CNGB: China National Gene Bank

Unbeknownst to me I've been skyping with a collaborator who has been working from this location.

SCMP: China opens first national gene bank, aiming to house hundreds of millions of samples

China’s first national gene bank, claimed to be the largest of its kind in the world, officially opened on Thursday to store and carry out research on hundreds of millions of genetic samples. The centre, dubbed China’s Noah’s Ark by mainland media, aims to collect 300 million genetic samples at its base in Shenzhen when all two phases are complete

... Cao said it was in China’s national interest to have its own gene bank rather than storing samples in other countries. “Cooperation is the global trend but it is more secure to preserve data in China since the variations among the genomes from different races could be used in both good and evil ways,” Cao said. ...

DNA Dreams at Harvard

This is a panel discussion of the documentary film DNA Dreams (see below), about BGI and its Cognitive Genomics Lab.

DNA DREAMS

Moderator: Dr. Evelynn Hammonds, Director of the Project on Race & Gender in Science & Medicine, Hutchins Center for African & African American Research/Barbara Gutmann Rosenkrantz Professor of the History of Science

Panelists include: (L to R)
1. George Church, Robert Winthrop Professor of Genetics, Harvard Medical School
2. Bregjte van der Haak, Filmmaker
3. Arthur Kleinman, Director of the Harvard University Asia Center and Professor of Anthropology and Medical Anthropology at Harvard University
4. Peter Galison, Pellegrino University Professor, Director of the Collection of Historical Scientific Instruments, Harvard University

Peter Galison is dismissive of "single parameter" measures of cognitive ability. George Church replies quite effectively. Certainly anyone who has thought seriously about IQ or g knows that it is only a crude measure of (compressed approximation to) a multi-dimensional set of mental abilities. I wonder how Peter would react to learning that his grandchild would be born with a mutation depressing the meaningless "single parameter" in question to an SD below normal. Would he just shrug it off as unimportant?

I believe this is the entire documentary:

Preimplantation genetic diagnosis and screening using next generation sequencing

This BGI study reports pre-implantation sequencing of hundreds of blastocysts. 42 ongoing pregnancies were achieved, with 24 babies born thus far.

Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing

Background
Next generation sequencing (NGS) is now being used for detecting chromosomal abnormalities in blastocyst trophectoderm (TE) cells from in vitro fertilized embryos. However, few data are available regarding the clinical outcome, which provides vital reference for further application of the methodology. Here, we present a clinical evaluation of NGS-based preimplantation genetic diagnosis/screening (PGD/PGS) compared with single nucleotide polymorphism (SNP) array-based PGD/PGS as a control.

Results
A total of 395 couples participated. They were carriers of either translocation or inversion mutations, or were patients with recurrent miscarriage and/or advanced maternal age. A total of 1,512 blastocysts were biopsied on D5 after fertilization, with 1,058 blastocysts set aside for SNP array testing and 454 blastocysts for NGS testing. In the NGS cycles group, the implantation, clinical pregnancy and miscarriage rates were 52.6% (60/114), 61.3% (49/80) and 14.3% (7/49), respectively. In the SNP array cycles group, the implantation, clinical pregnancy and miscarriage rates were 47.6% (139/292), 56.7% (115/203) and 14.8% (17/115), respectively. The outcome measures of both the NGS and SNP array cycles were the same with insignificant differences. There were 150 blastocysts that underwent both NGS and SNP array analysis, of which seven blastocysts were found with inconsistent signals. All other signals obtained from NGS analysis were confirmed to be accurate by validation with qPCR. The relative copy number of mitochondrial DNA (mtDNA) for each blastocyst that underwent NGS testing was evaluated, and a significant difference was found between the copy number of mtDNA for the euploid and the chromosomally abnormal blastocysts. So far, out of 42 ongoing pregnancies, 24 babies were born in NGS cycles; all of these babies are healthy and free of any developmental problems.

