Private Cheap Genome Sequencing

[Mary Ward]

Hi Folks,

I want to sequence my genome, but I want to keep the information confidential. I am interested in learning about some gene markers associated with health and genealogy.

I would like to do this without making the bizzilion primers to do this on a hacker scale, but I am not opposed if there is a primer library for me to reference.

Recommendations?

THANK YOU :)

-Mary, mar...@gmail.com

[Abizar Lakdawalla]

send it out to get sequenced, a whole genome costs about us$1500 to 3000. a whole exome (protein coding part of the genome) costs about $500 ish. you get a list of variants plus the raw data.

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[Skyler Gordon]

Getting the genome sequenced is most likely going to be the easy portion of this process. If you want to process all that data that is going to come back, which is generally in the form of 150-450 base pair segments that are then overlapped based on sequence continuity, you are either going to need to contact a company that will both sequence and process the data for you (which will be more expensive), or find a way to search for what you are looking for yourself. 

The hard part about this, is that the raw sequences will most likely be sent to you in a bunch of packets of roughly 50,000 sequences that you'll have to search through to find what you want. To process a single one of these would be simple, but to process all of them at once would require a computer program that utilizes a distributed framework (i.e. Hadoop), unless you happen to have a super computer or server system just laying around. 

To summarize - getting lots of sequence is not difficult, but finding something in it (your needle in the needle stack) is more difficult and requires some programming knowledge (it's a bit more complex than Crtl+F).

I hope this helps. 

-Skyler 

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[Jason Bobe]

Hi Mary - 

For commercially available clinical WGS, check out Veritas:

https://www.veritasgenetics.com/

The most privacy-assured genomes will probably come from having your own sequencer, e.g. minion. Not aware of DIYers tackling this yet. Certainly possible, hopefully more soon. If privacy is main concern, of course analysis would then need to be local too, of course. Raising a few hurdles. There was y-combinator start-up that tried to create a local storage device for secure, local processing of genomes for the privacy minded, not sure if around anymore. Stanford interpretome was a browser based tool that used your genome locally. 

more options available of course w/o bullet proof privacy, e.g. see

https://www.openhumans.org/activity/genevieve-genome-report/

Jason

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[Abizar Lakdawalla]

The data you get back is already analyzed. Illumina provides you an iPad preloaded with your data and a user friendly genome browser. You will need a doctors note to get this done. https://www.understandyourgenome.com/

Other providers will provide you with a minimum of a file called a VCF file that shows the changes in the genome compared to a reference file. This can be opened by many viewers including text parsers.

Example shown below

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[John Griessen]

On 07/08/2017 03:46 PM, Abizar Lakdawalla wrote:
> You will need a doctors note to get this done.

If it's like that, will they really drop their copy of the data in the memory hole?
Enquiring minds wanting to know and all...

[James Clement]

Just curious why you require privacy? I've had my whole genome sequenced three times. I was on the Board of Knome and had it done for the first time back in 2009. I'm a public member of Harvard's Public Genome Project and OpenHumans, which I think are great ways to share your data with medical researchers. I've publicly "outed" myself and have as part of my various public profiles the following:

I am Personal Genome Project participant #145, and my PGP ID is hu82E689. If you're interested, you can download my genome, SNPs, etc. data at https://my.pgp-hms.org/profile/hu82E689. Additional public data is available about me here: https://www.openhumans.org/member/JWCLEMENT/ If you discover anything interesting using this data, please let me know.

Most recently (December, 2016), I had my whole genome sequenced by Veritas Genetics for $1,000. They''re using the new Illumina HiSeq 10x, which is producing very good data. Expect about 6 months from the day you provide a sample (I prefer blood to saliva, since you don't have to deal with computationally discovering and deleting the bacterial DNA that would be in the saliva).

If you're just looking for genealogical and health data, for $199 you can have 23andMe sequence just a small portion of your genome and then download that data and run it on Promeathease.com. 23andMe has a good ancestry section to their online reports.

Good luck,
James

[Cathal Garvey]

Privacy is the right to disclose. If you have no option to *not* disclose, then you don't have that right anymore.

You choose to disclose, so you are exercising that right: good for you, that's your choice.

But, I would not choose to disclose my DNA to the world. Not only for me, but for the many others who share parts of my DNA. Bioethics is hard!

This is why private-by-default is the only way to guarantee our rights. And the EU GDPR will, I hope, make big strides toward that end in European personal genetics.

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