4 ms·

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 t

by arjie 1y ago

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 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 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.

dash2 1y ago
The obvious question: why are you so relaxed about revealing your whole DNA to the world?
- arjie 1y ago
  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 https://wiki.roshangeorge.dev/w/Observation_Dharma
r0ze-at-hn 1y ago
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.
zorgster 1y ago
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.

by arjie 1y ago

dash2 1y ago

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

arjie 1y ago
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 https://wiki.roshangeorge.dev/w/Observation_Dharma

r0ze-at-hn 1y ago

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.

zorgster 1y ago

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.