Hacker News Reader

Comment by thrtythreeforty | Hacker News Reader

Is there a way I can get this kind of analysis done and retain control of all the data that gets created? I have been interested in learning details about my genotype for a while, but not at the expense of having 23andMe keep a copy for whatever purpose they desire now or in the future.

View on HN

I work in human genetics and largely wonder the same thing. Short of sequencing your own genome, I'm not enthusiastic about most privacy policies.

To add context, I also am involved in public large-scale genetic studies (as a participant who has provided genetic data) such as All Of Us. There, I have no misapprehension that people will be studying my data.

I'm just saying that on the commercial side of things, I haven't found a satisfying consumer-facing way to pay for sequencing as a service (where I'm not trying to sequence at scale) without any strings attached.

Yes, find a local sequencing provider and arrange to do a SNP chip or whole genome sequencing. In the contract ask that they delete your data after delivering it to you. This will be:

1. Expensive - probably at least 2 - 3 thousand dollars.

2. Require you to do your own analysis.

Obviously you can't be 100% sure they will delete your genomic data, but they have no incentive to keep it.

Don’t they have every incentive to keep it?

Such as? I’ve worked in genomics labs, they would be quite happy to delete stuff.

Why to delete anything sellable? I always do all kinds of illegal copies of somebody's PD on all places I ever worked as employee. Typically by stealing some papers from garbage because photographing takes too much time per one 'drop'. With enough wit of choosing workplaces I use to have some incomes from my strategy.

Jesus christ dude don't admit to crimes on a public forum

Any chance you're making a joke/point about someone else?

study it, sell it? Sadly, it seems privacy has gone out of fashion. I am happy to hear the genomics labs you've worked in would be happy to delete it.

There are thousands of sequenced human genomes available to access for research purposes (1000 genomes project, UK biobank etc) so one additional genome adds no marginal value.

They also have an incentive not to be sued for some astronomical figure if (more likely when) the data is found not to have been deleted.

Or find a European genetics laboratory that offers this service.

Even though you may not be European, the lab will need to follow the much stricter data protection policies of the EU and will probably not have a different handling for non EU customers (but ask them).

I write this as someone who has worked at one of those in the EU.

Since you are in the field, would you give some names of such labs in the EU? The quality of results when searching for "European genetics laboratory" aren't great.

> the lab will need to follow the much stricter data protection policies of the EU

But will they still retain it indefinitely on a server somewhere? If yes, it will leak eventually. Or the government will lobby to get access to it to "protect the children".

I think that they have to delete the data per your request to be GDPR compliant since no law requires keeping such date.

Re 2: do you know of tools that don't involve the cloud and allow you to do such analysis? Ideally FLOSS. I could only find DbSNP and SNPedia but they are datasets, not sure if there are tools built on top of that like Promethease.

Re WGS there are a lot of well established tool chains that are FLOSS (eg https://github.com/bcbio/bcbio-nextgen). You could run alignment and variant calling on a beefy workstation. A laptop would potentially work. Easy to test this with publicly available raw data. Another option: The sequencing provider often will run alignment and some default variant calling for you. Annotating and analysing these variants can be done on pretty much any computer, all with open source software. A SNP chip is even easier to deal with as the computational requirements are less.

Interpreting the results is a more manual process. Really depends on what you are interested in.

Talk to your doctor. Genetic tests ordered via your physician may be covered by patient privacy laws in ways that 23andme customers aren’t.

Read the fine print though because you get what you pay for.

you will not get the richness of detail that 23andme provides though, since the results are mostly based off training data from other submissions to 23andme. Which is why it gets better over time; I was shown to be 20% Chinese, but now 4 years later my profile there reads that I'm completely Korean

Knowing your geographical ancestry - which, to me, seems slightly ridiculous, versus knowing some genetic predisposition for disease or problems like the one discussed above with caffeine or, say, ibuprofen, don't seem to be comparable in the slightest.

Their ancestry data is known to be quite dubious. They're really just guessing for the most part.

> I was shown to be 20% Chinese, but now 4 years later my profile there reads that I'm completely Korean

> you will not get the richness of detail that 23andme provides though

That richness you describe almost seems to be fabricated "vanity metrics" rather than anything useful

I think Nebula makes the promise of anonymizing your data and permanently deleting it once the retention period has expired.

https://nebula.org/whole-genome-sequencing-dna-test/

The easiest test I can think of given GPs description is to take your blood pressure, abstain from coffee for a week (?) and then take a new blood pressure. It's not an RCT so it won't be definitive, but it may suggest to you whether further investigation is likely to pay off.

(Unless, of course, other confounders affect blood pressure unrelated to this effect. But for me personally, my blood pressure is usually fairly constant, at least compared to a 20 mmHg drop.

> The easiest test I can think of given GPs description is to take your blood pressure, abstain from coffee for a week (?) and then take a new blood pressure.

That entirely depends on how strong the caffeine dependency of OP is. For someone like me it would be anything but "easy" for first 2-3 days at least due to withdrawal symptoms (headache, poor concentration, tiredness).

Several months ago I saw a study claiming that decaf coffee prevents withdrawal symptoms, even if you know it's decaf. I was getting headaches pre-coffee in the morning, and tried it, and it worked so well I quit caffeinated coffee without any trouble. Just felt a little slow and sleepy the first week.

https://www.sydney.edu.au/news-opinion/news/2023/02/14/decaf...

The article you linked says it _reduced_, not _prevented_ the symptoms in people who knew it was a decaf.

Sorry, I misspoke, and that's my experience. I still had slight symptoms, but they were reduced by at least 90%. I'd found it pretty difficult to quit coffee before, but switching to decaf was effortless.

Related question: I have my genome but I find that the reports on polygenetic scores that you receive from [popular consumer WGS sequencing provider] are lacking accuracy. Is there a platform/ community of personal genetics enthusiast that crowdsources such analysis?

I haven't done a DNA test before, but I assume the identity verification is lax at best.

Would it be practical to just generate a "burner" persona to attach your test to? Yes your data technically will exist, but will be effectively anonymized

If anyone you're closely enough related to also gets sequenced, it will effectively de-anonymise you

Reply on news.ycombinator.com