Conclusions
This study provides the first evaluation of the clinical outcomes of NGS-based pre-implantation genetic diagnosis/screening, and shows the reliability of this method in a clinical and array-based laboratory setting. NGS provides an accurate approach to detect embryonic imbalanced segmental rearrangements, to avoid the potential risks of false signals from SNP array in this study.

SCI FOO 2014: photos

The day before SCI FOO I visited Complete Genomics, which is very close to the Googleplex.

Self-driving cars:

SCI FOO festivities:

I did an interview with O'Reilly. It should appear in podcast form at some point and I'll post a link.

Obligatory selfie:

Those genius babies

This video has almost a million views. I think it's very well done :-)



Don't forget to respond to the reader survey.

Sequencing and GWAS

A very nice discussion of the challenges associated with sequence data, as opposed to SNP array output, in GWAS. All of these issues are familiar to our team as we work with our high cognitive ability sample at BGI.

8 Realities of the Sequencing GWAS

For several years, the genome-wide association study (GWAS) has served as the flagship discovery tool for genetic research, especially in the arena of common diseases. The wide availability and low cost of high-density SNP arrays made it possible to genotype 500,000 or so informative SNPs in thousands of samples. These studies spurred development of tools and pipelines for managing large-scale GWAS, and thus far they’ve revealed hundreds of new genetic associations.

As we all know, the cost of DNA sequencing has plummeted. Now it’s possible to do targeted, exome, or even whole-genome sequencing in cohorts large enough to power GWAS analyses. While we can leverage many of the same tools and approaches developed for SNP array-based GWAS, the sequencing data comes with some very important differences.

...

These caveats of the sequencing GWAS, while important, should not detract from the advantages over SNP array-based experiments. Sequencing studies enable the discovery, characterization, and association of many forms of sequence variation — SNPs, DNPs, indels, etc. — in a single experiment. They capture known as well as unknown variants.

Sequencing also produces an archive that can be revisited and re-analyzed in the future. That’s why submitting BAM files and good clinical data to public repositories — like dbGaP — is so important. Single analyses and meta-analyses of sequencing GWAS may ultimately help us understand the contribution of all forms of genetic variation (common, rare, SNPs, indels) to important human traits.

The Gene Factory (New Yorker)

LETTER FROM SHENZHEN: THE GENE FACTORY

A Chinese firm’s bid to crack hunger, illness, evolution—and the genetics of human intelligence.

BY MICHAEL SPECTER

A well-balanced article about BGI in the New Yorker.

I am misquoted about our current ability to predict height from genomic information, despite an hour on the phone with the Harvard-educated fact checker. There is also some confusion in that paragraph concerning the correlation between height and IQ and its relevance to the broader discussion  :-(

Chris Chang has the wise, last words in the article :-)  Click for larger version.

Single cell sequencing in PGD and cancer treatment

Note, the BGI Cognitive Genomics group with which I am associated is not involved in the work described below. Aneuploidy means an abnormal number of chromosomes within a cell, indicative of chromosomal abnormality. The most common type is Down Syndrome.

Single-cell Sequencing Makes Strides in the Clinic with Cancer and PGD First Applications (Genomeweb, October 02, 2013)

Single-cell sequencing is quickly entering the clinic with initial applications in cancer and pre-implantation genetic diagnosis and screening, researchers reported this week at the Beyond the Genome conference in San Francisco, Calif., which was sponsored by Genome Biology and Genome Medicine.

Within the field of pre-implantation genetic diagnosis and screening, BGI is already using single-cell sequencing to screen for aneuploidies prior to in vitro fertilization, and a team from Peking University is testing both single-cell transcriptome sequencing and single-cell whole genome sequencing for applications in IVF.

Meantime, a team from Harvard University has demonstrated through single-cell sequencing that circulating tumor cells from lung cancer patients show unique copy number variation profiles, while another group from Cold Spring Harbor Laboratory has tested single-cell sequencing methods in prostate cancer patients to monitor response to treatment and identify biomarkers and drug targets.

