Get genotyped for free ( If your IQ is high enough)
post by David Althaus (wallowinmaya)
I've just watched this talk about Genetics and Intelligence by Steve Hsu1, a theoretical physicist and Scientific Advisor to the Cognitive Genomics Lab of BGI (formerly the Beijing Genomics Institute), probably the leading genomics research center in the world.
Apparently, the main reason he gave this talk was to recruit volunteers for a study from the Cognitive Genomics Lab with the goal of investigating the genetics of human cognition.
From their homepage:
We currently seek participants with high cognitive ability. You can qualify for the study if you have obtained a high SAT/ACT/GRE score, or have performed well in academic competitions such as the Math, Physics, or Informatics Olympiads, the William Lowell Putnam Mathematical Competition, TopCoder, etc.
Automatic qualifying criteria include:
- An SAT score of at least 760V/800M post-recentering or 700V/780M pre-recentering; ACT score of 35-36; or GRE score of at least 700V/800Q.
- A PhD from a top US program in physics, math, EE, or theoretical computer science.
- Honorable mention or better in the Putnam competition.
If you qualify as a participant, we may send you a DNA saliva kit. After you return this kit, we will genotype your DNA, and the data will eventually be available to you on this website, in a format compatible with many 3rd party interpretational tools.
I guess there are quite a few Lesswrongers smart enough to qualify for this study. If you want to advance Science and get genotyped for free check out their website for further information.
1: Steve Hsu has an awesome blog called "Information Processing". He writes about the genetics of intelligence, economics, psychometry, career advice for geeks, physics, etc.
Comments sorted by top scores.
comment by gaffa ·
2011-10-02T22:09:20.428Z · LW(p) · GW(p)
Actually, they will not sequence your genome - they will genotype you. It's actually quite a difference and I would recommend changing the title of this post. So what they do is use a so called "SNP chip" to test your genotype at a large number (hundreds of thousands) of positions known to be polymorphic in the human population (http://en.wikipedia.org/wiki/SNP_genotyping). This is the same technology currently used by personal genomics companies such as 23andMe, and it's not particularly expensive.
Sequencing a genome is done by totally different technologies, and can potentially determine your entire genome sequence (whereas in the genotyping case you are restricted to the particular loci that were included on the chip). It it also still considerably more expensive.
Replies from: jkaufman, wallowinmaya
↑ comment by jefftk (jkaufman) ·
2013-02-23T21:46:39.019Z · LW(p) · GW(p)
I signed up for this back in March 2012, sent in my spit in September, and according to an email I got today they're actually sequencing my full genome. So it turns out the original title was correct (at least in my case).
↑ comment by David Althaus (wallowinmaya) ·
2011-10-03T17:10:55.435Z · LW(p) · GW(p)
Thanks for correcting my error.
How should I name the title? What about "SNP genotyping for free! ( If your IQ is in the 99,9th percentile) "
( The problem is that some people, like me, may not know the term. Which makes for bad marketing :-) )
Replies from: gaffa
↑ comment by gaffa ·
2011-10-03T18:23:06.585Z · LW(p) · GW(p)
I think "Get genotyped for free" would work, I don't know how many people will not fully understand what is meant but it'd be hard to come up with something else without getting non-snappy.
Replies from: wallowinmaya
comment by gwern ·
2012-01-28T18:50:51.367Z · LW(p) · GW(p)
Continuing; general media coverage:
- Newsweek: http://www.thedailybeast.com/newsweek/2011/04/24/high-quality-dna.print.html (mentions company funding but not how much the high-IQ sequencing will cost)
- http://www.susanohanian.org/show_research.php?id=381 South China Morning Post (found in LexisNexis, this is an open web copy)
"That could change soon. As mentioned earlier, for example, the BGI in China plans a study to look specifically for intelligence genes. And according to Nick Martin of the Queensland Institute of Medical Research, in Australia, dozens of GWAS investigations of behavioural and cognitive links are now under way. So as not to be caught with the dark-matter problem that has bedevilled the study of genetic disease, plans are afoot to consolidate these studies into “meta-analyses” big enough to detect otherwise-hidden effects. If all goes well, the old arguments about the role of nature and nurture in human development may soon be seen in a new light."
