, that's cool! Is your neighbor? Your friend? Your cousin? Should they be obligated to divulge their own medical information just because you're fine divulging yours?

More to the point, he didn't even share it. The concern here is re-identification and he chickened out of sharing his identity.

No, he gave the path to reidentify him

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

#143

Post by pessimizer »

hazza_n_dazza wrote: post #56
YXNjaGVyZWdlbgo wrote: post #10

Earlier quoted context omitted.

I can only recommend this article about bmj: https://respectfulinsolence.com/2021/11/15/wtf-happened-to-t...

I cannot recommend that article. Science exists in a realm of science, just because a major medical organisation is misunderstood dosen't make them 'antivaxxers'. BMJ is asking for open data, something I think many people here could utilise and find value in.

> Science exists in a realm of science,

What does this mean? That article is very specific, and is not sensational. He's been complaining about the BMJ for some time, and not just about these vaccines.

edit: open data is fine and good. The BMJ demanding it here is intentional sensationalism and part of a continuing pattern.

Incidentally, emember that antivax wasn't even a thing until The Lancet unleashed it on the world. Journals are often badly behaved in order to make headlines.

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

#144

Post by shrubble »

YXNjaGVyZWdlbgo wrote: post #10
diroussel wrote: post #3

The BMJ seems to be on good form. First publishing the whistle blower account of pfizer [1], and now this call for raw vaccine trial data. I commend them on this approach, and can only hope that the vaccines are as safe and effective as we have been told. [1] https://www.bmj.com/content/375/bmj.n2635 - "Covid-19: Researcher blows the whistle on data integrity issues in Pfizer’s vaccine trial"

I can only recommend this article about bmj: https://respectfulinsolence.com/2021/11/15/wtf-happened-to-t...

I find the author's take to be lacking in understanding of how contracting companies are hired and managed.

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

#145

Post by jeromegv »

drcross wrote: post #45
ceejayoz wrote: post #20

Earlier quoted context omitted.

Quoted post unavailable.

The chairman of Thompson Reuters, who professionally fact check information for Facebook, is on the board of Pfizer which is a grave conflict of interest and there's been repeated examples of them lying outright so all bets are off on who you may suggest is being misleading.

So you think that all studies AND hospitalization data that show the benefit of the vaccines now that billions of people are vaccinated are... FALSE... across hundreds of countries... because the chairman of ONE news organization is on the board of Pfizer?

I appreciate how antivax people love to share this fact like this is the ULTIMATE argument as to why the vaccine is actually BAD.

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

#146

Post by throwawaygh »

nradov wrote: post #141
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…

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-...

Notice that this is a policy document outlining a process, and that one outcome of following that process can be not sharing the data! It's not as simple as "follow these rules and you can share the data". It can also be "follow these rules, which tell you not to share the data".

It's also possible to reach an outcome that the data can be shared but must be de-identified in a way that precludes important statistical tests. Any sparse feature is incredibly powerful for re-id, and combined with other features might be difficult to share without running afoul of de-id best practice. The problem: rare medical conditions that must be accounted for in a statistical study of vaccine side-effects are examples of sparse features. So you can share the dataset, but not in a way that's useful for a non-GIGO statistical study.

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

#147

Post by nextos »

throwaway09223 wrote: post #129
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…

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, 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.

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

#148

Post by bshipp »

rvnx wrote: post #136
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…

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 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.

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

#149

Post by rvnx »

throwawaygh wrote: post #146
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-...

Notice that this is a policy document outlining a process, and that one outcome of following that process can be not sharing the data ! It's not as simple as "follow these rules and you can share the data". It can also be "follow these rules, which tell you not to share the data". It's also possible to reach an outcome that the data can be shared but must be de-identified in a way that precludes important statistical…

The thing is; in practice, how can you re-id someone that has a very rare medical condition if you don't already know that the person has this very rare medical condition ?

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

#150

Post by jjulius »

NicoJuicy wrote: post #142
throwawaygh wrote: post #116

Earlier quoted context omitted.

More to the point, he didn't even share it. The concern here is re-identification and he chickened out of sharing his identity.

No, he gave the path to reidentify him

Right, which - perhaps to your point - demonstrates how a seemingly innocuous piece of data left in a dataset could be used to, with relative ease, identify that individual.
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