5 ms·

I do clinical genomics. Highly recommend you to find a university hospital that can do genomic analysis for you. The IUIS IEI list has ~500 known genes that cou

I do clinical genomics. Highly recommend you to find a university hospital that can do genomic analysis for you. The IUIS IEI list has ~500 known genes that could be causal if you have some variant in one of these genes. The key is a good bioinformatic interpretation and clinical follow up. There are even some good commercial options that might be able to detect a causal variant. These guys can do it after order via healthcare professional https://blueprintgenetics.com/patients/?group=ordering-patients https://blueprintgenetics.com/patients/?group=ordering-patie... or these guys can do it from home; first the genome sequencing and then the immune panel report https://dantelabs.com/products/autoimmunity-panel https://dantelabs.com/products/autoimmunity-panel Likelihood of finding causal variants has doubled in last 5 years. * IUIS page: https://iuis.org/committees/iei/ https://iuis.org/committees/iei/ * latest version of gene list: https://static-content.springer.com/esm/art%3A10.1007%2Fs10875-022-01289-3/MediaObjects/10875_2022_1289_MOESM2_ESM.xlsx https://static-content.springer.com/esm/art%3A10.1007%2Fs108... * from this paper: https://link.springer.com/article/10.1007/s10875-022-01289-3 https://link.springer.com/article/10.1007/s10875-022-01289-3 Great info also in IPOPI website https://ipopi.org/about-ipopi/mission-and-objectives/ https://ipopi.org/about-ipopi/mission-and-objectives/

dangero 4y ago
Thanks so much for this information I'm definitely going to look into this.
- janeway 4y ago
  Sorry, I added some links in an edit just now - in case you missed them originally.
  - dangero 4y ago
    I ordered a Dante Labs kit actually -- that seems like a solution I can afford and at least then I will have my genome on disk for anyone who wants to see it.
    - janeway 4y ago
      Good call IMO. If they still offer the download options, take all files: fastq, bam, vcf. Fastq is the raw data and can be used again as methods improve. Download it twice and check the files are the same. The problem with fastq is that it could get truncated due to interrupted download and you would not really know. They probably offer some basic report with the 200$ genome. You can get interpretation reports added in future. Data from Dante labs is quite good. Good luck!
      - dangero 4y ago
        thanks for the tips, will do!
thewebcount 4y ago
FWIW, I can second this. My spouse is currently in the process of getting this done. Know up front that you'll have to fight insurance about it. They won't want to pay for it because they have no existing framework that says doing genomic testing will in any way help whatever you have. (And they're not wrong. It's entirely possible the genome sequencing won't turn up anything useful.) My spouse's doctor works at a university hospital as parent mentions. The other thing to know is that even once you do get it set up, it generally takes about 6 months before you get the results and the consult with the geneticist. And because there are multiple parties involved, everything moves glacially and nobody knows what anybody else is doing. It's frustrating, but I hope that it helps once it's finally complete. There are probably multiple companies that do this testing. We ended up going with Variantyx[0] because our doctor works with a geneticist who uses them. [0] https://www.variantyx.com https://www.variantyx.com
- PragmaticPulp 4y ago
  > My spouse is currently in the process of getting this done. Know up front that you'll have to fight insurance about it. They won't want to pay for it because they have no existing framework that says doing genomic testing will in any way help whatever you have. (And they're not wrong. It's entirely possible the genome sequencing won't turn up anything useful.) The whole genome sequencing linked above is $200, plus more if you want specific reports run against it (rather than doing it with 3rd party tools). $200 can still be a lot of money depending on the circumstances, but for most of us with tech jobs I'd gladly pay the $200 out of pocket and get it going right away while waiting for the glacial process of getting insurance and appointments coordinated.
FollowingTheDao 4y ago
I wish it was this easy. I am on permanent disability. I have PNP Deficiency which I discovered on my own through two genetic tests. https://rarediseases.info.nih.gov/diseases/4606/purine-nucleoside-phosphorylase-deficiency https://rarediseases.info.nih.gov/diseases/4606/purine-nucle... https://mayoclinic.pure.elsevier.com/en/publications/lupus-associated-functional-polymorphism-in-pnp-causes-cell-cycle https://mayoclinic.pure.elsevier.com/en/publications/lupus-a... https://www.researchgate.net/figure/Purine-nucleoside-phosphorylase-PNP-rs1049564-variant-enzyme-activity-and-mRNA_fig2_319408659 https://www.researchgate.net/figure/Purine-nucleoside-phosph... I suffered for years with a mood disorder which made them think every thingw as all in my head. I have consistently low WBC counts and not one doctor care sto look into it. I have an immune deficiency but all they see is the mood disorder brought on my the same gene polymorphism. https://link.springer.com/article/10.1007/s40263-022-00934-0 https://link.springer.com/article/10.1007/s40263-022-00934-0 https://link.springer.com/article/10.1007/s10875-011-9593-8 https://link.springer.com/article/10.1007/s10875-011-9593-8 Thanks for that link to Dante, I might do it since it has PNP on their list. But I have found that very high dose zinc increases my WBC and I think it is because it helps stimulate PNP https://pubmed.ncbi.nlm.nih.gov/1906845/ https://pubmed.ncbi.nlm.nih.gov/1906845/ https://academic.oup.com/nutritionreviews/article-abstract/42/8/279/1892606?redirectedFrom=fulltext https://academic.oup.com/nutritionreviews/article-abstract/4... But no one gives a sht about freaks like us. If they invested $100k when I was first sick they would have saved the 20 years of money they gave me for diability. It is so idiotic I hate it.
- janeway 4y ago
  Well I spend my life dedicated to “freaks like us”. For every one person who takes years to diagnose, there will be 100 in future that we can instantly treat. (1) it helps people who need it, and (2) it can unlock new mysteries of biology that we may never discover using traditional incremental biology. Best wishes.
  - FollowingTheDao 4y ago
    Why don’t you study me?
  - 4y ago

