New vs. Old: a Comparison of 23andMe's Health Reports and the Raw Data (enlis.com) 96
"With much fanfare," writes an anonymous reader, "last month 23andMe returned to reporting health information to their genetic service customers. How does their new service stack up?" According to the Enlis Genomics Blog, it's a good move but not perfect. The linked post explains that "the raw data from 23andMe contains significantly more health information than they are reporting in their health reports," and says "23andme has a long way to go to get back to reporting the same number of variants they were before the FDA ban. However – both the previous and new 23andMe reports pale in comparison to an analysis of the raw data. 23andMe’s new reports tell you about less that 1% of the health-related variants that are in their raw data." It's an interesting statistical blow-by-blow; the company making the comparison has a vested interest in you letting them run the numbers, but is not the only option.
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Says the man who's mother didn't take thalidomide [wikipedia.org]. Thank you FDA!
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How do you know? They might be typing with their flippers.
What? It could happen.
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Says the man who's mother didn't take thalidomide [wikipedia.org]. Thank you FDA!
Sometimes the FDA does good things and sometimes the FDA does bad things.
I've gone to a number of talks by experts in molecular genetics (i.e. experts in interpreting individual genome sequences to understand genetic disease) and I was a bit surprised that there's pretty much universal consensus that the FDA got it wrong when they shut down 23andMe's health reporting.
What you have to understand is that the quality of the underlying tests used by 23andMe was the same as what you'd get if you ordered the test
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But it never does anything out of the blue.
Some have p-souls, some have q-souls, but ... (Score:2)
Humans are different because they have souls.
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Well, you could try going to live like the San people. I suspect you're probably not smart enough to do that. Point being, intelligence is a difficult thing to quantify and an IQ test isn't necessarily the best tool to determine such. It's just not a good quantifier. We could also argue the relevance of morality and situational ethics. We could also discuss the impact of poverty on intelligence or, more specifically, how it correlates to test results. I'd also submit that the IQ, as mentioned, is hardly a g
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Every IQ tests proves it to the point where it is a statistical certainty.
Do you really believe skin color, bone shape, muscle mass etc can be determined by genetics but the brain is somehow immune?
The range of IQ scores of blacks and whites overlap. Many blacks are smarter than the average white, and many whites are dumber than the average black.
You cannot take any random black person and know if that single individual's IQ score is lower, average or higher than the mean IQ score for whites.
You especially cannot know, if taking one random black and one random white, which has the higher score. You can know the probabilities for the groups, but you cannot know for any two individuals. I find that most
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And yes, genetics is linked to physical characteristics, but there's been no proven link between race and those characteristics. Short Chinese people is a myth. It's mostly a product of their lower protein diet, and not genetics, but a racist glancing at them who believes in eugenics would try to breed the
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You assume we compare poor impoverished blacks with everyone else.
Take the top 10% of every race and you will see blacks are always at the bottom, along with asians above whites and ashkenazi jews above all.
Would you mind explaining how an IQ test could be made to favor blacks above whites/asians/jews?
I can't see how that would work.
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That's trivially easy but it proves nothing. But would that test be a valid yardstick or predictor of ability & success within groups?
If you wrote the test in French, for example, it would make French people look a lot smarter than Americans. But would it be able to distinguish smart French people from their less intellectually gifted compatriots?
If the answer is no, you aren't testing what you claim to be testing. Some
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That's trivially easy but it proves nothing.
It proves the test is arbitrary, and not a measure of Racial Supremacy, as the OP suggested. You seem to be agreeing with my point, but disagreeing with my manner of presenting it.
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That would be the case, were it true. But it isn't, sadly. It is so much easier to just wave your hands and claim that we are all the same, but we aren't. It might not even be genetic. I suspect that anyone who was born with dark skin would see a similar, if less pronounced effect as the sheep wearing the scary mask: https://www.youtube.com/watch?... [youtube.com]
Human brains al
Re: Blacks are dumber than whites (Score:1)
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I see you, like the vast majority of people, have no idea what that term means. HINT: If you have a central bank, you aren't capitalist. HINT 2: If you have corrupt, thieving government officials, then you aren't anywhere NEAR capitalist. The role of government in a capitalist society is to prevent and punish aggression from within and without. Not to rob the people and enrich those in power.
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What you are saying is that there are no capitalist countries? If that's true in the same way there are no communist countries nor fascist ones. But that says little about anything.
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I've traveled a lot in Africa (Botswana, Uganda, Kenya, Namibia to name a few) and mud constructions are still pretty much the norm for most villages - concrete or modern construction is sometimes utilised, but oftentimes a family simply cannot afford those construction methods - so they resort to mud bricks which have been kiln dried. The only consistent modern material used is corrugated metal for the roof.
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And kiln-fired mud bricks are NOT the components used to make a mud hut. That would be sticks and mud.
