BGI is the leading sequencing institute in Asia, with interests in a variety of genomic fields.

When it comes to genomics, China seems a little like the proverbial kid in the candy store – she wants a taste of everything. Of course, unlike the child, China might be making a bid to own the candy store outright as well. The Beijing Genomics Institute (BGI), now located in Shenzhen, is the leading genomics facility in China, and all of Asia. BGI has striven to make a name for itself in every major international genome sequencing project of the last decade. The International Human Genome Project, the International Human HapMap Project, sequencing SARS, the Sino-British Chicken Genome Project, etc. It was also responsible for completely sequencing the rice genome, the silkworm genome, the giant panda genome…the list goes on an on. By the end of this year BGI will have 128 of Illumina’s HiSeq 2000 platforms, 27 of AB’s SOLiD 4 systems, and many other sequencing devices. At full capacity this means they will be capable of the equivalent of 10,000+ human genomes per year. And they are still growing. BGI may not be the largest genomics facility in the world, but it is has phenomenal support from its government, ambition to expand quickly, and a hand in dozens of major sequencing projects. You can’t talk about the future of genetics without talking about China.

In late 1999 the Beijing Genomics Institute started to build China into a world leader of genetic research. In the decade that’s elapsed since, they’ve put their name on some major developments. Here are just a few of the biggest newsmakers:

• First Asian Diploid Genome Project – The first sequenced genome for a person of Asian descent in late 2007. Published in Nature 2008.
• Cloned Pigs – BGI was instrumental in creating handmade clones of pigs in 2008.
• Giant Panda Genome Project – BGI sequenced the Giant Panda (whose genome is roughly equal to a humans) on its own in just eight months in 2008-2009! Published in Nature 2009.
• Cucumber, and Rice Genome – Among the first sequences of complex plants used as food crops. Cucumber published in Nature 2009.
• Silkworm and Ant Genomes – Among the first sequences of a domesticated insect, and ecologically important insects. Ants published in Science 2010.
• SARS – Sequenced the SARS virus just hours after a Canadian team completed the first mapping of the pathogen.
• Ancient Human – BGI was the first to sequence an ancient human genome (a paleo-Eskimo). Published in Nature in 2010.

Since its inception, BGI has had a very ambitious attitude when it came to participating in world genomics. Every time they were presented with a new project, they basically said, sure, we’ll be a part of that. They contributed 1% to the Human Genome Project’s reference genome, and 10% to the Human HapMap Project. It was like they never met a sequencing project they didn’t like.

That attitude hasn’t seemed to wane at all. BGI is spearheading efforts that will sequence a wide variety of organisms. There’s the 1000Genomes Project aimed at producing a wide database of human genomes from people all over the world. They are also working to sequence 1000 plants and animals, and have already completed 14+ of the former and around 50 of the latter. In 2009, BGI launched its effort to map the genomes of 10,000 microbes – they’ve managed 800 bacteria, 100 fungi, and 100 viruses so far, with more finished every day. They are looking for collaborators to sequence 1000 Mendelian Disorders in humans. Completion of large genetic databases like these will be part of what could empower genetic research to finally make the discoveries the public has been waiting for since the first human genome was sequenced a decade ago.

Even while BGI is a testament to Chinese ambitions in genomics, it also speaks to the prominence of the US in that field. BGI relies heavily, almost exclusively, on sequencing technology rooted in California. Illumina’s HiSeq2000 and Applied Biosystems SOLiD 4 form the bulk of BGI’s machine workforce. To be fair, most of the world has focused on using these systems as well, and BGI is working to expand its hardware horizons, collaborating with OpGen on new optical sequencing methods. Still, when one sees BGI’s successes in genomics one also has to acknowledge that such capabilities weren’t developed in a vacuum. China’s sequencing projects, like every nation’s sequencing projects, have worked as part of a larger global effort.

The only real question, then, is how much will China simply be a part of that worldwide phenomenon, and how much will it lead? Even if the hardware is largely developed by California companies, those companies themselves are international entities. BGI is officially part of the sequencing club, recognized by Illumina as one of its associated world class facilities. BGI isn’t some second tier group working its way to the top, it’s already at the top, sharing space with the other lead genomics institutions around the world. If BGI and China continue to dedicate money, labor, and insight into genomics, they’ll be able to set the agenda for many sequencing projects around the globe. Actually, they’re already doing this with their various sequencing projects for microorganisms, plants, animals, and humans.

I know that many of us will view BGI’s growing importance through the lens of competitive national spirit. Yet no matter your feelings about China, you have to view BGI’s accomplishments as wonderful gifts to the global scientific community. Every genomics center around the world is going to have different specialties (Complete Genomics is dedicated to bringing down the costs of human whole genome sequencing, for instance) and it’s only through combining these disparate efforts that we’ll create the general understanding we need to move the field of genetics forward. It’s a team effort. Yay China, Yay us.

A map of the populations of major genome sequencing platforms around the world. Not yet updated for the end of 2010. Just some food for thought.