BGI's Fei Gao said that BGI has been testing a method published earlier this year in PLoS One for detecting copy number variants from single-cell, low-pass, whole-genome sequencing on couples undergoing in vitro fertilization.

In August, the first IVF baby that was sequenced before implantation was born healthy, he said, and since then more than 20 healthy babies have been born healthy following pre-IVF single-cell sequencing to screen for aneuploidies and large copy number variants. [ Italics mine. ]

Gao said that the BGI team first tested several kits for whole-genome amplification including ones that used multiple displacement amplification, degenerate oligonucleotide primed PCR, and a technique known as MALBAC developed by Sunney Xie's group at Harvard University. ...

... Gao said the team analyzed the samples for chromosomal aneuploidies and large copy number variants, and showed that the results were concordant with microarrays.

Next, they conducted a study of 41 couples that were undergoing IVF either because they were carriers of chromosomal abnormalities or had already had repeated miscarriages.

From those 41 couples, the team biopsied and sequenced 150 blastocysts. While 71 were identified as euploid, 25 had chromosomal aberrations, 40 had imbalanced structural aberrations, and 14 had both chromosomal and structural aberrations.

The sequencing test enabled the physician to choose only euploid blastocysts for implantation, Gao said.

... Separately, a team from Peking University is testing single-cell whole-genome sequencing using Xie's MALBAC technique, published in Science last year (IS 1/2/2013).

Fuchou Tang, an assistant professor at Peking University's Biodynamic Optical Imaging Center, said this week that his group is testing the technique on the 1st and 2nd polar bodies — by-products of the IVF process from which chromosomal numbers in the female pronucleus can be deduced.

The advantage of sequencing the polar bodies, as opposed to cells from the blastomere, is that there is no risk in harming a potentially viable embryo.

Tang's group has been collaborating with Xie's group, who presented at this year's Advances in Genome Biology and Technology meeting in Marco Island, Fla.

At the meeting, Xie said that in a pilot of six female donors, the technique could correctly infer embryo aneuploidy by sequencing to 0.1-fold depth (CSN 2/27/2013).

Since then, Tang's group has demonstrated that sequencing depth can be as low as 0.03-fold to accurately call aneuploidies, and he is now testing the technique to call point mutations that cause Mendelian disease.

... Aside from IVF applications, researchers are looking to single-cell sequencing to aid in cancer prognostics, diagnostics, and disease monitoring. Harvard's Xie has been using MALBAC to look at circulating tumor cells in lung cancer patients.

Circulating tumor cells are believed to be indicative of metastasis, which "accounts for 90 percent of cancer mortality," Xie said. "We need single-cell techniques to tackle this problem," particularly because cancer is so heterogeneous, and even more so after it metastasizes.

In a proof-of-concept study, Xie used MALBAC to do single-cell exome sequencing and in some cases whole-genome sequencing as well, of eight circulating tumor cells from one patient. He also sequenced the patients' primary and metastatic tumor and compared the mutational profiles from each. ...

Project Einstein

I met Jonathan Rothberg, a real pioneer in genetic sequencing technology, at Scifoo back in 2008 (see Gene machines). Jonathan's foundation is now backing an effort similar to the BGI Cognitive Genomics project. He may not remember, but we had a long conversation about this topic on the bus from the hotel to the Googleplex.

I've agreed to participate in Project Einstein (I am not worthy!) as a DNA donor, and I hope that our projects will someday share data and resources. Rothberg's attitude is typical of a true innovator: damn the critics, full speed ahead!

Nature: He founded two genetic-sequencing companies and sold them for hundreds of millions of dollars. He helped to sequence the genomes of a Neanderthal man and James Watson, who co-discovered DNA’s double helix. Now, entrepreneur Jonathan Rothberg has set his sights on another milestone: finding the genes that underlie mathematical genius.

