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Comment by aantix | Hacker News Reader

To determine whether you're a slow or fast caffeine metabolizer..

Wait for a sale at Nebula.org. Get your whole genome sequenced. ~$200. Having your whole genome sequenced could have added benefits down the road.

Download the .BAM file. It will be several gigabytes.

Use WSG Extract to generate the 23andMe raw data files.

https://www.geneticlifehacks.com/convert-whole-genome-file/

Connect that data file to Genetic Life Hacks. Take a look at the article on CYP1A2. This will show you whether you're a slow metabolizer or not.

https://www.geneticlifehacks.com/liver-detox-genes-cyp1a2/

The linked data file at GLF never uploads to the server. All analysis is local, client side.

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Thank you for this, I've wanted to do genetic testing for years but don't want it to be stored on anyone's server. Can you explain how it's not stored on any server? Like, you're downloading the .BAM file from Nebula; doesn't that mean they hold onto the data?

Anyone who does the actual sequencing has the data. I think they mean the final service that does the analysis runs locally in the browser. You still need to trust whoever does the sequencing.

I think the point is to prevent the data from being linked to your identify (name, address etc.).

Your identity can be reconstructed from relative's samples. If you submit your sequence its out of your hands forever. The only way to do this privately is to do the sequencing in your own lab.

I sequence my own genome in my own private lab. At least weekly. The rush when the sequencing begins. I almost can't help but sequence all over the place.

Nebula.org does the data sequencing.

They support anonymous sequencing.

https://nebula.org/anonymous-seq/

Genetic Life Hacks provides the analysis on a number of health and disease related topics. Their analysis is simply allele matching for any given topic (string comparisons). It's all done within the browser.

https://www.geneticlifehacks.com/faqs-about-genetics/#:~:tex...

> They support anonymous sequencing.

> https://nebula.org/anonymous-seq/

The button to purchase says "coming soon" for me.

Same for me (in the US).

...and now it's gone

23andme has a "report" about this called Caffeine Consumption. The markers they use are rs4410790 and rs2472297, whereas geneticlifehacks.com talks about rs762551. I'm not sure what to make of that, since that second 23andme one is "near" cyp1a2.

https://you.23andme.com/reports/wellness2.caffeine_consumpti...

This article seems to tie them together nicely: https://www.gbhealthwatch.com/Trait-Caffeine-Consumption.php

You can also search for the CYP1A2 gene using Nebula's gene analysis: https://portal.nebula.org/reporting/gene-analysis

Look at the variants to see if you have rs762551--that means you're a rapid metabolizer.

When I think about sequencing, I think about verifiability. With anonymity blinkers on, you could give me several gigabytes of random data and I'd have limited recourse.

Will Nebula give me an intelligible whole-genome data file if I happen to be a Golden Retriever?

Totally understand.

Luckily I had previously completed 23andMe, so I could cross reference that data with that generated by Nebula/WSG Extract.

My caffeine metabolism did match up.

You could check it against things that you know about yourself.

I know from my clinical history that I have mutations in the UGT1A1 gene that cause me to metabolize bilirubin differently. That is a relatively common mutation that occurs in roughly 2-3 percent of people. Unless I am lucky enough to have a random result that coincides with this, I could be fairly certain that this data is somewhat reliable. The problem thought, I don't know the degree of reliability.

nebula genomics uses chinese labs - would be careful about your data

Why?

Is the "Ultra Deep" analysis worth it over the standard "Deep" analysis?

When you are interested in heath issues, probably yes. For hobbyist the standard coverage will be enough.

I'm curious if there is a basic set of tests you can do with drinking locally to know one way or the other, as well?

Measure your blood pressure.

Measure before consumption. Take three different readings.

Measure at one hour intervals after caffeine consumption.

Fast metabolizers BP should return to baseline within a couple of hours.

Mine would remain elevated for 10-12 hours.

Did you measure your baseline blood pressure without caffeine as well?

Yes.

How many hours/days/weeks should you be caffeine free for the baseline BP?

A couple of days.

I usually have to go through a withdrawal headache first.

I'm assuming elevated is purely relative to your baseline?

Oddly, I don't think my blood pressure changes much at all. Will try this test again, though.

> Wait for a sale at Nebula.org. Get your whole genome sequenced. ~$200

Does anyone track these sales and send notifications? How exactly would someone wait for a sale?

nebula.org privacy policy.

https://nebula.org/blog/privacy-policy/

Do you have other alternatives which are more privacy preserving? The last time I heard about 23andMe was here in HN [1].

[1] https://hn.algolia.com/?dateRange=pastWeek&page=0&prefix=fal...

this is wonderful.

can i ask how you went about arriving at this workflow?

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