You use the VCF and a java project called the Exomiser, and it will give you output files with all the pathogenic variants marked
In my case and is the case with a lot of rare diseases you could have unique pathology and mutations in a certain gene but that don't show up as pathogenic in clin var. For example my family has a lot of autoimmune diseases and as expected my HLA genes are totally trashed. However none of these mutations have ever been seen and flagged before especially was WGS is so new.
If you only have a list of genes and the genomizer will give you a list of the genes that are the most heaviy affected, you can put them into this app to get some further data and idea about what kind of tissue expression or rare disease spectrums you may be dealing with: https://maayanlab.cloud/Enrichr/
you can make informed decisions on it like for example I have a defect in my thiamine transport gene, so now I follow a b1 megadose protocol. A lot of people do that with the basic 23and me methylation reports but this is more in depth. So in my family maybe this looks like parkinsonanism, autism, diabetes, muscle disease, metaboloic syndrome, but we're understanding these diseases to be more like mitochondrial diseases that are more systemic. The answers you get are often really just too cutting edge for GPs or even specialists to deal with and you have better luck just researching, biohacking or talking to a natropath. Genetics doesn't really have that place in general practice yet unless it's something like a very very clear pathogenic marker which honestly isn't the case in a lot of cases, or alternatively you end up having a "pathogenic" marker that we had no idea even exists in people who aren't gravely disabled. For example I don't have lissencephaly regardless of what my pathogeniticty says. instead in that case you look at the gene, and see the big picture which that it's linked to neurodevelopmental disorders, and I have autism so that could be a factor there. But autism != lissencephaly. WGS is so new
sadly the reality is though you can have all that and it almost puts you at a disadvatnage with doctors because you look crazy and sus claiming you have some HLA mutation or whatever. Who told you that? Oh well I data mined it...uh huh sure....honestly to get it back into the medical system and to be taken seriously you'd probably have to get a doctor to retest it, for example I can can spin this up to get my HLA alleles from my fastq https://github.com/nf-core/hlatyping
But no doctor is going to put that in my medical record until I convince them to run a blood test for the same damn thing.
if anyone wants to help me with my own genetic search woes and help me out or know solutions please let me know. if you want to help me publish or add to that guide somewhere let me know - i asked nebula if they wanted to print it on the blog and they said the'd be interested but I just never cleaned it up
> honestly to get it back into the medical system and to be taken seriously you'd probably have to get a doctor to retest it
The thing is, if you sequence your genome, you might have used a protocol that has a label on it: “Not for diagnostic purposes, research only“. A doctor shouldn’t take anything that’s not IVD-certified seriously(and for good reasons).
https://www.reddit.com/r/Nebulagenomics/comments/nhjfpa/how_...
You use the VCF and a java project called the Exomiser, and it will give you output files with all the pathogenic variants marked
In my case and is the case with a lot of rare diseases you could have unique pathology and mutations in a certain gene but that don't show up as pathogenic in clin var. For example my family has a lot of autoimmune diseases and as expected my HLA genes are totally trashed. However none of these mutations have ever been seen and flagged before especially was WGS is so new.
If you only have a list of genes and the genomizer will give you a list of the genes that are the most heaviy affected, you can put them into this app to get some further data and idea about what kind of tissue expression or rare disease spectrums you may be dealing with: https://maayanlab.cloud/Enrichr/
you can make informed decisions on it like for example I have a defect in my thiamine transport gene, so now I follow a b1 megadose protocol. A lot of people do that with the basic 23and me methylation reports but this is more in depth. So in my family maybe this looks like parkinsonanism, autism, diabetes, muscle disease, metaboloic syndrome, but we're understanding these diseases to be more like mitochondrial diseases that are more systemic. The answers you get are often really just too cutting edge for GPs or even specialists to deal with and you have better luck just researching, biohacking or talking to a natropath. Genetics doesn't really have that place in general practice yet unless it's something like a very very clear pathogenic marker which honestly isn't the case in a lot of cases, or alternatively you end up having a "pathogenic" marker that we had no idea even exists in people who aren't gravely disabled. For example I don't have lissencephaly regardless of what my pathogeniticty says. instead in that case you look at the gene, and see the big picture which that it's linked to neurodevelopmental disorders, and I have autism so that could be a factor there. But autism != lissencephaly. WGS is so new
sadly the reality is though you can have all that and it almost puts you at a disadvatnage with doctors because you look crazy and sus claiming you have some HLA mutation or whatever. Who told you that? Oh well I data mined it...uh huh sure....honestly to get it back into the medical system and to be taken seriously you'd probably have to get a doctor to retest it, for example I can can spin this up to get my HLA alleles from my fastq https://github.com/nf-core/hlatyping
But no doctor is going to put that in my medical record until I convince them to run a blood test for the same damn thing.
if anyone wants to help me with my own genetic search woes and help me out or know solutions please let me know. if you want to help me publish or add to that guide somewhere let me know - i asked nebula if they wanted to print it on the blog and they said the'd be interested but I just never cleaned it up