111–120 of 161 posts
Earlier quoted context omitted.
> But I do want to sequence it using a third-party Don't forget to change your DNA when the third party's database will eventually leak. (see the 21andMe's data leak: https://en.wikipedia.org/wiki/23andMe_data_leak )
what is the attack vector btw?
> "I have a VCF, I can run it through tools like VEP, ClinVar, gnomAD, PharmGKB (highly recommend), Gene Inspector, or Claude"
I am assuming my data is now within the hands of some of the very entities I do not want to have access to my data ... true?
I want to sequence, but I absolutely do not want any company or government or church to have access to my data. When the author says: > "I have a VCF, I can run it through tools like VEP, ClinVar, gnomAD, PharmGKB (highly recommend), Gene Inspector, or Claude" I am assuming my data is now within the hands of some of the very entities I do not want to have access to my data ... true?
Claude on the other hand - yeah you are giving your data away. But that step really isn't necessary.
By running a standard pipeline you could get a VCF (File containing the Variants in your genome) and each variant would be annotated. You can check all the annotated genes and figure out if these variants are pathogenic, likely pathogenic, likely not pathogenic or benign.
I don't want to sequence at home. But I do want to sequence it using a third-party that gives me all the raw data. I live in Europe and I'm just a simple consumer. Does anyone know how I can do this? What service would I use / you can recommend? Them not keeping it on their side would be a huge bonus of course but not sure I can ask for that much.
If a service doesn't give you the raw data for some reason you should be able to get it with a GDPR subject access request.
FTDNA gives you a vcf file, which contains the variant calls, but not the raw reads which those calls are made from (as in the BAM file). They do keep that data, because they charge extra for a BAM file download. It's almost certainly against the GDPR. Worse, I think they do it for anticompetitive reasons - they own the largest Y-DNA tree, and don't want you uploading your raw data to competing trees (in particular YFull).
> This is intended to be read by AI- please just copy and paste the URL of this and have ChatGPT walk you through it. If you have AR glasses, even better, since the AI can walk you through the whole protocol. What kind of magic is going on here, am I missing something?
Hi, author here- I intended it to be hands-free so you can upload to ChatGPT/Claude and talk to it. I found it easier to follow the protocol each time by talking to AI rather than having to read from the computer every time I had to check something, reducing context-switching You can still read it, though it is pretty dense
I would have done better in uni if the lab manuals were written like this
Earlier quoted context omitted.
what is the attack vector btw?
Finding yourself in a genetically-determined out group, and being treated differently / discriminated against because of it.
I think this whole fear is over blown anyway. I am in a genetic out group (schizoaffective disorder and yes my risk is genetic) and the benefits of getting my genetics run twice out weighed any risk that might have befallen me.
Has anyone succeeded in doing any of this? I always assumed if it were this simple, someone would be selling DNA kits on Amazon for a few thousand dollars.
Has anyone succeeded in doing any of this? I always assumed if it were this simple, someone would be selling DNA kits on Amazon for a few thousand dollars.
As a useful genome? Marginal. ONT will need a couple runs to get complete human genome coverage and the substitution error rate is still high compared to short reads. For a fraction of the price and effort you can get your DNA resequenced at 10 times the quality.
I guess if you are super-ultra paranoid you can do it all yourself at home, but honestly. You're not that special, and if someone really actually wanted your genome that bad they'd just take it from a used coffee cup.