2
$\begingroup$

I have some basic programming knowledge, and I would like to take a look at my genome and search for specific sequences related to mental illness and addiction.

The test costs only 1000$ in Spain and I can pay it, but I don't earn a lot of money and I would only pay for it if I could process it on my local computer with 32GB RAM.

Is human DNA too much big to process at a local computer?

$\endgroup$
7
  • 3
    $\begingroup$ What do you want to process? A sequence file is basically a text file which is not very big. You can download the reference genomes easily from the various repositories on the web. $\endgroup$
    – Chris
    Commented Aug 30, 2023 at 7:31
  • $\begingroup$ Thx. I want to have the file and write universities to ask for some genes I am curious to know if I have. Possible so? $\endgroup$
    – user76750
    Commented Aug 30, 2023 at 7:44
  • 2
    $\begingroup$ It all depends on what sort of analyses you want to do and what sort of information you get from the sequencing. There are a lot of open-source programs for genome alignment (often the first step in analysis) that will work perfectly well with 32 GB RAM, it might take a day or two to run the program. I suggest that you look into the analyses you want to do and then come back to this question. $\endgroup$
    – bob1
    Commented Aug 30, 2023 at 8:17
  • $\begingroup$ I'd say probably yes, but as others point out it all depends on the data you have and the analysis you want. From what I understand, most commercial tests don't provide raw sequence data, but a list of thousands of locations that are most variable in the genome, and which variants you have at those locations. This should be a lot less memory intensive. $\endgroup$ Commented Aug 30, 2023 at 15:57
  • 1
    $\begingroup$ Did you look at all the human genomes and genomics code on GitHub, search it for you own specific tasks: google.com/search?q=human+genome+project+github $\endgroup$ Commented Aug 31, 2023 at 11:00

1 Answer 1

4
$\begingroup$

I don't know what you mean by "process". Aligning to the human genome might be a strain on your computer, since it has to hold the whole index in memory, but I don't think you'll have to do that. If you get your genome as a fasta, that's just plain text. A vcf file with just the variants is even smaller.

Just don't expect to get much. The truth is, scientists don't know enough to be able to look at a genome and go "oh, that's your problem!", except for a small number of really detrimental things. You probably are not going to be able to find some "gene allele for addiction". You are almost certainly not going to find anything clinically actionable.

$\endgroup$
6
  • $\begingroup$ As a scientist, I am genetist anyhow. DNA has 4.5 billion years while human brain has 1my. I have been reading that trash psychiatrist write.I think they are lost.I think in the next decades there will be a bit of ligth in menthal health coming from DNA.I am diagnosed of schizoaffective wich is just a kind of schizophrenia. I have read delusional disorder genes (the disorder I think I have) are of the same family of schizophrenia ones. I want just to take a look at this... $\endgroup$
    – user76750
    Commented Aug 31, 2023 at 2:24
  • $\begingroup$ By the way I could see if I have for example Alzheimer genes. If this is possible and cost less than 1000$ I don't know why lots of people are not planing to do the same as me. For example for Alzheimer prevention is esential. They are doing blood test to try identify it soon. $\endgroup$
    – user76750
    Commented Aug 31, 2023 at 2:39
  • 2
    $\begingroup$ How about this. Before you spent the money, write up exactly what outputs you expect the sequencing group to give you, exactly what your plan is for "processing" it, and what actionable information you think is reasonable to expect from that processing. $\endgroup$
    – swbarnes2
    Commented Aug 31, 2023 at 5:14
  • $\begingroup$ @swabarnes Ok, I migth post more questions if I start the analysys, but most of them are for neurosciences site. $\endgroup$
    – user76750
    Commented Aug 31, 2023 at 5:15
  • 2
    $\begingroup$ For instance, before I mentioned vcf files, did you know what they are? Do you know what's in them, and what you can learn from them, and where to get the information required to interpret them? $\endgroup$
    – swbarnes2
    Commented Aug 31, 2023 at 5:16

You must log in to answer this question.