[Gatsky]

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.

[MrDresden]

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.

[hawk_]

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.

[caskstrength]

> 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".

[Kbelicius]

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

[est31]

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.

[Gatsky]

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.

[Gud]

Don’t they have every incentive to keep it?

[brigandish]

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.

[Gatsky]

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

[Gud]

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.

[Gatsky]

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.

[eimrine]

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.

[DANmode]

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

[snapcaster]

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