Rothberg and physicist Max Tegmark, who is based at the Massachusetts Institute of Technology in Cambridge, have enrolled about 400 mathematicians and theoretical physicists from top-ranked US universities in a study dubbed ‘Project Einstein’. They plan to sequence the participants’ genomes using the Ion Torrent machine that Rothberg developed.

The team will be wading into a field fraught with controversy. Critics have assailed similar projects, such as one at the BGI (formerly the Beijing Genomics Institute) in Shenzhen, China, that is sequencing the genomes of 1,600 people identified as mathematically precocious children in the 1970s (see Nature 497, 297–299; 2013).

... Rothberg has long been interested in cognition. He is also in awe of the abilities of famous scientists. “Einstein said ‘the most incomprehensible thing about the Universe is that it is comprehensible’,” he says. “I’d love to find the genes that make the Universe comprehensible.”

There is precedent to the concept of sequencing extreme outliers in a population in the hunt for influential genes. Scientists have used the technique to sift for genes that influence medical conditions such as high blood pressure and bone loss. Some behavioural geneticists, such as Robert Plomin at King’s College London, who is involved with the BGI project, say that there is no reason that this same approach won’t work for maths ability. As much as two-thirds of a child’s mathematical aptitude seems to be influenced by genes (Y. Kovas et al. Psychol. Sci. 24, 2048–2056; 2013).

... The Rothberg Institute for Childhood Diseases, Rothberg’s private foundation based in Guilford, Connecticut, is the study’s sponsor. But Rothberg won’t say who is funding the project, which other geneticists estimate will cost at least US$1 million. Some speculate that Rothberg is funding it himself. In 2001, Fortune estimated his net worth to be $168 million, and that was before he sold the sequencing companies he founded — 454 Life Sciences and Ion Torrent, both based in Connecticut — for a combined total of $880 million.

Rothberg is adamant that the project is well worth the time and the money, whoever is paying for it. “This study may not work at all,” he says — before adding, quickly, that it “is not a crazy thing to do”. For a multimillionaire with time on his hands, that seems to be justification enough.

Let me repeat the scientific motivations for this type of project. The human brain is arguably the most complex object we know of in the universe. Yet, it is constructed from a blueprint containing less than a few gigabits of information. Unlocking the genetic architecture of cognition is one of the greatest challenges -- now feasible in the age of genomics that Rothberg and others helped bring into existence.

For a discussion of previous GWAS results on general cognition, and their implications for the prospects of studies like Project Einstein, see First GWAS hits for cognitive ability. For general background on the science, watch this video. Or read these: MIRI interview, FAQ.

Deemed Naughty by Nature

Nature editorial condemns research in cognitive genomics. A slight exaggeration, but consistent with the level of reporting in the accompanying article. (Click through and vote in their poll!)

I am quoted as follows:

After this summer's furore over Miller's interview [in Vice Magazine, of all places; Miller referred to Chinese embryo selection for "genius babies"], Hsu played down the potential for abuse. “There's a big gap between finding a few hits and finding thousands of hits — enough to predict the trait on the basis of the genotype — and we were never saying we were going to get to that point,” he says. But in 2011, before the uproar over the study, Hsu told Nature: “I'm 100% sure that a technology will eventually exist for people to evaluate their embryos or zygotes for quantitative traits, like height or intelligence. I don't see anything wrong with that.”

The first quote refers to the discovery power of our sample of 2000 gifted individuals. We would be quite happy to find even one genome-wide significant hit. The second quote refers to my prediction for what will be possible eventually (perhaps decades from now). Juxtaposing the quotes this way is deliberately misleading.

Dreams of DNA machines

I'm often asked about the status of the BGI cognitive genomics project. A fairly long article about it appeared in WIRED recently. I have quite a lot of experience with the media from tech startup days, as well as from coverage of my physics and genomics research. My advice is to read everything with a grain of salt. Most journalists have the best intentions, but the complexity of the topics they try to cover makes their task extremely difficult.

