r/promethease

Just about ready to actually explode in frustration. I have been on Promethease since 2017 and now nothing works anymore! The site won’t let me generate a report that I can open from the report page, it emailed me some rubbish that doesn’t help instead, well what it’s emailed me is a html file (in a zip) which is impossible to open with any browser (from iPhone).

I have never used anything but a phone to access Promethease. I don’t have anything but a phone.

I am completely boiling in frustration at this point and I can’t take it anymore. It was already a hard enough site and now it’s actually impossible.

There’s a pinned post on this board about something on GitHub. I don’t know how to use GitHub, why would I? I have not the slightest interest whatsoever in learning to code and I have no means of assessing what’s safe to use, because I know nothing about it and I never have needed to and never will need to. I did at least try to open the link at the end of the page, and not a single flaming thing made sense. I don’t want to have to teach myself a fucking undergrad in fucking tech! I am a bio type not a fucking maths type!

Literally can’t cope. At this point MyHeritage can count themselves lucky I am too sick to be calling in a bomb threat, because they would deserve it.

This information is about me, it belongs to me, it’s my body, and its life or death serious…. And this is what they do to it?

Arghhhhhhhhhhhh

Allelix is Promethease-like tool that doesn't require uploading your genome to a third party or paying per report.

It takes your raw data file from 23andMe, AncestryDNA, FTDNA, LivingDNA, or MyHeritage and generates a report annotating your variants against ClinVar, PharmGKB (pharmacogenomics), GWAS Catalog, and SNPedia. Similar to what Promethease does, but:

• Free. AGPL open source, no cost, no account.
• Offline. Your genotype file never leaves your computer. The tool downloads public databases (ClinVar, PharmGKB, etc.) once, caches them locally, and runs everything on your machine.
• CLI-based. Three commands from zero to report:

Reports come out as HTML (like the screenshot), JSON, or directly in the terminal.

• Allelix auto-detects everything. Format (23andMe vs AncestryDNA vs ...), genome build (GRCh37 vs GRCh38) - it's all handled automatically.

It's not a 1:1 Promethease clone - the report format is different and it doesn't have Promethease's custom wiki content. What it does have is direct annotation against the primary source databases with full attribution, so you can see exactly where each classification comes from and verify it yourself. If you run allelix db update before analysis, you'll always have the latest information.

Pharmacogenomics mode (allelix pharmacogenomics your_file.txt) gives you a focused drug-gene interaction report from PharmGKB + CPIC data.

Methylation mode (allelix methylation your_file.txt) gives you a focused report on methylation pathway genes - MTHFR, MTR, MTRR, COMT, CBS, and related variants.

Extract (allelix extract your_file.txt --snps rs1801133,rs4680) prints the raw diploid genotype for specific rsIDs - useful for spot-checking a ClinVar or PharmGKB hit against what the array actually called.

GitHub: https://github.com/dial481/allelix

Allelix v1.2.0 Sample Report

I used this is 2019 to analyze my genome. Do you have newer updates to the infomation you can provide?

Hey everyone.

Just a question, does anyone know if there’s anything about ancestry that’s worse than other tests? Is it worth getting retested at another provider if I used them? I realize now I should’ve used 23andme.

Hey everyone,

My psych nurse recently recommended that I look into pharmacogenetic (PGx) testing because I have a brutal history with medication side effects (and as a natural redhead, I apparently have some gene variations that make me process certain drugs weirdly anyway).

My nurse mentioned commercial panels like GeneSight or Genomind, and while my insurance covers a chunk of it, I’m trying to see if I can save some money or do the data deep-dive myself.

I already have raw DNA data from 23andMe. Can I just upload that raw data to Promethease to get accurate pharmacogenetic info regarding psychiatric medications (like how I metabolize antidepressants/anti-anxiety meds)?

Specifically wondering:

1. Does Promethease actually flag the specific liver enzyme variants (like CYP2D6, CYP2C19, etc.) that dictate psychiatric drug metabolism?
2. Is the formatting readable enough to figure out dosing/side-effect risks, or is it a massive headache to cross-reference compared to a dedicated clinical report?
3. If you’ve used Promethease for this exact reason, was it actually helpful or did you end up just needing a clinical test anyway?

Appreciate any insight! Thanks in advance!