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Bricks? That's not what most of us call mud. :P
Claiming that mud huts is some indicator of intelligence (as the clueless fuck above tries to do) is in itself laughable - if anything it is an indication of intelligence. There are less complex huts that can be made but mud is cheap, ecologic, easy to work with and (if used correctly) a near perfect match to the climate. Why build western style houses when they would be much more expensive and much harder to maintain where the weather is extremely wet for long
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If you don't believe that, then you don't believe in racial discrimination. Skin color doesn't directly dictate characteristics. IE an all white or an all black society can and have historically been equally barbarous or ascendant. But mix the two together and something strange happens. The society stratifies according to skin tone. This has happened in many entirely separate cultures (India being a good examples--dark skinned South Indians have r
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Nope, sorry. This is shown in videos of the youngest children. Babies focus more on white dolls than black ones. Facts won't go away just because they are uncomfortable.
Also, just waving your hands around and saying "that isn't so" isn't proof.
"we grew up too poor to afford the *luxury* of being racist. We had more important things to worry about than the color of our friends skin"
You act as if that is some kind
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White skin is bad for you, in that it increases skin cancer. Light colored eyes are bad for you as well, as you more quickly lose your sight in old age. Yet these characteristics have been strongly preserved. There must be a reason for that.
Yes, that's called vitamin D.
UV light do two things to the skin : damage it, which is bad, and give vitamin D, which is good. You can't separate the two.
As a result, people from the north, where there is very little sunlight especially during the winter, have light skin as a way to get as much vitamin D as possible, whereas people from near the tropics where there is plenty of sunlight have dark skin as a natural sunscreen to prevent UV-related skin damage.
The eye color is related to the skin color because
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So, human skin color determines other characteristics?
Human skin certainly determines the susceptibility to certain kinds of cancer. And skin color correlates well with incidence of sickle cell anemia. And skin color correlates well with salt sensitivity (for heart disease, not taste). Skin matters for lots. But it hasn't been shown to correlate for many other things. It seems reasonable to assume it will correlate with some physical characteristics (like gender and height), and mental characteristics. But so far, no conclusive links have been found. An
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So, human skin color determines other characteristics?
Usually not, but it often correlates with other characteristics. For example, white skin tend to correlate with long nose although AFAIK they are completely separate traits. There are other indisputable correlations between skin color and other biological traits. So I don't think it is much of a stretch to assume that there are correlations with higher functions too.
Interracial procreation can blur these differences but we need both a change of mindset and a few generations to get there. Sexual preference s [okcupid.com]
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Everyone submit your DNA! (Score:2)
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Or you're aware of how easily mistakes are made, how flawed the testing is and how the statistics are misunderstood and misrepresented.
I'm far less likely to be prosecuted for a crime I didn't commit if my DNA isn't available to be wrongly matched with that of a criminal.
can't deal with that Elephant in the Room (Score:2)
Predictive testing (Score:3)
According to the data, one can predict the stupidity of a Slashdot comment by whether the poster is an Anonymous Coward. Studies have proven this time and time again.
Data, like hips, don't lie.
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You can call him Pontiff and his last name is Ratzo, he'd not make this up. They can't tell lies on the internet, you know.
Open Source Personal Analysis Tool (Score:3)
Instead of opening your data up to yet another corporation by trusting someone else to analyze your raw data, why not create an open source application that you can download to analyze your raw genetic data? I'm sure the molecular biologists out there would be more than willing to help contribute.
Re: Open Source Personal Analysis Tool (Score:2)
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It would be awesome to have a small finger sticker and analytics device, like used for diabetes blood sugar testing kits, that, maybe, hooked into a USB port and did the work there and was able to spit the data out. Then you could do all sorts of things, up to and including things like removing any easily identified PII and sharing the results with the research communities of your own volition.
They took a bunch of blood when I joined the military. While this was, indeed, many years ago (mid 1980s when I wen
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You do not think such a device would be used by the authorities like in GATTACA?
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Well then I'd be on the lookout for agents with little stabby pens. Just because it can be abused doesn't make me not want it.
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The data is quite simple. At the most basic level it's just a photo of bright spots on a chip, as read by the machine. Knowing that spot A corresponds to variant A and spot B to variant B, an algorithm then decides ("calls"), depending on the relative brightness whether the person has variants AA, AB or BB (or impossible to tell). This is the only real processing and there IS open source software for that (packages for R, most famously CRLMM).
So, the whole point is getting the variant calls, ie what sort of
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At this point, SNP genotyping is pretty much obsolete for health-related uses because you can now get a full genome sequence for about $1,000 from just a few drop of saliva
No way. Two lanes of HiSeq (the most economical method) will net you about 10X coverage (assuming uniform coverage, which you won't get) for about $3000 at academic prices. For SNP calling, 20-30X is usually considered the minimum, with 50-60X being preferred. And then there is still the cost of DNA isolation, library prep, QC to factor in. The $1000 (human) genome is still quite a ways away.
SNP genotyping can still be useful for detecting losses or duplications of large parts of a chromosome ("structural" variations)
Maybe you are just being lazy with your terminology, but SNP genotyping, by definition, does not look for structural
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SNP genotyping can still be useful for detecting losses or duplications of large parts of a chromosome ("structural" variations)
Maybe you are just being lazy with your terminology, but SNP genotyping, by definition, does not look for structural variations. SNP == single nucleotide polymorphism. There are separate arrays to look for these variations, but they are not SNP arrays.