Couldn't help but be bemused by http://www.cnn.com/2009/WORLD/asiapcf/08/03/china.dna.children.ability/ & http://www.bionews.org.uk/page_46453.asp - if ever phenotype should be screening off genotype...
And on the topic of whether they will use the results? http://www.nytimes.com/1998/08/16/world/scientists-debate-china-s-law-on-sterilizing-the-carriers-of-genetic-defects.html?pagewanted=all&src=pm came up in a search:
The 1994 law, whose main purpose is to guarantee prenatal and pediatric health care to poor women and children, nonetheless contains two small but controversial articles dealing with genetic counseling. They stipulate that couples undergoing their required premarital physical examination be informed of any genetic problems. But articles 10 and 16 then direct doctors to ''take steps'' to ''prevent childbearing'' -- through sterilization or long-term contraception -- should a problem be detected. And the law is unclear as to who should make the decision regarding sterilization -- the doctor or the couple. Dr. Griffiths said that many scientists and human right advocates were concerned about the ambiguity, particularly given the charges of forced sterilization that have plagued China's one-child family program. Article 10, for example, says that physicians must give ''medical advice'' to couples who have been ''diagnosed with certain genetic diseases of serious nature which are considered inappropriate for childbearing.'' It continues, ''The two may be married only if both agree to take long-term contraceptive measures or to take a ligation operation for sterility.'' It is unclear how many people have been sterilized or forbidden to marry under the law, since Professor Qiu said that provinces were generally still preparing to implement it. But local laws requiring sterilization under narrower circumstances already exist. In 1988, Gansu province in northwest China passed a law requiring compulsory sterilization of people with I.Q.'s under 49. Several other provinces subsequently adopted similar provisions.
...When Xin Mao, a Chinese geneticist now working in England, polled genetic counselors from 37 countries on whether reducing defective genes in the population was an important goal of their work, all respondents in China said ''yes,'' while fewer than 6 percent in Canada and 5 percent in the United States agreed....Dr. Mao's research also found that Asian physicians were more inclined than their Western colleagues to recommend sterilization in cases of genetic problems. Only 3 percent of genetic counselors in the United States said they would advise a couple where both man and woman carried a gene linked to cystic fibrosis to undergo sterilization, compared with 52 percent of Chinese counsellors.
From another South China Morning Post article, "Genetic data on IQ could mislead, academics say":
Three applicants who were rejected for government jobs after they were found to be carrying the thalassaemia gene sued the Foshan city government this summer, becoming China's first case of workplace discrimination because of the gene. China does not yet have laws against gene discrimination, although many employers measure intelligence to cull candidates from pools of applicants, through the use of aptitude tests.
comment by Zetetic ·
2011-10-01T23:33:20.619Z · LW(p) · GW(p)
I wonder how these criteria were decided upon. I don't see how a 1500 GRE score is at all comparable to an honorable mention on the Putnam. It seems like even getting a 20 on the Putnam (most years) is significantly more impressive than any GRE score.
Replies from: None
↑ comment by [deleted] ·
2011-10-02T02:16:18.235Z · LW(p) · GW(p)
I wouldn't be surprised if the two results are equivalent by the naive measure: the fraction of Putnam participants who get honorable mention or better might well be about equal to the fraction of GRE test takers who get a score of 1500 or greater.
The real issue here, of course, is self-selection. Lots of people take standardized tests because they want to apply somewhere that requires the score, which drives the GRE average down. On the other hand, most people who take the Putnam do so because they enjoy the challenge, and are more likely than average to be good at math. This drives the Putnam average up, compared to what it would be if every college student in the US took it.
Edit: I don't have combined statistics for the GRE, but between 5% and 6% of test-takers got 800 on the math section when I took it in 2010, while I estimate 700+ on the verbal section was about as likely. Obviously the two are correlated, but it seems reasonable to suspect that the combined percentage was less than the 2% of Putnam contestants who received an honorable mention or better.
