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Nebula Genomics – First to offer consumer anonymous sequencing

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Re: Nebula Genomics – First to offer consumer anonymous sequencing

#61

Post by kevinmchugh »

pointlessone wrote: post #20
danbruc wrote: 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.

It's interesting to imagine how this would've worked in 1995 or something, if the sequencing was possible. You'd have done the sample, and in response they'd send you three CD-ROMs. The first is the visualizer program which you'd install as an executable. The other discs are your genome*. If your spouse or kid got their genome sequenced, you'd get two more discs.

Every year the company would print an update to the disease database on more CDs, and make them available for a relatively small price, probably exclusively by mail.

Obviously there's some aspects of this that suck, but it's interesting to see how it's so much better for privacy, because data hoarding wasn't viable at scale or as a business.

* Two, because a genome is > 700MB, so it won't fit on a single disc. How annoying the size limit of a CD would've been if you had to solve this problem at work!

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#62

Post by renewiltord »

IMHO this stuff is not necessary. My DNA and that of my wife will be public. The rest of my family will volunteer theirs soon. And I am looking to expand the amount of public DNA from my ethnic group.

Given sufficient time, this information will be useful for the progress of science.

In some sense, this is part of a genetic adaptive mechanism. With a sufficiently tight-band public genetic release with full health history, it is possible that future science will bias to my genes.

Perhaps some of mine will be ones people desire and others not. But they will optimize to the ones that are studied. That means my genes will live on slightly preferentially.

Which, of course, means that I should encourage everyone else to keep theirs private.

Amusing thought. But I think we will all be for the better with our genomes public. It's okay if others won't submit theirs. We will submit ours and may humanity benefit from it.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#63

Post by anonymouskimmer »

romainsimon wrote: post #42
etdr wrote: 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?

IGV is very nice for viewing sequence data. I've never loaded anything into it that wasn't already prepared to be loaded into it, but this is probably fairly easy to do. It's really nice for viewing three-frame translation to look at the proteins encoded by DNA, but for eukaryotes you have to pay attention to mRNA splicing even if you know the boundaries of the protein coding sequences.

https://igv.org/doc/desktop/#UserGuide/reference_genome/

Edit: Since you use Nebula's service, have you emailed them to ask what they recommend for genome viewing and analysis?

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#64

Post by dyeje »

abecedarius wrote: post #58
vatys wrote: post #4

When I signed up for 23andme many years ago, it was via a friend in another country, who re-mailed it for me under a fake name and paid in cash. For some time I would log in through a locale-specific 23andme sub-domain until they eventually merged it all together. It wasn't long before they figured out who I was and placed me within my family tree. My fake name now lives among near and distant relatives I was not awa…

Consider a service which promised to scan your genome, send you the data file, and delete the sample, and their copy of the file on confirmation of your receipt. This is still vulnerable to dishonesty, but only transiently. There's nothing logically impossible about such a service, and I'd trust it modulo actual red flags. Too bad afaik nobody's offering it. Once they're archiving their copy I just don't see how they…

I thought about offering a product like this but the market seems tough given:

1. Most people don’t care about the privacy aspect

2. People who already got a test from 23andme, Ancestry, etc are unaddressable

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#65

Post by hifreq »

kevinmchugh wrote: post #40
vatys wrote: post #4

When I signed up for 23andme many years ago, it was via a friend in another country, who re-mailed it for me under a fake name and paid in cash. For some time I would log in through a locale-specific 23andme sub-domain until they eventually merged it all together. It wasn't long before they figured out who I was and placed me within my family tree. My fake name now lives among near and distant relatives I was not awa…

> While I truly appreciate the concept of bringing privacy and anonymity to this field, it's worth considering we are all quite easy to identify using these samples. Yes, as long as they have the data. If a company would process the sample, send me a thumb drive of my information, and not retain a copy, that data can't leak because it doesn't exist.

> not retain a copy

Unfortunately this is just one step away from a blog post where the CEO apologizes for letting down their customers by keeping copies of all data in an unsecured s3 bucket that was downloaded in its entirety by a 13 year old "hacker".

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#66

Post by hifreq »

vatys wrote: post #23
autoexec wrote: post #9

Earlier quoted context omitted.

> I just wanted to make it sufficiently difficult for when 23andme inevitably sold out, got gobbled up, or turned evil. You might as well add "hacked" to that list given recent events.

Yes, I definitely considered that as well. Basically, I knew that 23andme data would eventually exist outside 23andme, whether that be via hack, acquisition, or eminent domain. I accepted that and did it anyway, taking steps to at least not be directly associated with my sequence, even if my association can be inferred or derived later. My main concern is that their testing would identify something which in the futur…

There used to be a way to request full data deletion on their website. Probably too late to do it now for people who are included in the hack, but could still be a good idea to do it asap.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#67

Post by anonymouskimmer »

jsenn wrote: post #60

I wonder if there’s a way to physically encrypt the DNA before sending it off for sequencing—e.g. randomly permute the base pairs, send jumbled DNA to sequencing company, get digital results back, then decrypt them. Of course generating the physical “private key” and then turning it into something usable to decrypt the results would have to be much simpler/cheaper than the sequencing itself, otherwise you’re back at…

I think the major issues with this approach are:

1) You aren't sending them naked DNA which can be modified in a test tube, you're sending them epithelial cells that they extract the DNA from.

2) Any changes you make would mostly not be complete, and they're generating your reference genome from a consensus (to account for sequencing errors and DNA damage). This increases the odds that any randomization you do is basically swamped by the consensus algorithm. If the changes are not swamped then your decryption depends on knowing exactly which changes are from your encryption algorithm, and exactly which are from their consensus algorithm.

3) Bisulfite conversion, methyltransferases, general deamination, and the like make known changes to your genome that can easily be fully accounted for during analysis. There's no easily done "random" cryptographic technology that you can do on your DNA. And even if there was, it probably wouldn't be doable without already knowing your specific sequence.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#68

Post by celdon25 »

DevX101 wrote: post #39

Just looked at the team and it's founded by George Church, professor at Harvard/MIT. There's certainly been some great research to come from his labs, but this guy is on the board of almost every biotech company to emerge from the Boston area. His wikipedia says he cofounded 50 biotech companies, lol. There's a few of these 'rockstar' professors that collect companies like infinity stones from all the students to pas…

I’m pretty sure he has been involved. A friend of mine started a company where Church was an advisor, said he was a huge help. The same friend also was the one who recommended Nebula to me, and I was happy with the service.

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#69

Post by Dig1t »

This is amazing. I will actually pay for this.

Also cool to note that this service sequences your entire genome and lets you download the raw data. Which is not something 23 and Me offers.

You can open the data in an open source genome browser and read the raw information that encodes you. Which I just think is the coolest

Re: Nebula Genomics – First to offer consumer anonymous sequencing

#70

Post by [deleted] »

hifreq wrote: post #65
kevinmchugh wrote: post #40

Earlier quoted context omitted.

> While I truly appreciate the concept of bringing privacy and anonymity to this field, it's worth considering we are all quite easy to identify using these samples. Yes, as long as they have the data. If a company would process the sample, send me a thumb drive of my information, and not retain a copy, that data can't leak because it doesn't exist.

> not retain a copy Unfortunately this is just one step away from a blog post where the CEO apologizes for letting down their customers by keeping copies of all data in an unsecured s3 bucket that was downloaded in its entirety by a 13 year old "hacker".

[deleted]
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