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Old 2016-12-18, 22:29   #1
jasong
 
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Set some spit to 23andme, and I'm 99% honky, and 1% "brother"(black).


Closest relative I have on 23andme is probably a second cousin, which is likely because of their last name, Shipp. I'm pretty sure Shipp is fairly close on my family tree, so not surprising that I might have a second-cousin that's last-named Shipp. Although, if she's married and changed her name that would make it a weird coincidence.
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Old 2016-12-18, 23:51   #2
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Originally Posted by jasong View Post
Set some spit to 23andme, and I'm 99% honky, and 1% "brother"(black).
I bet you are more than 1% Neanderthal…

Did you do this for the ancestry data or the medical third party readers? Promethease was the best company I could find. Recently LiveWello announced a deal with a medical grade, full sequencing company. I think the costs for full sequence at over 99.99% accuracy was ~$500 USD or so. You can't rely on 23andme to make any medical decisions as the reliability/repeatability is far too low.
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Old 2016-12-19, 00:41   #3
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Quote:
Originally Posted by flagrantflowers View Post
I bet you are more than 1% Neanderthal…

Did you do this for the ancestry data or the medical third party readers? Promethease was the best company I could find. Recently LiveWello announced a deal with a medical grade, full sequencing company. I think the costs for full sequence at over 99.99% accuracy was ~$500 USD or so.
That would be for coding regions ('whole exome sequencing') only. The $19.99 test is even less powerful (just a few million common SNPs using a hybridization array).
When they list the 99.99% value, it is usually a misleading specificity measure, not sensitivity (in genomic variation the TN value is >> {TP, FP, FN} ). An average person has ~5 million variants over the genome, but only ~25 thousand of them are in coding regions (with the baseline of 20 million true negatives over coding regions, and as much as 2.5 billion over the whole sequenceable genome).
WGS even at high volume is still a few times higher than the $1k future goal. Even at reagent cost, it is currently ~$2.5k.
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You can't rely on 23andme to make any medical decisions as the reliability/repeatability is far too low.
They are an entertainment value company.
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Old 2016-12-19, 03:13   #4
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… it is usually a misleading specificity measure, not sensitivity….

WGS [Whole Genome Sequencing] even at high volume is still a few times higher than the $1k future goal. Even at reagent cost, it is currently ~$2.5k.

They are an entertainment value company.
This is extraordinarily good information and a succinct breakdown of where the field is and what you get for what. I wonder if companies that purport to be more accurate should also be viewed as for 'entertainment value'? Hypochondriasis is a powerful ailment, and placing 'hope' in services like these -- making 'medical' decisions -- seems like dangerous ground…

Here is the company that was advertised: https://genos.co/
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Old 2016-12-19, 03:25   #5
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I am working exactly in the field. (In the Children's Hospital, the Genomics Institute. We are sequencing WGS for critically ill newborns primarily, and other children too.)

If one is healthy, they should not waste their money sequencing themselves. Not just yet.
There are many serious questions one should ask themselves prior to sequencing. (in popular culture, one reflection is in House M.D, the side character "Thirteen"'s story)
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Old 2016-12-19, 23:40   #6
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Quote:
Originally Posted by flagrantflowers View Post
I bet you are more than 1% Neanderthal…

Did you do this for the ancestry data or the medical third party readers? Promethease was the best company I could find. Recently LiveWello announced a deal with a medical grade, full sequencing company. I think the costs for full sequence at over 99.99% accuracy was ~$500 USD or so. You can't rely on 23andme to make any medical decisions as the reliability/repeatability is far too low.
Slightly off-topic question:When was it discovered that African and Australian natives(blacks) tend to not have a lot of Neaderthal DNA in them? I seem to remember that being a thing I liked to gloat over back in the early 90s when I had to face down racist high-schoolers trying to convince me not to hang with "niggers." (the quotes are because I only use the word when I talk about racism...or in anger, because I have major faults)