Replies from: Zetetic, Dreaded_Anomaly
↑ comment by Zetetic ·
2011-10-02T07:32:31.802Z · LW(p) · GW(p)
I think the real issue is that comparing the GRE quantitative section to the Putnam isn't reasonable.
I wouldn't be the least bit surprised if there are tons of people who are not capable of scoring anything at all on the Putnam, yet have perfect GRE quant scores.
In any event, seeing researchers using the naive measure (if this is indeed what they did) to compare what are blatantly apples and oranges makes me feel a bit uneasy.
Replies from: chrchang
↑ comment by chrchang ·
2011-10-02T11:10:47.891Z · LW(p) · GW(p)
We are aware that the SAT and GRE quant sections have low ceilings, which is why you also need a very high verbal score to qualify through one of those tests alone. But some extremely intelligent people fail to clear the verbal cutoff (especially likely when English isn't their first language), so we figured it was worth mentioning that performance on the level of Putnam Honorable Mention gets you in regardless of your standardized test scores.
Also keep in mind that these are just automatic qualifying criteria. We'll admit a fair number of volunteers who don't satisfy any of them.
Christopher Chang, BGI Cognitive Genomics
Replies from: Zetetic
↑ comment by Dreaded_Anomaly ·
2011-10-02T03:09:49.023Z · LW(p) · GW(p)
On the GRE in 2010, 800M was ~94th percentile, while 700V was ~97th percentile. The math section is just too easy for many students in engineering, physics, mathematics, and so forth.
comment by rocurley ·
2015-03-22T05:33:02.089Z · LW(p) · GW(p)
For those of you still waiting, got an email to the effect of: We did it, sorry it took so long, it'll be uploaded in 3 weeks. Also they said that more than half were not yet done.
Replies from: rseiter, gwern
↑ comment by rseiter ·
2015-03-30T18:12:24.759Z · LW(p) · GW(p)
I received a similar email and was able to download my genome file a few days ago. The file is 23andMe format output by Plink. It was text even though it had a .gz suffix. I had trouble uploading the file to Promethease, but was able to get it working by changing the header to one copied from an actual 23andMe file and removing the missing (--) SNPs. Unfortunately, despite being ~125MB (~5x the size of an example 23andMe file I have) my file is missing many of the 23andMe SNPs (7948 genotypes annotated in Promethease vs. 20k+ for the 23andMe example). I have an email in to BGI requesting additional information. For example, Promethease directly supports the dbSNPAnnotated.bz2 Complete Genomics file and I was hoping to get a copy of that file for my data.
Have you had any success analyzing your results? Would anyone be interested in starting a discussion group for analyzing our BGI results?
Replies from: VincentYu, RichardKennaway, sideband
↑ comment by VincentYu ·
2015-04-04T05:58:16.406Z · LW(p) · GW(p)
Are you sure you've downloaded your entire genome file? My uncompressed file is about 500 MB, and I got about 26000 annotations on Promethease. It seems like your file might have gotten truncated during the download.
Short step-by-step guide for those who want to get their genome annotated by Promethease:
- Use the 'Download All Files' link on the SpiderOak page to download your genome file.*
- Unzip then gunzip to get the raw text file
- Open the file in a text editor. Remove all the commented lines at beginning of the file except the last one (i.e., keep the line starting with
# rsid; Promethease chokes if you don't) and save. This is required to get Promethease to recognize the file.
- (optional) Compress the edited file with zip, gzip, or bzip2 to save upload time and bandwidth.
- Upload to Promethease and follow the directions there.
* I advise against downloading the
Replies from: rseiter
genome.txt.gz file directly because for some reason SpiderOak has
Content-encoding: gzip in their HTTP response header, which means that browsers will transparently uncompress that file. This makes me uneasy because there is no checksum provided for the (somewhat large) plain text file, so we have little protection against corruption and truncation. In contrast, by using 'Download All Files' to download everything in a zip, the data's integrity will be automatically verified against CRC-32 checksums when we unzip and gunzip locally.
