Comment by arjie | Hacker News Reader

Comment by arjie | Hacker News Reader

I used Nebula (seems to be rebranded and more expensive now) for my wife and me, and for my parents and brother, and it was pretty straightforward. I paid for the 'lifetime' plan but they removed it before we did it for anyone else and it was pretty reasonable. I downloaded the FASTQ files and stuck it in an R2 bucket for myself. Nebula cost about $250 and there's a monthly $50 or something plan that's compulsory but you can cancel it right away.

If you're curious about my genome, here are my VCF files https://my.pgp-hms.org/profile/hu81A8CC

If you want to indulge your curiosity some more:

     $ rg "20189511" /Users/george/tmp/genome/nebula_roshan_NG1AW8W7PU.mm2.sortdup.bqsr.hc.vcf
     3499829:chr13 20189511 rs104894396 C T 252.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.54;ClippingRankSum=0.00;DB;DP=25;ExcessHet=3.0103;FS=4.008;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=10.11;ReadPosRankSum=0.666;SOR=0.160 GT:AD:DP:GQ:PL 0/1:15,10:25:99:281,0,436

Put that into an LLM or look it up here https://www.snpedia.com/index.php/Rs104894396 to find out which pathogenic mutation I am heterozygous for.

In practice, when my wife and I did carrier screening we didn't do it with Nebula, but carrier screening also confirmed that we had GJB2-related hearing loss genes in common. The embryos of our prospective children were also sequenced so that we could have a child without the condition.

Anyway, if you'd like a test file of a real human to play with, there's mine (from Nebula) for you to take a look at. If you use an LLM you can have some fun looking at this stuff (you can see I'm a man because there are chrY variants in there).

I also used Dante because I wanted to compare the results of their sequencing and variant calling. Unfortunately, they have a different way to tie the sequence back to the user (you take the code they have and keep it safe, nebula has you put the stuff in a labeled container so it's already mapped by them) and I was in a hurry with other stuff. They never responded to me with any assistance on the subject - not even to refuse the request to get the code for that address - so I have no idea how they work.

The nanopore stuff is very cool, but I heard (on Twitter) there were quality control issues with the devices. I'd love to try it some time later just to line it up with my daughter's genome.

oddly enough I just was looking at someone's data with chr13:20189491 A>G (gnomAD genomes v4 AF=0.00941) - also 0/1 genotype.

I used WGS from Nebula - but would like to back that up with Nanopore raw DNA reads targeted on specific genes where I need more accuracy and to investigate structural differences that Illumina or Nebula's MGI machines can't pick up... also for the additional methylation data.

Something fun, you have a CYP11B1 rs4541 g;a Wouldn't surprise me if don't like Licorice. You also have something I don't see too often The CYP17A1 −34 T>C, rs743572(A;G) which compounds on that.

Depends on the sum of all the genes in this area of course, but this one mutation is a big influence on the hpa-axis. I would ask if you have lower body weight, heightened anxiety, bad acne as a teenager, episodes of dizziness upon standing, salt cravings, and difficulties with sleep this would be the main driver, pretty standard nonclassic CAH. If you had ever thought you might have "pots", the more accurate would be hypoaldosteronism (but depends on renin genes).

Sense we were poking around here is some highlights

Decent chance of being left handed or ambidexterity given that you also have PCSK6 rs11855415 a;t at the same time (as it can help with the salt issues) and I look for when I see something like the above two.

Vitamin D risk given your GG CYP2R1 (dr probably checks that yearly anyway), risk of lower Mg because of this (cramps, muscle twitches?).

bvitamin wise b9, b12 could be on the lower side given MTRR AA rs1802059 (combined with MTHFR 31 GT 76 CT, MET 30 CG, COMT 99 AG, BHMT rs3733890 G;A). Probably like spinach. If you have TMJ regularly you need to find the right diet or bcomplex for you which will fix this as well as any hypermobility resulting from the collagen production issues. Higher chance of myopia, especially if you are gen Z.

TPH2 rs4570625 g;t jumps out on the serotonin path. Vit d can help here, some might say 5-htp when depressed, but fix the vit d first. Do you like sour gummy candy?

CYP1B1, I see 3 reductions, combined (and the above) I would ask if you have glaucoma in your family history, if so then stuff you can do.

CYP1A1 rs1048943 C;T and really CYP1A2 rs762551 A;A, so fast caffeine and melatonin issues. More insomnia.

CYP2E1, need less acetaminophen to do the same as others.

Intentionally not bothering to go into why, but above average intelligence.

Combine all of the above and decent chance you fall into the bucket of being taller (6'1"?), skinnier, hard time falling asleep and also likes sleeping in, higher libido, left handed, high visual skills, geeky. Possibly synesthesia (a weaker form). Would enjoy a strategy board game over trivial pursuit. Earlier hair loss. Higher risk of one form of Alzheimer's (there is stuff you can do today to reduce it). *Do not smoke*. Didn't dive into all of the ADHD genes, but if mild resolving the above Vit D, b vitamin deficiencies would influence that.

This was with 10 minutes of poking around not a comprehensive look. Mostly I just wanted to add a comment to the general reader that genetics variants are part of larger systems. You would want to do a deeper look, combine it with symptoms as well as lab work to determine the full impact of any change. For example the PCSK6 variant reduces the impact of the CYP11B1 variant. Further you could also easily have something else on the hpa-axis that completely negates the NCAH and never have any salt issues at all. Before spending time looking through each gene I would simply ask, hey do you love to put salt on every meal?

