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Nebula Genomics – First to offer consumer anonymous sequencing

nebula.org

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Re: Nebula Genomics – First to offer consumer anonymous sequencing

#41
post #36

I had my genome sequenced by Nebula. Honestly I know I shouldn't have from a privacy standpoint (especially since I signed up with my real name and details) but the idea of having my entire genome stored on my hard drive was too tempting for me, and now that's what I have. I have started looking into the software to analyze it, and I'm happy that it's a purchase that will be valid my entire life.

I was the same way. I have a genetic condition in my family of unknown origin and the risk of anything happening. My genetics outweighed the possibility, and what turned out to be the evidence of what my even partial genome could uncover.

Unfortunately, I was the only one in my family who understood this and the rest were too afraid to get the test done even though people in my family have died of this disease.

A few years ago I tried to get my full genome from nebula but they messed up my order really badly and it took over a year to get my money back. But it looks like they might be cleaning up their act and the $250 price is really tempting.

Since our disorder is polygenic, there’s still a lot of questions I have so I’m probably going to get a nebula run as well.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#42
post #36

I had my genome sequenced by Nebula. Honestly I know I shouldn't have from a privacy standpoint (especially since I signed up with my real name and details) but the idea of having my entire genome stored on my hard drive was too tempting for me, and now that's what I have. I have started looking into the software to analyze it, and I'm happy that it's a purchase that will be valid my entire life.

I did the same thing. Have you found any software to analyze it?

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#44
I find this fascinating. I once was considering getting my whole genome sequenced from Nebula but then I realized that their sequencing was being done by Beijing Genomics Institute (BGI). The quality of sequencing from BGI is very high, but the reality is it has some fairly established ties to the PLA (to the extent that it's considered for sanctions by lawmakers). There's been concern in the bioinformatics community for years that the CCP/PLA, through BGI, has been amassing substantial genomics data on people (most notably pregnant women). Unclear why, but – given the authoritarianism – the mind can go places. That's the thing with running any genomics-oriented organization; at minimum, pretty sordid optics can emerge if you're not careful.

I bring this up because Nebula is clearly making a play for anonymity which, in my mind, is strange. Perhaps deceitful. The thing about genetic data, especially WGS, is that it's hopelessly not anonymous. Sure, it can be protected, but given the world we live in (hacks, data brokers, etc.), it's the type of data that will likely get out into the wild. This past week at 23 and Me is a case in point. The comment from another poster here about whether they delete it or not is an important one. I suspect they don't; for a while Nebula was touting a setup where they held onto your data and you could license it for use by pharmaceutical companies or researchers and receive payment. Not sure if that's still a thing. Either way, I find the notion of "anonymity" here very dubious, even if you pay with Monero or similar, use a PO box, etc. But that's kinda the reality – these genomics companies aren't especially open about a several key facts when you get your genome sequence. Another example is that they don't make clear that when you get your genome sequenced you are effectively unmasking the genome of your extended family.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#45
post #29

If you have a publicly available photo of yourself (e.g. public social media), it's possible to match that to your genomic sequence. I.e. you already have to be anonymous online to have a chance that a private company cannot reidentify you. https://www.science.org/doi/10.1126/sciadv.abg3296

Seems like the technique only works in highly controlled scenarios (e.g. you have tens of phenotypes and images and want to have a better than random chance of assigning one to the other):

> Nevertheless, re-identification risk in the wild does not appear to be especially high. While we observe a success rate as high as 25%, this is only achieved when the genomic dataset is extremely small, on the order of 10 individuals. In contrast, success rate for top 1 matching drops quickly and is negligible for populations of more than 100 individuals. Moreover, it should be kept in mind that this result assumes that we can predict the phenotypes perfectly.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#46
post #18

Why do they build this Rube Goldberg system? Do consumers demand that they can access their data from everywhere so keeping it on some server is necessary? Do they need the data from everyone to do statistics on them? Is it related to selling the analysis software as a subscription? All in comparison to the obvious solution, send in a sample, receive the resulting data. Plus some offline analysis software that you ca…

One of the services they provide is giving you reports on new genetic studies and how it relates to your DNA. Another is online genome browser. Both require access to your genome. If you only want to sequence your DNA you can do that, download your files and delete your account. They promise to delete your genome once you close your account.

Do they promise not to share the information with third parties who won't delete my genome when I close my account?

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#47
Yeah, another round of these "anonymous" services.

It's better than having your name slapped into it, but let's be honest here unless you have all your material and tools inside your home with no Internet connection, all these things are NOT anonymous by definition.

Case in point: 23andMe

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#48
They insist that they have a genome sequencing company but when I attempted to use them it became apparent that any success happens despite their equipment and processes, rather than because of it. Months of waiting led to admonitions that no valid samples could be found, which then precipitated further waiting for test kits to be re-sent and new tests to be run. Although they eventually refunded my fee (after about a year in total of waiting), that only happened despite their customer service. I was left with the impression that they were selling something that sometimes might work but hoping that you'd be willing to hang around for months or years until you win the lottery and their process actually generates genomic data. Avoid.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#50
post #36

I had my genome sequenced by Nebula. Honestly I know I shouldn't have from a privacy standpoint (especially since I signed up with my real name and details) but the idea of having my entire genome stored on my hard drive was too tempting for me, and now that's what I have. I have started looking into the software to analyze it, and I'm happy that it's a purchase that will be valid my entire life.

I did the same thing. Have you found any software to analyze it?

It's all command line tools, one is called samtools and another is called picard, there might be another one I'm forgetting.

The interesting this with the data is that it isn't your raw genome, it's the entire data from all the sequencing runs of 30 or whatever base pairs (I got my scan done at the 30x level which is supposed to mean that on average every base pair is read 30 times). So it's not like you can just read your DNA directly in one string (not sure why I want to do that but I like the idea of a single file containing just all my nucleotides in sequence). The next step for me, when I go back to it, is to get on the forums for those above tools and ask how to do the things I want, there are a LOT of subcommands.

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