↑ comment by rseiter ·
2015-04-05T16:42:35.953Z · LW(p) · GW(p)
Thanks for the explanation and tips! I used your procedure and ended up with the same 131MB file. Interestingly I did not need to remove the "--" entries. I have been exchanging email with BGI and they indicated files could have significantly different number of entries (but I am surprised at >3x!). Is there any chance your sequencing had greater than 4x coverage? My VCF file is queued up and should be available in a few months which should help clarify what I am seeing.
Replies from: VincentYu
↑ comment by RichardKennaway ·
2015-03-30T20:16:38.810Z · LW(p) · GW(p)
I signed up with 23andMe, a few days before getting that letter from BGI. I'm currently waiting for both results. Can anyone point me to a good resource for studying what the data mean and what I can do with them?
Replies from: rseiter
↑ comment by rseiter ·
2015-03-30T20:38:07.174Z · LW(p) · GW(p)
I think Promethease (http://promethease.com) is a good and inexpensive ($5) start. If you have both sets of results I would recommend using 23andMe given my experience with uploading BGI data. Web searching "promethease review" will give some details and alternatives. Hopefully those of us in the BGI study can work out a good way of analyzing that data.
comment by gwern ·
2012-01-28T18:49:24.046Z · LW(p) · GW(p)
Apropos of that, that's part of the Chinese effort http://duende.uoregon.edu/~hsu/talks/ggenomics.pdf :
Headquarters in Shenzhen, China. Raised funding of US $ 1.6 billion. Nearly 5000 employees (1000 in software development alone). More sequencing power than all of US or Europe combined. Aims to become leading platform for sequencing and bioinformatics. Soon to hit 1000 genomes sequenced per day at $ 5k cost per genome. Previous successes: participant in original Human Genome Project (1 percent), rice genome, Panda genome, Tibetan altitude adaptation, early hominid sequence, over 1000 Han genomes sequenced.
Seek 10^3 or more subjects with IQ +3 SD or higher (roughly 1 in 1000). Conveniently pre-filtered population: students invited to training camps for physics, math and informatics Olympiads. Each student ranked roughly top 5 in his or her province, roughly 100 per subject per year in China. Math ability, possibly as high as +4 SD, general intelligence probably roughly +3 SD. Randomized testing to check these estimates.
Expect full sequencing (not just SNP genotyping) of 10^5 to 10^6 individuals within next few years. (Recall, BGI should reach rate of 10^3 per day within a year!) Probably paid for by science agencies of national governments. (Total cost roughly US $1 billion or so ... comparable to first genome sequenced by Human Genome Project!) IF sufficient phenotype data is collected about these individuals, will have very well-powered GWAS studies within next few years – enough statistical power to capture a good fraction of total additive variance (about .6 for intelligence).
I was struck by Hsu's estimate of how well the selection would work if the optimistic estimates about how many alleles they find works out:
Suppose that we have 100 g-affecting loci, each with minor allele frequency (MAF) of 0.1 and an average effect of 0.02.
• Instead of using a random sperm cell to conceive, a couple might go through 500 cells and choose the one with the most + alleles.
• If all couples in the population do this, what will happen to the level of g?
In the offspring generation, the mean level of g will increase by 0.2 SDs.
• Consequences will be especially prominent at the tails ...