While I cannot give a comprehensive update, I can state that

1. 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.

2. 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.

In other news, the documentary DNA Dreams (about our project) has won the Film & Science Award and has been selected by various film festivals throughout the world, including in Italy, France, USA and Denmark and the Grand Competition of Pariscience. It has also been acquired by several international broadcasters, including Sweden (SR), Japan (NHK), Germany and France (ARTE). See trailer below.



DNA dreams.


My comments on the documentary from an earlier post:

1. As you might expect, it emphasizes sensational aspects of our research -- genetic engineering, drugs for cognitive enhancement, etc. These are all possibilities, obviously topics we discussed at the behest of the film makers, but of course for now our work is basic research with no near term applications. (Basic research tends to be less interesting to viewers than science fiction extrapolations.)

2. I find the video visually interesting, but at times it emphasizes the alien or sinister. Even the musical background seems chosen for this purpose.

3. Several important members of our team have little or no role in the documentary, despite being interviewed extensively during its making. I suppose the director was limited in what she could include, given the 60 minute format. The young woman who leads the cloning team is not actually part of our group.

History will remember their names

Or maybe not ... ;-)  Note the absence of snail shells.

WDIST and PLINK

News from BGI Cognitive Genomics.

31 May 2013: We have started the process of returning genetic data to our first round of volunteers. Everyone who was sequenced will be contacted within the next few weeks.

We are also starting public testing of our new bioinformatics tool: WDIST, an increasingly complete rewrite of PLINK designed for tomorrow's large datasets, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling and others. It uses a streaming strategy to reduce memory requirements, and executes many of PLINK's slowest functions, including identity-by-state/identity-by-descent computation, LD-based pruning of marker sets, and association analysis max(T) permutation tests, over 100x (and sometimes even over 1000x) as quickly. Some newer calculations, such as the GCTA relationship matrix, are also supported. We have developed several novel algorithms, including a fast Fisher's exact test (2x2/2x3) which comfortably handles contingency tables with entries in the millions (try our browser demo!). Software engineers can see more details on our WDIST core algorithms page, and download the GPLv3 source code from our GitHub repository.

Nature News: Chinese project probes the genetics of genius

This article is mostly correct -- see my comments below in [[ brackets ]]. As usual the Chinese connection is emphasized in the title, even though Plomin (Kings College London) is the more experienced researcher in this area, and most of our DNA samples come from US citizens.

To clarify, my main motivation for understanding the genetics of cognition derives from the observation that the human brain, the most complex object we know of in the universe, is produced from a genetic code of only gigabits in length. How, exactly, this works is one of the greatest scientific mysteries. Genomic selection and other "spin-offs" from this research are of secondary interest.

Nature News: The US adolescents who signed up for the Study of Mathematically Precocious Youth (SMPY) in the 1970s were the smartest of the smart, with mathematical and verbal-reasoning skills within the top 1% of the population. Now, researchers at BGI (formerly the Beijing Genomics Institute) in Shenzhen, China, the largest gene-sequencing facility in the world, are searching for the quirks of DNA that may contribute to such gifts. Plunging into an area that is littered with failures and riven with controversy, the researchers are scouring the genomes of 1,600 of these high-fliers in an ambitious project to find the first common genetic variants associated with human intelligence.

[[ SMPY qualifiers scored at the 1 in 10k level on the math portion of the SAT. Due to the positive correlation between M and V they almost all have V scores in the top half of one percent. ]]

The project, which was launched in August 2012 and is slated to begin data analysis in the next few months, has spawned wild accusations of eugenics plots, as well as more measured objections by social scientists who view such research as a distraction from pressing societal issues. Some geneticists, however, take issue with the study for a different reason. They say that it is highly unlikely to find anything of interest — because the sample size is too small and intelligence is too complex.