dangero 4y ago

Thanks so much for this information I'm definitely going to look into this.

janeway 4y ago
Sorry, I added some links in an edit just now - in case you missed them originally.
- dangero 4y ago
  I ordered a Dante Labs kit actually -- that seems like a solution I can afford and at least then I will have my genome on disk for anyone who wants to see it.
  - janeway 4y ago
    Good call IMO. If they still offer the download options, take all files: fastq, bam, vcf. Fastq is the raw data and can be used again as methods improve. Download it twice and check the files are the same. The problem with fastq is that it could get truncated due to interrupted download and you would not really know. They probably offer some basic report with the 200$ genome. You can get interpretation reports added in future. Data from Dante labs is quite good. Good luck!
    - dangero 4y ago
      thanks for the tips, will do!

thewebcount 4y ago

FWIW, I can second this. My spouse is currently in the process of getting this done. Know up front that you'll have to fight insurance about it. They won't want to pay for it because they have no existing framework that says doing genomic testing will in any way help whatever you have. (And they're not wrong. It's entirely possible the genome sequencing won't turn up anything useful.) My spouse's doctor works at a university hospital as parent mentions. The other thing to know is that even once you do get it set up, it generally takes about 6 months before you get the results and the consult with the geneticist. And because there are multiple parties involved, everything moves glacially and nobody knows what anybody else is doing. It's frustrating, but I hope that it helps once it's finally complete. There are probably multiple companies that do this testing. We ended up going with Variantyx[0] because our doctor works with a geneticist who uses them. [0] https://www.variantyx.com https://www.variantyx.com

PragmaticPulp 4y ago
> My spouse is currently in the process of getting this done. Know up front that you'll have to fight insurance about it. They won't want to pay for it because they have no existing framework that says doing genomic testing will in any way help whatever you have. (And they're not wrong. It's entirely possible the genome sequencing won't turn up anything useful.) The whole genome sequencing linked above is $200, plus more if you want specific reports run against it (rather than doing it with 3rd party tools). $200 can still be a lot of money depending on the circumstances, but for most of us with tech jobs I'd gladly pay the $200 out of pocket and get it going right away while waiting for the glacial process of getting insurance and appointments coordinated.

FollowingTheDao 4y ago

I wish it was this easy. I am on permanent disability. I have PNP Deficiency which I discovered on my own through two genetic tests. https://rarediseases.info.nih.gov/diseases/4606/purine-nucleoside-phosphorylase-deficiency https://rarediseases.info.nih.gov/diseases/4606/purine-nucle... https://mayoclinic.pure.elsevier.com/en/publications/lupus-associated-functional-polymorphism-in-pnp-causes-cell-cycle https://mayoclinic.pure.elsevier.com/en/publications/lupus-a... https://www.researchgate.net/figure/Purine-nucleoside-phosphorylase-PNP-rs1049564-variant-enzyme-activity-and-mRNA_fig2_319408659 https://www.researchgate.net/figure/Purine-nucleoside-phosph... I suffered for years with a mood disorder which made them think every thingw as all in my head. I have consistently low WBC counts and not one doctor care sto look into it. I have an immune deficiency but all they see is the mood disorder brought on my the same gene polymorphism. https://link.springer.com/article/10.1007/s40263-022-00934-0 https://link.springer.com/article/10.1007/s40263-022-00934-0 https://link.springer.com/article/10.1007/s10875-011-9593-8 https://link.springer.com/article/10.1007/s10875-011-9593-8 Thanks for that link to Dante, I might do it since it has PNP on their list. But I have found that very high dose zinc increases my WBC and I think it is because it helps stimulate PNP https://pubmed.ncbi.nlm.nih.gov/1906845/ https://pubmed.ncbi.nlm.nih.gov/1906845/ https://academic.oup.com/nutritionreviews/article-abstract/42/8/279/1892606?redirectedFrom=fulltext https://academic.oup.com/nutritionreviews/article-abstract/4... But no one gives a sht about freaks like us. If they invested $100k when I was first sick they would have saved the 20 years of money they gave me for diability. It is so idiotic I hate it.

janeway 4y ago
Well I spend my life dedicated to “freaks like us”. For every one person who takes years to diagnose, there will be 100 in future that we can instantly treat. (1) it helps people who need it, and (2) it can unlock new mysteries of biology that we may never discover using traditional incremental biology. Best wishes.
- FollowingTheDao 4y ago
  Why don’t you study me?
- 4y ago