The talk isn't really citable, but there's "BGI Cognitive Genomics Lab: Proposal for Gene-Trait Association Study of g"
There are some delicious discussions in there; for example, on weaknesses in previous research (this sort of discussion is why I tend to skepticism, as in my previous email on genes):
Several positive findings from candidate gene studies of g have been reported [13, 19, 34, 35, 75, 79, 88]. However, given the consistent failures to replicate these findings [41, 56, 63], it appears that most or all of these reports are false positives. The poor track record of candidate gene studies is not peculiar to research on g but rather is characteristic of research on a wide variety of traits. In retrospect this trend is not surprising. Researchers performing candidate gene studies have labored under the illusion that a lax statistical significance threshold is acceptable if the total number of tested hypotheses is small. As succinctly explained by the Wellcome Trust Case Control Consortium, however, the critical factor is not the number of tested hypotheses but rather the prior probability that any given hypothesis is correct . Now consider the fact that there are more than 10^7 SNPs with a minor allele frequency (MAF) exceeding .01 in the human species [1, 52]. Any reasonable prior probability that one of these SNPs has a detectable effect on a particular phenotype must be extremely small. Since prior probabilities do not depend on the amount of data gathered, extremely strong evidence of association is required to overcome a conservative prior probability, regardless of how many loci are examined in a particular study. Theoretical calculations and practical experience have shown that any associations clearing a significance threshold of 5 × 10^−8 will attain a high posterior probability of being authentic [43, 66, 99]. Since candidate gene studies have not employed significance thresholds anywhere near this strict, statistical considerations provide a sufficient explanation for the inconsistent results under this approach.
Here's information on Big Five and heredity:
A paper in press by de Moor and colleagues reports a GWAS of the Big Five personality traits . Although these personality traits do not include g, the results are nevertheless arguably relevant. The discovery sample consisted of 17,375 adults; five in silico replication samples totaling 3,294 adults were also employed. Genome-wide significance was obtained for Openness to Experience near the RASA1 gene (p = 2.8×10^−8 ) and for Conscientiousness in the brain-expressed KATNAL2 gene (p = 4.9 × 10^−8 ). However, the replication samples did not show significant associations between the top SNPs and the personality traits, although the direction of effect of the KATNAL2 SNP on Conscientiousness was consistent in all replication samples.
The results of the de Moor study are sobering. Compare its number of hits (one at best) with those from the initial studies of height:
- The GWAS of 13,664 individuals by Weedon and colleagues uncovered seven loci showing evidence of association at p < 5 × 10^−8 , all of which were later replicated ; and
- The GWAS of 15,821 individuals by Lettre and colleagues also uncovered seven loci showing evidence of association at p < 5 × 10^−8 , all of which were later replicated .
According to the comprehensive analysis of the GIANT Consortium, there are only ten common variants associated with height that account for more than 0.1% percent of the variance in that trait . It appears, then, that the variants most strongly associated with the Big Five personality traits may not even account for 0.1% of trait variance.2
comment by taiyo ·
2011-10-01T20:38:02.834Z · LW(p) · GW(p)
Thank you for this info. I've signed up. I think this flipped my mood from gloomy to happy.
Incidentally, this is the second study I've signed up for via the web. The first is the Good Judgement Project which has been a fun exercise so far.
comment by Xachariah ·
2011-10-01T22:18:01.699Z · LW(p) · GW(p)
Is anyone aware of a cheap/free way to check your SAT scores online and provide documentation for this survey? The last time I had need of my SAT scores was nearly a decade ago, and my best memory is "really high and I got scholarships a lot," which I don't think would count officially.
Replies from: MinibearRex, Hyena, lavalamp
comment by gwern ·
2011-10-03T00:54:25.013Z · LW(p) · GW(p)
I remember when this was announced; I eagerly checked my old SAT & GRE scores and... I was short by a few dozen points. Oh well. Genomics is falling so fast I'll just have it done in 10 years or so for next to nothing.
comment by Dreaded_Anomaly ·
2011-10-02T05:01:33.635Z · LW(p) · GW(p)
Watching the talk linked below, at about 35:26 he mentions some new results on the comparison of IQ similarity to genetic similarity. Does anyone know where to find these results?
comment by [deleted] ·
2011-10-02T02:36:27.710Z · LW(p) · GW(p)
I will be happy to take the free stuff, thanks! But seriously...the GRE is kind of easy.
Replies from: Benquo
↑ comment by Benquo ·
2011-10-02T16:45:41.998Z · LW(p) · GW(p)
Easy for you? Do you think your experience was typical?
