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Exome sequencing: $250


BrianMDelaney

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This sounds too good to be true: $250 for exome sequencing. Maybe it's only for bulk purchases. Well, if so, we might be able to get enough people interested.

 

To begin with: count me in, unless someone has reason to believe BGI isn't reliable.

 

I'll write to them and ask for details. I might be happier with 75X or 100X coverage, to be honest. I'll ask about prices for that, as well.

 

Interesting take on BGI here at the Singularity Hub,

 

- Brian

 

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Brian,

 

I'm all for citizen science and self-experimentation, but I'm wondering, what is it exactly you hope to learn from spending $250 on exome sequencing, beyond what you get from 23andMe? People are skeptical enough (probably with good reason) about trying to interpret even some of the more well-established genetics correlations available from 23andMe. When I look at my 23andMe data with Promethease, all I get is more confused. How do you plan to use the data from BGI to improve you health / longevity practices?

 

I thought today's Dilbert cartoon was quite apropos!

 

J9qruvu.png

 

:)xyz

 

--Dean

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Brian,

 

I'm all for citizen science and self-experimentation, but I'm wondering, what is it exactly you hope to learn from spending $250 on exome sequencing, beyond what you get from 23andMe?

 

Well, not to be snarky, but the answer is in your question: I hope to learn about relevant genetic variations beyond what I got from 23andMe! There are tons. At least once a week I come across a paper referencing a variation in a SNP that confers tremendous protection, or risk, for a condition I don't want (or, in a few cases, such as the condition of longevity, one I do want) and would like to know whether I have it, but I can't know because the SNP wasn't on the V3 chip. Now, these variations are generally rare, of course, otherwise I already would have paid for a full genome scan. But while $250 isn't nothing, it seems well worth the potential benefit. In addition, I have a lot of fun with my huge file of genetic data. It would be even more fun if the file were bigger. 

 

- Brian

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Thanks Brian,

 

I guess I don't have quite the confidence you have in the validity of studies of the health / longevity impact of individual SNP variations, or the ability to do anything about it even if the information is valid.

 

But I will admit I've taken eye health a lot more seriously (sunglasses, lutein supplements, etc.) since learning I'm likely at increased risk of macular degeneration based on my 23andMe data. 

 

--Dean

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I guess I don't have quite the confidence you have in the validity of studies of the health / longevity impact of individual SNP variations, or the ability to do anything about it even if the information is valid.

 

Well, it depends greatly on what sort of, and how many health problems one has....

 

Imagine the risk of macular degeneration was one of a dozen or more serious risks you thought you had based on family history or your 23andMe results.

 

As to validity, there are single studies in which one can have great confidence, in my view. The rare, protective APP variation found in the Icelandic database is one example.

 

http://www.ncbi.nlm.nih.gov/pubmed/22801501

 

Brian

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Thanks Brian,

 

 

 

As to validity, there are single studies in which one can have great confidence, in my view. The rare, protective APP variation found in the Icelandic database is one example.

http://www.ncbi.nlm....pubmed/22801501

 

Interestingly, the SNP of the Amyloid-beta Precursor Protein (APP) gene discussed in this article (rs63750847) is included in my 23andMe data.  Unfortunately neither my wife nor I have the 'T' allele for this SNP, which appears to dramatically reduce the risk of Alzheimer's disease by decreasing amyloid-beta production in the brains of the 1 in 10,000 people of European descent that carry it. I presume you weren't one of the lucky one's either Brian...

 

--Dean

 

-------------

[1] Nature. 2012 Aug 2;488(7409):96-9. doi: 10.1038/nature11283.

A mutation in APP protects against Alzheimer's disease and age-related cognitive
decline.

Jonsson T(1), Atwal JK, Steinberg S, Snaedal J, Jonsson PV, Bjornsson S,
Stefansson H, Sulem P, Gudbjartsson D, Maloney J, Hoyte K, Gustafson A, Liu Y, Lu
Y, Bhangale T, Graham RR, Huttenlocher J, Bjornsdottir G, Andreassen OA, Jönsson
EG, Palotie A, Behrens TW, Magnusson OT, Kong A, Thorsteinsdottir U, Watts RJ,
Stefansson K.

The prevalence of dementia in the Western world in people over the age of 60 has
been estimated to be greater than 5%, about two-thirds of which are due to
Alzheimer's disease. The age-specific prevalence of Alzheimer's disease nearly
doubles every 5 years after age 65, leading to a prevalence of greater than 25%
in those over the age of 90 (ref. 3). Here, to search for low-frequency variants
in the amyloid-β precursor protein (APP) gene with a significant effect on the
risk of Alzheimer's disease, we studied coding variants in APP in a set of
whole-genome sequence data from 1,795 Icelanders. We found a coding mutation
(A673T) in the APP gene that protects against Alzheimer's disease and cognitive
decline in the elderly without Alzheimer's disease. This substitution is adjacent
to the aspartyl protease β-site in APP, and results in an approximately 40%
reduction in the formation of amyloidogenic peptides in vitro. The strong
protective effect of the A673T substitution against Alzheimer's disease provides
proof of principle for the hypothesis that reducing the β-cleavage of APP may
protect against the disease. Furthermore, as the A673T allele also protects
against cognitive decline in the elderly without Alzheimer's disease, the two may
be mediated through the same or similar mechanisms.