Earlier large studies with the same goal have failed. But scientists from BGI’s Cognitive Genomics group hope that their super-smart sample will give them an edge, because it should be enriched with bits of DNA that confer effects on intelligence. “An exceptional person gets you an order of magnitude more statistical power than if you took random people from the population — I’d say we have a fighting chance,” says Stephen Hsu, a theoretical physicist from Michigan State University in East Lansing, who acts as a scientific adviser to BGI and is one of the project’s leaders.

“If they think they’re likely to get much useful data out of this study, they’re almost certainly wrong,” says Daniel MacArthur, a geneticist at Massachusetts General Hospital in Boston. He is not against intelligence studies in principle, despite the visceral reactions they provoke in some people. “Studying intelligence is useful for understanding cognitive function, or diseases” that affect it, he says. But he questions whether the study will work.

[[ Not exactly sure what Dan means by "useful data" here. It's true that we don't anticipate getting more than a few genome-wide significant hits from a GWAS analysis. We may get zero! ]]

... Both Plomin and Hsu are passionate enough to take a shot, although their goals differ. Hsu is focused on the genetic basis of extreme intelligence. “My primary interest is why Einstein or Hawking is different from a normal person,” he says. Plomin is sequencing high-performers as a way of homing in on genes that affect intelligence in the broader population. If enough of these are discovered, he thinks that it may be possible to predict someone’s intelligence from an early age, and to offer help to children who are at risk of learning disabilities.

[[ This may give the false impression that it's a different genetic mechanism that gives rise to "extreme" intelligence as opposed to normal variation. ]]

Publicity around the project has spawned some extreme reactions. An article published in March entitled ‘China is Engineering Genius Babies’ in the US arts and culture magazine VICE branded the study “a state-endorsed genetic-engineering project” that will allow parents to predict the IQs of embryos and selectively breed ever-smarter children. (“That’s nuts,” says Hsu.) “Intelligence does push a lot of buttons. It’s like waving a red flag to a bull,” says Plomin. He argues that there is nothing wrong with using genetic information as the basis of educational interventions. “I’m interested in predicting learning problems early rather than waiting until kids get to school and then fail,” he says. ...

The talented 1 in 10,000

David Lubinski sent me a copy of his latest paper from a longitudinal study of individuals who scored at the 1 in 10k level (normalized by age) on SAT-M or SAT-V before 13. This population is similar to the one whose DNA we are using in our intelligence GWAS.

How can a brief test administered to a 12 year old be so good at picking out individuals who are likely to be exceptionally successful at age 38? If I hadn't been repeatedly told otherwise by "experts" I might conclude it had some validity ;-)

Who Rises to the Top? Early Indicators

Youth identified before age 13 (N = 320) as having profound mathematical or verbal reasoning abilities (top 1 in 10,000) were tracked for nearly three decades. Their awards and creative accomplishments by age 38, in combination with specific details about their occupational responsibilities, illuminate the magnitude of their contribution and professional stature. Many have been entrusted with obligations and resources for making critical decisions about individual and organizational well-being. Their leadership positions in business, health care, law, the professoriate, and STEM (science, technology, engineering, and mathematics) suggest that many are outstanding creators of modern culture, constituting a precious human-capital resource. Identifying truly profound human potential, and forecasting differential development within such populations, requires assessing multiple cognitive abilities and using atypical measurement procedures. This study illustrates how ultimate criteria may be aggregated and longitudinally sequenced to validate such measures.

