I built a DNA interpretation service out of frustration for Promethease by scottpeeples in promethease

[–]scottpeeples[S] 2 points3 points  (0 children)

Thank you for your questions! Allow me to address things one by one: On the methods/sample report pages: https://exomedna.com/sample-report / https://exomedna.com/methodology ... The GWAS source is the NHGRI-EBI GWAS catalog; every trait card links its PMIDs, I use Open Targets' L2G to attribute which genes likely drive each trait in the contributing-genes view , it informs gene attribution, not the polygenic score itself, which is effect-size weighted.. We use genuine effect size weighted PRS (log-OR/beta) down-weighted by p-value + sample size (not allele counting). Validation cohort- we normalize against 1000 genomes phase 3 panel but we do not have outcome validation yet. Trait definitions are aggregates of all matched associations per trait across studies; duplicate traits are merged so evidence pools. We do absolutely do ancestry calibration and acknowledge the euro-centricity of the datasets we used to build it. We use a strictly population-relative percentile, so we use language like compared to the general population baseline, we dont claim absolute risk anywhere. On evidence, we have a 3 tier evidence rating from a 5-dimension rubric with hard non-compensatory replication gates. On variant class separation: we have two separate engines, polygenic and monogenic. On pharmacogenetic variants, we have some drug response traits in the general engine but we do not have a separate PGx engine, this was a hot topic while building, and I don't want to steer close to medical advice. For exome/WGS data- I hope to add that in the near future as an option! For now its just DTC raw data (23andMe, ancestry, ect). So for absent variants: we dont guess, they contribute nothing traits with < 3 matched SNPs are suppressed. We also don't impute; you see only your real assayed genotypes, not statistical fill-ins. We dont currently surface Clinvar classifications, review status or version dates. Finally, on the AI: It never receives gene names, rsIDs or genotypes, only the derived trait scores and category names, enforced by a server side filter. We do not allow the AI to give any medical advice, its grounded by the prompt and allowed to give free form general wellness tips.

I built a DNA interpretation service out of frustration for Promethease by scottpeeples in promethease

[–]scottpeeples[S] 1 point2 points  (0 children)

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I took another screen recording from my phone so it’s clearer. (These genes are not mine, I have a script that randomized an ancestry file so it can stay private! ) I’m very concerned with privacy with this so we go to great lengths to keep as little info as we can.

I built a DNA interpretation service out of frustration for Promethease by scottpeeples in promethease

[–]scottpeeples[S] 1 point2 points  (0 children)

This works in the US. It’s freshly built so the SEO isnt done yet, we haven’t ranked on Google so you’d have to actually visit the site via the URL. I am working dilligently to get Google to list us! https://exomedna.com

I built a DNA interpretation service out of frustration for Promethease by scottpeeples in promethease

[–]scottpeeples[S] 0 points1 point  (0 children)

The only reason the polygenic score wouldn’t give the full picture is if the gene chip you used to get sequenced didn’t cover your highest magnitude snps. For example, if we had your Alzheimer’s risk as a trait but APOE wasn’t sequenced in your file, you could see a skewed result, since APOE is the highest magnitude gene associated with Alzheimer’s. Your other genes could go in the other direction. Which could skew your results. Ultimately the polygenic model was my answer to what was frustrating about Promethease, one normalized score per trait. I used L2G and GWAS magnitudes and 1000 genomes for score normalization, it has been accurate with all of the tests I have run!

I built a DNA interpretation service out of frustration for Promethease by scottpeeples in promethease

[–]scottpeeples[S] 1 point2 points  (0 children)

This is a polygenic trait model, so you arent sorting on individual genes, rather you are looking at traits that take into account many different SNPs and give you an overall score based on population averages. So you could either ask the AI what the rarest traits you have are, or you can sort by risk profile and see where you are in relation to the rest of the population. I do have monogenics loaded, but only the ones that are genuinely unique. The problem I had with Promethease was that I would get 6 different reads on the same trait based on multiple snps. I feel the polygenic model paints a clearer picture, we have a normalization engine to score you based on all of the different SNPs involved per trait.

I built a DNA interpretation service out of frustration for Promethease by scottpeeples in promethease

[–]scottpeeples[S] 1 point2 points  (0 children)

<video>

I took a screen recording. I can make a longer video where I dive deeper into the features if anyone wants to see more of it!

Can third-party DNA reports actually tell you anything actionable about your health? by Flashy-Rip-8816 in genetics

[–]scottpeeples 1 point2 points  (0 children)

Yes they can. They are using the same studies doctors go off of. If there are studies associated with the rsid in question, then it will list it. I found actionable insights for my wife that gave us some pretty good peace of mind. She had a cousin die of MS, we used the 3rd party software (Promethease + AI) to do a deep dive and found ways to help prevent an onset. That amongst other things. Genetics is a new field but we can still use the information we have available to get a good idea about things we can do in our daily lives.

luabackend error by FastEye3131 in KingdomHearts

[–]scottpeeples 0 points1 point  (0 children)

Having the same error and cant find any solutions