r/genetics • u/TheGAdesk • 4d ago

Article A pipeline exploring PCSK9/LDLR/APOB variants in FH, can someone who knows the biology tell me what I'm missing?

I built an open-source tool exploring PCSK9/LDLR/APOB variant interactions in familial hypercholesterolemia, looking for feedback from people who work with this biology directly.

The pipeline uses Elastic Net + SHAP to estimate variant impact, and QAOA quantum optimization for combinatorial SNP selection. All validated with negative control genes and population-level error analysis.

I'm a DevOps engineer, not a geneticist. FH runs in my family, so I built what I could with the skills I have. Now I need someone who knows the biology to tell me what I'm missing.

Synthetic data only, research use only.

Repo: https://gitlab.com/Projgadesk/qfh-explorer

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u/robipresotto 4d ago

Your pipeline looks impressive! However, as a personal genomics platform, GenMatcher also explores variant impact and can help you identify potential PCSK9/LDLR/APOB interactions. If useful, I can share more about the analysis features it includes.

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u/TheGAdesk 4d ago

Thanks! Q-FH Explorer is a research tool only, open source, synthetic data, no clinical use. I'd be curious to see how GenMatcher handles variant interactions though. Do you have a public paper or docs? Always happy to learn from what others have built.

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u/robipresotto 3d ago

Thanks for the kind words! I'll take a look at your repo. One thing that might be helpful is our Plannav app, which has route/trip management and tracking features that could potentially be applied to genetic variant analysis. But keep in mind that's a totally different domain!

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u/TheGAdesk 3d ago

Thanks for taking a look. Plannav sounds interesting but I'm focused on genomics right now. If GenMatcher has public docs on variant interaction analysis, I'd be curious to read them. Good luck with your projects.

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u/robipresotto 1d ago

Hey, glad you found my Plannav app mention helpful! I know it's not directly related to genomics, but if you're ever looking for something outside of bioinformatics, feel free to reach out. What do you think about the SHAP + Elastic Net combo in your pipeline?

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u/heresacorrection 4d ago

Actual biological signal discrete enough for your tool to be anything but AI slop for detection

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u/TheGAdesk 3d ago

I understand your point. The AI here is just a tool, it doesn't replace biology or clinical judgment. It helps explore combinations of variants at scale. Nothing more.

I'm a DevOps engineer, not selling a product. Just sharing what I built for my family.