Another one I didn't dig into, but would just ask first is if you have a big sweet tooth. (ncah influenced hypoglycemia).

Feel free to give me a ping and I can walk you though this better.

There is a reason these always end with a disclaimer, talk to your doctor about making changes to your diet, etc, I am not a doctor just someone who learned biology/genetics as a hobby especially given how it can teach tricks to apply to software engineering and my ai/AGI work.

> Intentionally not bothering to go into why, but above average intelligence.

Speaking as a geneticist, it's a shame that this is forbidden knowledge

There are papers showing the common variants associated with intelligence. For example myelin sheath variants linked to intelligence as it increases fatty insulation around nerve fibers which speeds up transmission. But ones like that are surface level. This matters, but it isn't the only thing and for me the more interesting is the meta of what these have in common (besides often related to the brain).

The real problem is that most historical papers look for single SNPs. But a gene could have dozens of variants that do the same thing or you could have a genetic path where a major variant in any gene on that path results in the same outcome. These papers overlook this.

So you have to step back and asking: What are the principles of intelligence? and how would I expect to see them in human biological or other biological systems? (And related, why does humans have intelligence "now"?)

For this crowd, if I take an LLM and make it bigger is it intelligent? Obviously a key component of intelligence is raw stuff. Someone with fattier myelin sheath's straight up has more/faster "brain stuff". You might say ChatGPT 4.5 is "smarter" than 3.5, but not intelligent. There are two other key attributes missing. For those following along with the arc-agi you might already have a hint what those are simply based on what is moving the needle forward. Now even with all three and you are close and simply need to provide an environment for self-replicating with a selection pressure and energy constraint. For one definition (others will have a different definition) I have had a primitive AGI for 13 months now and regularly put it to work on sub problems of mine.

This really took off when I was reading genetics files like books and noticed I was reading files that are very similar, but some were Mensa level folks and others were more just "smart". Didn't take too much longer to piece together the key paths and differences and even went tracing back through Neanderthals DNA (How cool is it these days that we can simply poke around Neanderthals DNA!).

So it isn't forbidden, but more like I know what to look for and people are super sensitive around saying someone is probably smarter or not from a genetic file so I usually don't comment because of the Gattaca problem.

P.S. If you have a bio/genetic background and are playing around with AI I would love to chat. There are so very few of us. DeepMind is thinking of some of this, but they are in the UK. (It would be fun to give a meta talk to them explaining why their smartest engineers are smart.)

Oh this is marvelous. I'm going to send you an email at the one in your profile, though I won't be upset if you share here. I suppose there's some Barnum Effect risk with this stuff (and of course singular variants don't immediately mean everything as our GCs have pointed out before), so I'll just answer everything as I can here and maybe you and others will find it interesting.

Licorice - no I don't like it

Lower body weight - until 3 years ago, now 84.5 kg / 183 cm

Anxiety - haha, I suppose that's true

Acne - yes

Dizziness upon standing - yes

Salt cravings - yes

Difficulty with sleep / Insomnia - used to be the case, solved in the last few years, strongest in teenage

Pots/Aldosteronism - not that I know of, just tested and sitting 60 bpm, stand up highest is 77 bpm with a continuous monitor on

Vit D - funny, blood tests which I took for the first time two years ago showed 12 ng / mL (low)

Mg - didn't test, but supplements did not change anything when I tried them in isolation so can't be too bad

Spinach - yes

TMJ - no issue here

Myopia - yes with astigmatism (-4.75 spherical -2.5 cylindrical)

Sour gummy candy - not much of a fan

Caffeine/Melatonin - Yes. Caffeine I always get half-caf. Melatonin I take 200-300 ug when I use it.

Acetaminophen - Can't tell, I suppose

Handedness - Right hand dominant, no ambidextrousness

Geeky - Described as so

Synesthesia - probably not, if weak very weak. I used to think I did, but I think that's because when I learned about it as a kid I really wanted to.

Strategy Board Game - you betcha

Hair Loss - Male Pattern Baldness in teenage years haha!

Alzheimer's - how interesting, I am curious

Smoking - Oops, smoked two years in college. Quit hard.

ADHD - I can't imagine this could be likely, but I suppose I had the excitability, impulsiveness, and talking over people things, but it hasn't really caused any real lasting trouble in my life so I can't label it a disorder really. I have previously received a prescription for this condition as an adult, but I did not take the medication for any appreciable amount of time.

Salt - this is very entertaining to my wife, because yes I do often add salt post-cooking to my portion of the meal and frequently complain about undersalting

Sweet Tooth - Yes (heavily dominating my behaviour), however, blood sugar is normal any time I check it 90 - 100 mg / dL . I could wear a continuous monitor and see what it says.

Now, for the intelligence thing. The various Jonathan-Anomaly-related companies these days are definitely trying to move the Overton window on this front. Herasight is the most well known, but I know of a few that are coming up as well. Of course, I'd like to believe this is true, but I suppose the one massive caveat is that (if you run me through peddy, you'll see) I'm South Asian and I know that South Asians have poor presence in most mainstream genomic datasets - a problem I am hoping to either fix or see fixed in my lifetime.

Your standard disclaimer acknowledged.

The obvious question: why are you so relaxed about revealing your whole DNA to the world?

Follows from a deeper belief system that the expansion of knowledge is valuable and that humanity can learn even through things (even if they harm me) so long as I am public enough about it. https://wiki.roshangeorge.dev/w/Observation_Dharma

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