The authors note that about 2% of the US general population earn doctoral degrees (JD, MD, PhD), whereas about 22% of gifted students who test at the top 1% level do so, and 44% percent of this population (in the 1 in 10k population there were many times more PhDs than MDs and JDs). From the paper:

... Other investigators have observed the importance of ability patterning for differential accomplishments in education and the world of work among talented students (Gottfredson, 2003; Wai, Lubinski, & Benbow, 2009), and even students in the top 1% of ability (Gohm, Humphreys, & Yao, 1998; Park, Lubinski, & Benbow, 2007). However, the current investigation studied participants who were profoundly gifted (top 1 in 10,000), as indicated by at least one SAT score. Moreover, for 94% of these participants their less impressive SAT score placed them in the top 1% of ability—and the lower score for 78% was in the top 0.5% (see Fig. S1 in the Supplemental Material); almost all members of this sample had both mathematical and verbal reasoning abilities higher than those of the vast majority of Ph.D.s in any discipline (Wai et al., 2009, Figs. 6 and B1).

... More than 7% of participants held tenure at research intensive universities (including many considered the best in the world) by the time they were age 38. The 14 attorneys were predominantly working in positions of significant responsibility for major firms or organizations. The 19 physicians were also highly accomplished: Seven were assistant professors, 2 were directors of major private practices, and 1 codirected a hospital organ-transplant center serving more than 3 million people. Rather than working for established organizations, 14 individuals founded companies of their own. Two individuals were vice presidents at Fortune 500 companies; 2 others were Fortune 500 senior hardware or software engineers. Several participants were active in government agencies at local and federal levels—one advised the president of the United States on national policy issues.

On the radio: NPR's On Point

I'll be on live (I think) for an hour starting at 11 AM eastern. If you dial in, you might be able to ask me a question on the air :-)

WBUR On Point. (More on the show and its host here.)

"To join the conversation on the air, call us at 1-800-423-8255 during a live broadcast."

Genius Babies

The internet headline was “engineering genius babies” out of China. Not true. But the reality is very interesting. We’ll check it out.

Guests

Nita Farahany, Professor of Law, Philosophy, Genome Sciences & Policy at Duke University School of Law, and a member of the Presidential Commission for the Study of Bioethical Issues.

Lee Silver, Professor of Molecular Biology and Public Affairs at Princeton University, Co-editor of the journal of the International Mammalian Genome Society, Fellow at the American Association for the Advancement of Science, and author of “Remaking Eden: Cloning and Beyond in a Brave New World” (1997).

Dr. Steve Hsu, member of the core team at BGI’s Cognitive Genomics Lab, Vice President for Research and Graduate Studies and Professor of Theoretical Physics at Michigan State University.

Here's the audio:

Genetic Architecture of Intelligence

Video from a talk I gave recently at the Cognitive Science Forum at MSU. This is a more reliable source of information about the BGI intelligence study than coverage in the popular media  :-(

A Genetic Code for Genius?

Another BGI Cognitive Genomics story, this time in the Wall Street Journal. I think coverage in the popular press is beneficial if it gets people to think through the implications of future genomic technology. It seems likely that the technology will arrive well before our political leadership and punditocracy have a firm understanding of the consequences. (In support of my point, see the comments on the article at the WSJ site; more at Marginal Revolution.)

WSJ: ... Mr. Zhao is a high-school dropout who has been described as China's Bill Gates. He oversees the cognitive genomics lab at BGI, a private company that is partly funded by the Chinese government.

At the Hong Kong facility, more than 100 powerful gene-sequencing machines are deciphering about 2,200 DNA samples, reading off their 3.2 billion chemical base pairs one letter at a time. These are no ordinary DNA samples. Most come from some of America's brightest people—extreme outliers in the intelligence sweepstakes.

... "People have chosen to ignore the genetics of intelligence for a long time," said Mr. Zhao, who hopes to publish his team's initial findings this summer. "People believe it's a controversial topic, especially in the West. That's not the case in China," where IQ studies are regarded more as a scientific challenge and therefore are easier to fund.

The roots of intelligence are a mystery. Studies show that at least half of the variation in intelligence quotient, or IQ, is inherited. But while scientists have identified some genes that can significantly lower IQ—in people afflicted with mental retardation, for example—truly important genes that affect normal IQ variation have yet to be pinned down.