That's one of the funniest things about racism, the fact that if you believe in the Theory of Evolution, one might argue that blacks are superior to whites, but kept down socio-economically by society.
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Old 2016-12-20, 01:15   #7
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If one is healthy, they should not waste their money sequencing themselves. Not just yet.
Do you have an idea of when "yet" would be? Ten years?
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Old 2016-12-20, 23:27   #8
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Do you have an idea of when "yet" would be? Ten years?
My guess is that even once you have done it once it would be worthwhile doing it again in a few years or at least rechecking for diseases. When you start doing it and how frequently is up for discussion. We don't know the function of the majority of genes still.
Once full genome mapping becomes cheap enough that it is regularly used in fairly large trials our knowledge about how genetics relate to diseases will increase massively. I believe is around $1000 currently. I don't know how much cheaper it needs to get but the price has been decreasing at a very quick rate over the last few years. As recently as 2007 the price was at $1m. It is possible that the price will hit points where it stagnates for a few years but I imagine it is fairly likely we will see $100 genomes within 5 years.
https://en.wikipedia.org/wiki/$1,000_genome
https://www.genome.gov/sequencingcostsdata/
It was interesting learning about this sort of thing on my Med Stats MSc.

Last fiddled with by henryzz on 2016-12-20 at 23:29
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Old 2016-12-21, 00:06   #9
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Good post.

There are a couple considerations: 1. not only the test will become cheaper, it will also become more precise (Similar to the Asimov's question: "shall we fly to Alpha Centauri tomorrow and reach there in 50,000 years, or wait for 25 years and reach there in 25,025 years - and with less discomfort?"). 2. The associations from an allele that you might have to a disease, or even more importantly, to 'which of the three lines of treatment will be more successful for this individual' is almost non-existent (or at least very specific, as in "one case out of hundreds") right now - but will steadily grow. 3. If you do the test now and then will actually need it only 10 years from now (for a specific condition that you may or not develop), you may be told then, 10 years later, that those old tests are incompatble with current state of analysis/diagnosis - and you will have to repeat it anyway.

So, it's best to do it then. 5 or 10 years from now.

Quote:
Originally Posted by House-pedia
"Thirteen" has a 50/50 chance of having inherited Huntington's disease from her mother, but she initially refuses to be tested for it as not knowing allows her to live with hope.
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Old 2016-12-21, 10:40   #10
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Well, having as a file 3 Gbytes of letters for $2.5K does not help you live better, so it is like having an expensive art piece/portrait. Of course if there is one misspell telling you positive/negative for disease, it is interesting (if you are ready to know that).
On the other hand at least WES is a stable information. No matter what will be available 10 years from now, one's exome will always have the same As, Ts, Cs and Gs. They will never change right? There is a huge question if some of the bases are potentially modified, which might be possible to probe in just couple of years, but it will still be C for example.
It is important to know which copy of a gene comes from mom or dad and that is far from being reported in WES.
The question about Alpha Centauri is for the humanity, the question on one's own genome is personal. What if you are 75? Should you wait 20 years?
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Old 2016-12-21, 14:06   #11
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Quote:
Originally Posted by Batalov View Post
Good post.

There are a couple considerations: 1. not only the test will become cheaper, it will also become more precise (Similar to the Asimov's question: "shall we fly to Alpha Centauri tomorrow and reach there in 50,000 years, or wait for 25 years and reach there in 25,025 years - and with less discomfort?"). 2. The associations from an allele that you might have to a disease, or even more importantly, to 'which of the three lines of treatment will be more successful for this individual' is almost non-existent (or at least very specific, as in "one case out of hundreds") right now - but will steadily grow. 3. If you do the test now and then will actually need it only 10 years from now (for a specific condition that you may or not develop), you may be told then, 10 years later, that those old tests are incompatble with current state of analysis/diagnosis - and you will have to repeat it anyway.

So, it's best to do it then. 5 or 10 years from now.
Also very good points. I would personally put a lot of weight on family history over any lack of confirmed genes currently as to whether you are likely to get something. Genetic research is in its infancy. Part of the issue is that multiple testing is such an issue due to the number of genes. It is inevitable that we are missing a lot due to this. Even with this though false results will slip through the cracks. I have heard numbers like only 80% of Med Stats results published are confirmed by another study. That figure varies a lot between fields. Psychology studies were particularly bad(~30% from memory)
Genetic research does routinely adjust for multiple testing which may mean that the false positive rate is better than other fields. I am willing to be that the false negative rate is higher though.
https://en.wikipedia.org/wiki/Multip...risons_problem
There are many unsolved problems in this sort of research. There is much improvement in methods needed. I also have a lot more to learn in order to understand the issues better.
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