[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".

[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.