$250 exome scan??

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Gilgamesh
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$250 exome scan??

Postby Gilgamesh » Mon Dec 07, 2015 5:34 am

Hi everyone. I returned to Europe a few days ago and am (re-)setting up house. I'll be more engaged at ApoE.Info within a few days, but, for now, something amazing written by J11 that I noticed during my automatic check of the wiki site for changes is worth empasizing here in the forums, as well:

Full exome sequencing
BGI $250 promotion for 50x. Seems like a great deal!

http://bgi-international.com/exome-sequ ... promotion/
This is an extraordinary deal indeed! Perhaps we could get group discounts? I'd prefer 75X or even 100X coverage -- but we could surely get a volume deal on that, as well.

Hope everyone is well!
G

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Julie G
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Re: $250 exome scan??

Postby Julie G » Mon Dec 07, 2015 10:08 am

Nice to see you arrived safely, G. Can you (or anyone) explain in a sentence or two how using this exome scan could offer tangible benefit our members. Thanks!

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Re: $250 exome scan??

Postby J11 » Mon Dec 07, 2015 10:34 am

First of all, G thank you very much for acknowledging my contribution.
Another feather in my cap I would say.

I am very glad that you suggested the idea of a group buy.
I have sent them an email I have not received a reply yet.
On their email form they asked for a company name, I had to make one up.
Perhaps if I had mentioned Apoe4 Forum they would have been more interested.

I would think that at a $250 price point we could rustle up a whole swarm of customers for them.
At such a price point, there might not be that much profit in it for them, they probably are thinking of this more as a wholesale price.
Yet, I could well imagine that a company like BGI likely has a truly huge sequencing center with a tremendous amount
of invested capital and it is quite possible that most of their machines most of the time are mostly unoccupied.
Further, we all know that it should not be that long before there is another substantial move down in prices.

$250 50x seems like a cry for help!
I think at such a price we can help them.

I would be interested to know whether they would include phasing with the exome scan for a modest extra fee.

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Re: $250 exome scan??

Postby J11 » Mon Dec 07, 2015 4:13 pm

Looks like BGI has just given us all a big early Christmas present!

I just received a reply from my basic inquiry, they want to play ball!
It might be a good idea to actually identify ourselves as from Apoe4 forum.
This is just awesome! This price point could bring exome scanning down to the consumer level.

It could greatly help me in my search for our family's dementia causative variant.

I think if we spread the word around we could generate an absolute ton of business for them.
Funny that their marketing department is now pretty much me!
They were sure quiet about this offer.
We paid about $1000 a year ago for a 65x exome scan.
This one would be a lot cheaper and probably in some technical ways better.

With group buying power, perhaps we could ask about phasing.
A company like BGI is at the forefront of mass sequencing. Not so long ago an American company came up with
a toaster that adds index units unto DNA allowing phasing this could be very helpful.

BGI is also interested in exploring the research landscape.
They might be interested in helping us out if we could articulate a strategy for finding Alzheimer disease variants as in my family.
There would be quite a bit of prestige gained by a company that could actually make some headway in deciphering Alzheimer
familial dementia. At the moment, there is nearly a complete blank in understanding the genetics of this form of dementia.

Would like some confidence building signals from them regarding the legal side of their DNA custodial care.

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Re: $250 exome scan??

Postby Julie G » Mon Dec 07, 2015 4:33 pm

J11, good news. If you try to arrange a group buy, our organization is formally called: Apoe4.Info, Inc. In case you need it, free to send any formal communique to: Admin@apoe4.info.

To rally support from members, please take a few minutes to let us know how this opportunity could benefit us:
Can you (or anyone) explain in a sentence or two how using this exome scan could offer tangible benefit our members. Thanks!

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Re: $250 exome scan??

Postby J11 » Mon Dec 07, 2015 5:08 pm

A wide-scale roll out of exome sequencing would allow for the immediate identification of very narrow regions containing Alzheimer variants.
Knowing the identity of the variant causing familial Alzheimer's could be crucially important.
It is entirely possible that some variants causing Alzheimer's might already have effective forms of treatment.

(For example, one pathway identified as causing AD involves iron metabolism.
There are already treatments that can address iron overload disorders.)

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Re: $250 exome scan??

Postby J11 » Mon Dec 07, 2015 5:22 pm

G, in terms of upping the coverage level, when we did our exome scan a year ago we were able to buy an extra 20x of coverage for $100.
Most of the cost relates to set up. Once the sequencers are rolling the marginal cost is quite .. well marginal.

Considering how much the price has fallen they might now only be asking $50 (or less for) for the extra 20x of coverage.
Believe that would surely be worth it.

It can be so frustrating when you hit onto a variant with low coverage and wished that you had paid another $100 to bump up the coverage even more. Depending on the prices, you could just go nuts and bump coverage up to 100x, if that would now only cost an extra 100 or so.
Our first round of sequencing was starting to get quite pricey near $1000, so at a certain point we just had to pass on anteing up for another round.

One of the outstanding questions that I would like to address with BGI is the idea of empty sequencing. Some parts of our loved one's genome were sequenced an extraordinary number of times (up to 400 times coverage). Those runs essentially had no value. Reading the same variant 400 times offers no marginal value. The reason this happens is on an exon there would typically be a big pile up about 100 base pairs in. The ends and the valleys along long exons could wind up with low or no coverage. I will be very interested to know how BGI could address this issue. In their email reply they mentioned that they use BGI's exome capture kit and Agilent V5 capture. I will be very interested in knowing how these kits could be tweaked in order to fill in the low coverage areas from our original exome scan.

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Re: $250 exome scan??

Postby SusanJ » Mon Dec 07, 2015 5:27 pm

J11, or G, are there any researchers who might benefit from looking across our members if we had the exome scans done? I have to admit this is beyond my skill set, but I'd be willing to provide data (anonymously) if someone else could make sense of it.

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Re: $250 exome scan??

Postby J11 » Mon Dec 07, 2015 5:27 pm

Sure would be great to have some hands in the air on this one.
$250 is an overwhelmingly awesome price.

I posted on the forum not so long ago that if you wanted 2x coverage using Sanger sequencing that this would cost over $100.
For ONE SNP!
An entire exome sequence is 60 MILLION BASE PAIRS!

Anyone want a brochure or something from BGI?
It is pretty obvious that the next generation of sequencing is approaching and they have gotten quite worried.
For customers this is an amazing opportunity, to access a mature technology at a very reasonable price.

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Re: $250 exome scan??

Postby J11 » Mon Dec 07, 2015 5:38 pm

I am sure there would be a whole bunch of researchers that would be interested in this.
I have known for quite some time that we could work out our the genetics of our family's AD, though
I was thinking in terms of many thousands of dollars. I could not justify spending that much money.

BGI's newest price point has greatly changed the landscape.

The thing that needs to be kept in mind is that with widespread sequencing you could get away from needing to exactly identify near relatives who might be within 7 or so generations from you. This is the typical genealogical depth available on Ancestry.com. Before the 17th Century
you really have to wonder how accurate a purely genealogical approach might be. However, with an exome scan, all you might need is somewhat who carries a common variant without needing to know about the exact family relationship.

Susan, as you mentioned, I think there would be quite a few people at BGI that would be quite motivated to help us. BGI is very interested in the scientific implications of their work. If we can package this for them as a community of highly motivated dementia families that are willing to unravel the genetics of their Alzheimer's (for a reasonable price) and are offering them a substantial publication opportunity, then they might be able to offer us a fair amount of guidance.


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