You can certainly use SNP arrays to look at losses, duplications, and copy number changes in general - this is done routinely. Full SNP array data gives you not just variant calls, but also signal intensity etc. for each probe. You can't look directly at other forms of structural variation like translocations and inversions, although it may be possible to pick up focal copy number changes at the breakpoints.
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Macrogen up in Korea has the highest certifications available - better than CLIA in terms of raw data quality - guaranteed to be as good as if Illumina did the sequencing for you itself. And they offer 30X whole genome for $1,000 (an extra $100 to extract the DNA from saliva). They also offer combined whole genome and 100X exome for $1,500.
Right, sure, go ahead and send your sequencing to Korea. What is the cost to have it done by MacrogenUSA, the subsidiary that can actually do FDA-approved work? $1000 doesn't even cover the cost of the materials, so who knows what they are pulling to advertise that.
But 23andMe was pure speech - there weren't offering anything physical - only information.
The issue is, what do people do with that information? If they run out and start seeking a bunch of new age remedies for perceived ailments because they don't understand enough about genetics to know what they are looking at, then it can be a rea
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At this point, SNP genotyping is pretty much obsolete for health-related uses because you can now get a full genome sequence for about $1,000 from just a few drop of saliva - well the raw data, at least - a custom interpretation for a suspected genetic condition might easily run you $20K. SNP genotyping can still be useful for detecting losses or duplications of large parts of a chromosome ("structural" variations) - but mainly because the analysis software is more mature.
I am aware of the difference between the cost of data and the cost of healthcare resulting from said data, but the poster was explicitly asking about the relevance of "open source" raw data so that he could do the interpretation himself. I am also explicitly mentioning arrays, because this is the cheapest technology and the one used by 23andme. Nevertheless, this kind of technology (and yes, the genome too!) has not made a very meaningful impact in clinical practice, with the obvious exception of clinical g
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...why not create an open source application that you can download to analyze your raw genetic data?
Many, if not most of the major analysis tools are already freely available (usually even fully open source).
Let's say your raw data is a full genome sequence reads from an Illumina sequencer (which costs about $1,000 from a few drops of saliva at the going rate). Well, first thing you're going to do is map your raw reads to a reference genome. The most common reference genome in use is freely available from the NCBI ftp site that is provided by the US NIH. And there are plenty of free read mappers available
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23andMe use SNP arrays (custom Illumina BeadChips) rather than NGS at the moment. The 'raw' data they supply isn't really raw at all, but a processed list of several hundred thousand variant calls:
http://www.snpedia.com/index.p... [snpedia.com]
You can convert this into something standard like VCF, which most tools that deal with variants will read.
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The 'raw' data they supply isn't really raw at all, but a processed list of several hundred thousand variant calls:
No, but it is cheap, which is not to be underestimated. If we want affordable healthcare, we have to care about cost and not just the new shiny. The other thing is, focusing on select variants allows them to do a targeted analysis. In a world plagued by systems biology, people like to think a "global picture" is always better, but having some idea what you are looking for before you start collecting data makes your statistical analysis, you know...meaningful.
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That was really just a comment for biology geeks about the kind of data they provide. With a true raw file, you can get more out of SNP array data (e.g. genomic copy number). The 23andMe pricing is pretty keen, though, perhaps only about double what what you'd pay an academic service provider to run a SNP array of similar size (you'd get full raw data, but would have to do the DNA extraction and data interpretation yourself). An exome costs about 10x the price of the cheapest SNP array, and a whole genome m
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And getting back on topic, 23andMe was focused on just that problem: putting together a website that could help ordinary people understand their genomes. And the FDA shut them down
The FDA requires analytical verification ( does the test or service accurately and reproducibly provide the data that you are saying within acceptable margins of error? ) and clinical validation ( can the results of the test or service be reliably associated with specific health outcomes, after accounting for statistical significance and effect sizes? ) for medical devices and services sold in the USA. 23andMe has to go through this process as does every medical services company. This is not a conspiracy. T
Slashvertising (Score:5, Informative)
Clearly nobody read the link, because it's one big fat ad for a third-party genome-analysis tool and nobody's complained yet. Come on, people, keep up!
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I thought about trying their service but for $199 I'll pass.
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I thought about trying their service but for $199 I'll pass.
I thought about trying their service but for the ultimate invasion of privacy [scientificamerican.com] and an open door to future violations of human rights, I'll pass. I really want to know what they have to tell me but I certainly am not willing to find out under these terms. Now, when I can do it anonymously...
medical information is regulated (Score:2)
Ok, this is very simple, and something all the developers here need to know.
If you're reporting medical information in the US, you need all of the processes you use to generate that health information to go through the FDA before you ADVERTISE you can do it (yes, your website is an advertisement). Fitness is fine any time, go crazy with that. Medical information, only after FDA approval. If you think you may be doing something health related, go find a regulatory consultant and find out what you need to