Replies from: drc500free, None, quentin, erratio
↑ comment by drc500free ·
2011-10-02T19:39:27.082Z · LW(p) · GW(p)
Easy enough that it can't really distinguish 2 SDs from 3 SDs at the top end.
Though it's possible that it's already an SD above the population mean to begin with since it's only college grads. I don't think these researchers are looking for a very precise cutoff.
↑ comment by [deleted] ·
2011-10-02T17:20:47.420Z · LW(p) · GW(p)
Of course I am aware that I did unusually well, and I don't think that everyone can get a perfect score on the quant section, but last I checked, like one in 20 test takers does. To me, that suggests they could usefully make it a lot harder. Maybe I'm underestimating the difficulty of getting a 700 verbal, though. (I didn't think it was particularly more difficult than the SAT critical reading section, and I expect people to have a lot more practice reading dense academic prose at the end of undergrad than they did at the end of high school, but I can believe I'm not great at distinguishing degrees of difficulty in that range.)
↑ comment by quentin ·
2011-10-03T23:31:07.263Z · LW(p) · GW(p)
I was briefly excited as I met both GRE and SAT cutoffs. But now I'm feeling guilty and debating whether or not to apply; I'm certainly not in the 99.9th percentile. I absolutely love this community but I don't really post because I sincerely feel inadequate.
I'm easily in the 5th percentile, but I feel like an imposter with my standardized test scores: the tests are SO damn easy and don't measure anything of substance. GRE verbal tests your ability to recall obscure words, and the math tests your ability to maintain focus through 2 hours of trivial middle-school math. I didn't study at all.
Replies from: wedrifid, JoshuaZ, wallowinmaya
↑ comment by wedrifid ·
2011-10-04T00:00:11.871Z · LW(p) · GW(p)
the tests are SO damn easy
That's what being intelligent is supposed to feel like!
But now I'm feeling guilty and debating whether or not to apply
Guilt is overrated. They say you qualify. Therefore you do. It's their study. In fact, if you do qualify but don't think you should then you are biasing their data against genes for low self esteem.
↑ comment by JoshuaZ ·
2011-10-03T23:48:35.304Z · LW(p) · GW(p)
If you meet their samples then you should go for it. If they've already decided that those are the metrics they want to use then that's what matters for their data gathering purposes.
Also, if you have GRE and SAT scores in that range, while it is possible that they aren't really a reflection of intelligence in the 99.9th percentile (ignoring for now what intelligence means in any useful sense) one is almost certainly well above the 95th percentile.
↑ comment by David Althaus (wallowinmaya) ·
2011-10-04T09:34:31.423Z · LW(p) · GW(p)
Please sign up. Do you really believe that your perception of your abilities is more accurate than that of objective tests?
And if you believe that you aren't that intelligent, then why do you trust your reasoning and not that of the researchers who designed the study? Do you think they've made some great error in selecting these criteria? Do you think you are smarter than them? ;)
Either way, you definitely should sign up.
Oh, and you don't have to be in the 99,9th percentile. The 99,865th percentile totally suffices! ;)
↑ comment by erratio ·
2011-10-02T17:19:06.042Z · LW(p) · GW(p)
Typical for who? For the general population? For the people on LW? For the people I personally hang out with, or who are attending the same school as me?
I suspect that for the kinds of people who generally hang out on LW.. yeah, it's not challenging. I often feel stupid compared to the people here, and I breezed through it without any special preparation. But judging by the amount of GRE prep material out there and the number of people moaning on grad school forums about whether they'll be admitted with their low scores, I guess there are lots of people who find it difficult.
comment by [deleted] ·
2015-07-28T23:31:46.407Z · LW(p) · GW(p)
Since risk from individual SNP's 'should' not be aggregated to indicate an individual's risk based on multiple sources of evidence, how are the magnitudes for genosets determined?. Can bayes or another method be used to interpret a promethease report?