PMID: 22801501

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Dean, no, I'm not one of the rare lucky ones, alas. But imagine I had a great genetic risk for Alzheimer's, and was indeed one of the lucky ones, but didn't know it because rs63750847 wasn't on the chip(s) used by 23andMe. I would want to find out my rs63750847 status! And that's just one of many, many examples. New ones appear in the literature all the time, and the rate at which they're appearing will only increase. For example, wouldn't you love to learn that your APOE-ε3 is actually the rare, protective APOE-ε3b? (Even APOE-ε4b is protective, it appears.) Well, you can't with your 23andMe data. But you could with a full exome scan. Is that alone worth $250? For some people, sure! Others, no. But that's just one of many, many examples.

 

(By the way, the abstract from the link I gave is posted in full in your response. Was that intentional? Or did it "auto-expand" or something?)

 

- Brian

 

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Brian,

 

I too am someone who likes to have more information, although I'm  less interested in finding out about positive health markers (genetic or otherwise) I may carry than I am about negative ones. Why? The former just make me feel good, while the later might spur me to make important dietary / lifestyle changes that could significantly impact my health or longevity, like in the case of macular degeneration mentioned earlier.

 

(By the way, the abstract from the link I gave is posted in full in your response. Was that intentional? Or did it "auto-expand" or something?) 

 

It was (obviously) intentional. I too found the study you referenced quite interesting, and thought others might as well. But your original description of it was rather terse and cryptic ("The rare, protective APP variation found in the Icelandic database is one example."), so I thought it likely that others wouldn't bother to follow your link.

 

So I expanded on your description, and included the text of the abstract, for the benefit of others now, and for people searching the forums in the future for topics like "amyloid beta", "A673T gene" or "alzheimer's disease", none of which you mentioned.

 

--Dean

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I too am someone who likes to have more information, although I'm  less interested in finding out about positive health markers (genetic or otherwise) I may carry than I am about negative ones. Why? The former just make me feel good, while the later might spur me to make important dietary / lifestyle changes that could significantly impact my health or longevity, like in the case of macular degeneration mentioned earlier.

 

Makes sense, though, for me, knowing something positive would mean some changes to my regimen already made could be relaxed or stopped. In any event, there are plenty of rare SNPs with bad implications, to be sure!

 

 

 

(By the way, the abstract from the link I gave is posted in full in your response. Was that intentional? Or did it "auto-expand" or something?)

 

It was (obviously) intentional.

 

Not obvious to me – thus my (entirely sincere) question! I thought you might be using (or unintentionally misusing) some sort of browser plug-in or something that did that; or that it might be a setting here in the forum software (I still don't know what half the buttons I above the compose window do!). And I was reading on my smartphone, whihc didn't reveal the well-composed nature of your post (which I see now on my computer). Sorry for any implied snarkiness.

 
In any event, you're certainly right that I should have said more, and that the use of keywords -- either in one's message, or in the "keyword" field (both will enable searchers to find the post more easily) -- should be encouraged! I'll remember that next time!
 
Best,
Brian
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  • 3 weeks later...

Thanks to Al Pater for the following recent tip about a SNP that might have relevance for people wondering how much CR might help them.

 

 

Asunto: [CR] SIRT1 genetic variants associate with the metabolic response of Caucasians to a controlled lifestyle intervention--the TULIP Study.

Fecha: Sat, 26 Dec 2015 04:27:42 -0800

De: Al Pater

Para: CR@lists.calorierestriction.org

 

SIRT1 genetic variants associate with the metabolic response of Caucasians to a controlled lifestyle intervention--the TULIP Study.

Weyrich P, Machicao F, Reinhardt J, Machann J, Schick F, Tschritter O, Stefan N, Fritsche A, Häring HU.

BMC Med Genet. 2008 Nov 12;9:100. doi: 10.1186/1471-2350-9-100.

PMID: 19014491 Free PMC Article

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2626584/

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2626584/pdf/1471-2350-9-100.pdf

 

 

Conclusion

 

SIRT1 plays a role for the individual lifestyle intervention response, possibly owing to decreased basal energy expenditure and a lower lipid-oxidation rate in rs12413112 X/A allele carriers. SIRT1 genetic variants may, therefore, represent a relevant determinant for the response rate of individuals undergoing caloric restriction and increased physical activity.

 

Small effect, but still, it would be nice to know my status on that SNP. Alas, it’s not included on the V3 chip 23andMe used on me.... (Any V4ers out there who can check their status?)

 

I have this experience a lot: seeing a study about a SNP and not knowing my status for that SNP. Thus (to repeat) my interest in BGI's offer.

 

- Brian

 

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  • 2 weeks later...

 


This sounds too good to be true: $250 for exome sequencing. Maybe it's only for bulk purchases. Well, if so, we might be able to get enough people interested.

 

To begin with: count me in, unless someone has reason to believe BGI isn't reliable.

 

I've been sequenced for BGI Cognitive Genomics (as have several people I've known) and we still haven't gotten results back.

 

From certain people I know who have worked in BGI, it seems that BGI may be struggling in certain ways...

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