The Hong Kong researchers hope to crack the problem by comparing the genomes of super-high-IQ individuals with the genomes of people drawn from the general population. By studying the variation in the two groups, they hope to isolate some of the hereditary factors behind IQ.

Their conclusions could lay the groundwork for a genetic test to predict a person's inherited cognitive ability. Such a tool could be useful, but it also might be divisive. ...

Inside China’s Genome Factory

Another BGI profile, this time in MIT Technology Review.

Technology Review: ... In its scientific work, BGI often acts as the enabler of other people’s ideas. That is the case in a major project conceived by Steve Hsu, vice president for research at Michigan State University, to search for genes that influence intelligence. Under the guidance of Zhao Bowen, BGI is now sequencing the DNA of more than 2,000 people—mostly Americans—who have IQ scores of at least 160, or four standard deviations above the mean.

The DNA comes primarily from a collection of blood ­samples amassed by Robert Plomin, a psychologist at King’s College, London. The plan, to compare the genomes of geniuses and people of ordinary intelligence, is scientifically risky (it’s likely that thousands of genes are involved) and somewhat controversial. For those reasons it would be very hard to find the $15 or $20 million needed to carry out the project in the West. “Maybe it will work, maybe it won’t,” Plomin says. “But BGI is doing it basically for free.”

From Plomin’s perspective, BGI is so large that it appears to have more DNA sequencing capacity than it knows what to do with. It has “all those machines and people that have to be fed” with projects, he says. The IQ study isn’t the only mega-project under way. With a U.S. nonprofit, Autism Speaks, BGI is being paid to sequence the DNA of up to 10,000 people from families with autistic children. For researchers in Denmark, BGI is decoding the genomes of 3,000 obese people and 3,000 lean ones.

Beyond basic science, BGI has begun positioning itself as the engine of what’s expected to be a boom in the medical use of genome scans. In 2011, for instance, it agreed to install a DNA analysis center inside the Children’s Hospital of Philadelphia, a leading pediatric hospital. Ten bioinformatics experts were flown in from Shenzhen on temporary visas to create the center, which opened six months later with five sequencing machines.

As the technology enters clinical use, the number of genomes sequenced in their entirety could catapult into the millions per year. That is what both the Philadelphia hospital and BGI are preparing for. “They have the expertise, instruments, and economies of scale,” says Robert Doms, pathologist-in-chief of the children’s hospital. ...

BGI cleared to acquire Complete Genomics

Sequencing is a fast moving field with many competing technologies. The claim that the acquisition of Complete Genomics has national security implications is highly implausible. Earlier posts here and here.

NYTimes: ... BGI-Shenzhen, said in a statement this weekend that its acquisition of Complete Genomics, based in Mountain View, Calif., had been cleared by the federal Committee on Foreign Investment in the United States, which reviews the national security implications of foreign takeovers of American companies. The deal still requires antitrust clearance by the Federal Trade Commission.

Some scientists, politicians and industry executives had said the takeover represented a threat to American competitiveness in DNA sequencing, a technology that is becoming crucial for the development of drugs, diagnostics and improved crops.

The fact that the $117.6 million deal was controversial at all reflects a change in the genomics community.

A decade ago, the Human Genome Project, in which scientists from many nations helped unravel the genetic blueprint of mankind, was celebrated for its spirit of international cooperation. One of the participants in the project was BGI, which was then known as the Beijing Genomics Institute.

... Some other executives at American sequencer manufacturers said they saw no cause for concern. “I can’t believe they can come up with a rational explanation of why this is a national security issue,” said Michael W. Hunkapiller, the chief executive of Pacific Biosystems.

Jonathan M. Rothberg, who runs the Ion Torrent sequencer division of Life Technologies, also said the acquisition “does not appear to raise national security issues.”