Even genetic epidemiology textbooks seem pessimistic: about the usefulness of the genetic research underpinning precision medicine:
‘...for the repeated failure to replicate positive findings in genetic epidemiology (102; 103) and remains the subejct of an important ongoing debate (101-105)’
-pg. 26 on chapter 1. An Introduction to Genetic Epidemiology
The references in question are about the impact of population stratification on genetic association studies. That doesn’t seem to substantiate such a broad stroke about the non-replicability of genetic epidemiology. I don't know what to make of these findings.
Damnit, can't post images in-line with comments. So, here is a link to a screenshot of those references
It suprises me that entrepreneurial machine learning analysts don’t beg for genetic research to identify how combinatorial patterns of genes to be able to characterise individual risk. It seems like if/once they can get hold of that information, the sequence from genetic science to consumer actionable health information is bridged.
So where are the 'lean gene learning machine' startups? I certainly don’t have the lean gene to do it myself. I don’t know machine learning.
Regulatory issues seems like the biggest hurdle. To the best of my google-fu, 23andme doesn't even disclose what it's 'Established Research' genes are. So, once regulatory hurdles are summounted, lots of useful research will flood out.
comment by whatagrl ·
2013-03-17T16:59:39.880Z · LW(p) · GW(p)
I haven't had my IQ tested in so long. But back in the 1970s, via the Stanford Binet and the Wechsler (WISC) I qualified for the gifted education program (MGM- Mentally gifted minors) with scores of 142 and 144 respectively. I did not take the SAT as my family was poor and it was certain I wouldn't attend college, or at least, not a four year university. As it turned out, I did finish with my BA degree (financial aid and working odd jobs).
Anyway, I have already had my genotype (and other genetic information determined) via saliva sample sent to labs at 23andme.com, and I have the AA genotype. According to articles on 23andme.com, this genotype is prevalent among those with higher I.Q.s . It will be interesting to see if your findings corroborate these findings.
comment by A113 ·
2013-02-20T00:21:54.387Z · LW(p) · GW(p)
Apparently selection is still ongoing: I got an email today saying they're sending me the kit. What kind of information should I expect when the results come back? I've never been genotyped before, so I don't know if this will be telling me stuff I already know, listing risk factors for diseases, declaring me genetically nonhuman, or what. I'm a step behind the rest of you on what genotyping actually does.
Replies from: erinys
↑ comment by erinys ·
2013-09-14T06:00:59.040Z · LW(p) · GW(p)
Although I got the email 2/23/13 saying my results were expected in May, I haven't gotten anything yet, and the site says it is still being sequenced. The results will be encoded. You will need a program to decode it. When you log into the site, at the top one of the options is Software. Under that, they list several programs that can be used. If anyone can make sense of it, I'd love to learn how. Just because I was a mathematical idiot savant at one point doesn't mean that part of my brain didn't shrivel up and die once real life happened.
On the website, it eventually updated the due date on sequencing to July. Never got an updated email.
Has anyone gotten results? Is anyone else still waiting?
I didn't become involved through that route, but I was a participant in the Study of Mathematically Precocious Youth. The majority of participants are from SMPY via the samples taken earlier by Dr. Robert Plomin, another researcher. The SMPY research emphasized gender at nearly every step. I haven't heard a word about it with this. For whatever reason, the non-verbal intelligence of males exceeds that of females. That is especially true of spatial intelligence, which seems to be specifically what they (ideally) are looking for.
So, any other gals here participating in this?
If anyone is still following this, if you fell slightly short in one area they still wanted people to apply. Those figures were simply for guaranteed inclusion. I think there was a crappy understanding of Western thinking and a lot of people self-excluded who should not have. It seems BGI only got 500-600 people on its own, the other 1500 were via Plomin. When I first read of this almost 2 yrs ago, there was mention of getting 10k volunteers.
I can't speak to the GRE, but on the SAT it is slightly unusual for people to do extremely well on both the verbal and the qualitative sections. For 2008, a GRE score of 700 was the top 4%. Those top 5% scoring 800 Math would not necessarily be top 4% Verbally, those would be largely English and liberal arts types (like me, 20 yrs after graduating college, nowhere near 800 on Math despite scoring that on the SAT 25 yrs before). Hitting 700 V & 800 M thins the herd, which was already reduced because not everyone goes to grad school, not all schools require tests, some take GMAT, etc.
Replies from: RichardKennaway
↑ comment by RichardKennaway ·
2013-09-14T06:28:58.988Z · LW(p) · GW(p)
I am in the same position: results expected in May (2013), status page now says July. I sent them an email in August but had no reply. As a non-American I don't have a GRE or SAT, but when I volunteered I just listed my educational record and career and waited to see what they said. I am wondering what their actual criteria for inclusion are, defined by who they have actually included.
Have any of their participants, on LW or elsewhere, received their data? Or is this whole thing just a ploy to get free DNA samples from smart Westerners in order to, I dunno, craft a deadly virus that only smart Westerners will succumb to? (Joke.)
Replies from: VincentYu, laofmoonster
↑ comment by VincentYu ·
2013-09-25T20:03:00.282Z · LW(p) · GW(p)
Have any of their participants, on LW or elsewhere, received their data?
Someone recently asked BGI Cognitive Genomics and received the following response (NB: most of that linked thread is about commercial sequencing using BGI's lab, not about the BGI Cognitive Genomics study):
Whole genome sequencing is complete, but proper postprocessing of the data is taking longer than we had anticipated.
More precisely, I inspected the files we could have returned in June, and found that they did not distinguish between high-confidence reference genome matches and no-calls. This is a common trait of research pipelines handling WGS data, but it would have made for highly incomplete reports from third-party personal genomics tools. We are currently working on fixing this, but I cannot yet give a reliable ETA (at this point, "July" is a placeholder for "I don't know yet").
The website will be updated as soon as I do have a reliable ETA, and you will receive an email when your data is about to be available for download.
Earlier, on August 18, Steve Hsu wrote:
I'm often asked about the status of the BGI cognitive genomics project. [...] While I cannot give a comprehensive update, I can state that
Volunteers who qualified for the study via cog-genomics.org and returned their samples by approximately September 2012 have all been sequenced on the Illumina platform, and will receive updates on the status of their genomic data relatively soon.
The relationship between BGI and Illumina has deteriorated since the acquisition of Complete Genomics by the former, which was vigorously opposed (ostensibly on national security grounds, believe it or not) by the latter. Our project has not escaped collateral impact from this development.
↑ comment by laofmoonster ·
2014-08-31T02:46:58.268Z · LW(p) · GW(p)
USA resident here, I submitted my sample in April 2013 and have not received data. The status page indicates they are still sequencing my genome. I emailed them twice to inquire on the timeframe for completion to no avail.
Replies from: RichardKennaway
↑ comment by RichardKennaway ·
2014-08-31T05:47:42.086Z · LW(p) · GW(p)
I had a reply from them in October 2013, saying:
I inspected the files we could have returned in early summer, and found that they did not distinguish between high-probability reference genome matches and low-certainty sites. While this is fine for some research purposes, it would have resulted in nearly useless reports from third-party tools. We're currently working on fixing this problem, but we can't yet give a precise ETA (the website's mention of "July" has, sadly, become a placeholder for "I don't know yet").
We will update the website and send you another email when we are ready.
I believe some other people have received the same. When I log in to their website and look at my status page, it says:
We're pleased to report that sequencing has completed. We are now extracting high-probability genotype calls from the raw data, and will send you an email when the process is complete. (This is taking longer than we anticipated; apologies for the delay.)
comment by Metus ·
2011-10-02T17:58:54.197Z · LW(p) · GW(p)
Sadly, since I did neither grow up in the USA, nor participate in any competition due to disinterest, I am surely not eligible for this study but I am very much interested in the findings since IQ seems to be correlated with the risk of some serious mental disorders.
Edit: I would also be very interested in a study that examines the genetic basis for other personality traits, like conscientiousness or extraversion.