[image credits: BGI, Pathogenomics]
[sources: BGI]

Open up your financial umbrellas, Complete Genomics is going to make it rain. The Mountain View startup has built a name for itself as one of the premier providers of whole genome sequencing for humans. Now we are just days away from their IPO. According to the filing statements with the SEC, Complete Genomics will offer 6 million shares of their stock at a price between $12 to $14. To encourage prospective investors to leap at their offer, the company released details of its current and future production. At the beginning of the year, the worldwide total number of human genomes ever sequenced was less than 300. Complete Genomics produced that many in the third quarter of 2010 alone. They hope to produce 400 genomes per month by the end of the year. These are big numbers, and they’re likely to get bigger. Much much bigger. In our interview with CEO Cliff Reid back in January, he claimed that Complete Genomics would sequence 1 million human genomes by 2014, and at prices substantially lower than any on the market today (possibly < $1000). The race to establish whole genome sequencing supremacy is underway, and this IPO will be a sign of how much faith the public has that Complete Genomics can come out on top.

It’s been a big season for genome sequencing. Ion Torrent, a company developing CMOS based DNA sequencing technology was purchased by Life Technologies for $375 million. Critical parts of the CMOS approach to DNA were actually licensed to Ion Torrent earlier in the year by DNA Electronics, a UK company looking to develop handheld genetic scanners that we’ve discussed before. Pacific Biosciences (NASDAQ: PACB), which has developed optics based DNA sequencing tech, had its IPO at the end of October and raised around $200 million. BGI, China’s premier genome institute recently announced it was teaming up with OpGen to further their own optical approach to DNA sequencing. Everywhere you look, from the EU to California to Asia, forces and finances are gathering to see who will provide the next generation of genome testing and analysis.

This heightened activity in the field may be just what Complete Genomics needs to fuel their IPO. With Ion Torrent selling for $375 M and Pacific Biosciences raising $200 M at a similar share price (~$16), Complete Genomics gets a good idea of what it can raise. The $86 million it hopes to pull in through its stock offering will nearly double what it has gained through venture investments. Complete Genomics gathered $39 million in venture funding this August putting it up to around $91 million in total. With another $86 M, Complete Genomics would have the funds to expand its new sequencing centers aggressively – a key requirement if they are to develop as quickly as Cliff Reid seems to be planning. Investors may look at Complete Genomics’s competitors recent financial gains, compare their tech to CG’s rapidly growing capabilities,and flock to the IPO.

Yet such investments are not without their concerns. Even while raising venture funds, Complete Genomics was fighting off patent infringement lawsuits from Illumina - perhaps their main rival in whole genome sequencing. Genetic testing based on SNP (single nucleotide polymorphisms) has faced growing concerns over accuracy and relevance in the light of real and perceived errors. The field of genetics, in general, has faced criticism for the lack of real world benefit for patients in the ten years after the first human genome was sequenced. Investors may see Complete Genomics’ cheap whole genome sequencing, which provides phenomenonally more data than SNP tests, as the technology that will come to dominate genetics and reconfirm its importance in medicine. Or they may see the uncertainty in genetics as a great reason to avoid investing in the field altogether.

The same factors which make investments a risk make them very exciting to techno-optimists like myself. I can’t say for certain that Complete Genomics will be the undisputed leader in whole genome sequencing. There’s too much potential competition from Illumina, and the CMOS and optical approaches developed by others are too attractive looking, to call things in Cliff Reid’s favor at the moment. Still, I do think Complete Genomics has the right approach to sequencing: specialize in one field (human genomes) and use economy of scale to push towards ever cheaper and larger production. 400 genomes a month by 2011 is an amazing accomplishment, especially as the costs for materials for each genome may be as low as $1800. The only way Complete Genomics is going to lose is if some other company can beat that. Either way, scientific research and personal genomics will have won. Cheap and fast whole genome sequencing will provide us with huge amounts of new genetic data that we can use to understand illnesses, and provide better healthcare. When your genome costs less than $1000 to sequence, millions all over the world will be encouraged to get themselves tested and claim an informed ownership of their own genetic information. Win or Fail, Complete Genomics’ IPO is another sign that the next DNA revolution is near.

[image credit: Complete Genomics]
[sources: Complete Genomics, SEC]

Europe’s leading genetic sequencing provider, GATC Biotech, recently announced that it would sequence 100,000 human genomes by 2014. Based in Germany, GATC plan on using sequencing technology from other industry leaders, including Illumina’s HiSeq2000 and Pacific Bio’s PacBio RS single molecule platform, to achieve their goal. They are reportedly already on target to finish 100 human genomes by the end of 2010. To facilitate the ramp up needed to hit the 100k mark in four years, GATC has created a new unit, and has grown their staff to 120 employees. They predict that sequencing customers will come from the pharmaceutical and diagnostic industries, as well as academia. While GATC isn’t adding any new technology to the whole genome sequencing game, they are a major force in Europe, and seem to have the resources necessary to make their goal a reality. With another company competing for sequencing dominance, the chances for cheap reliable access to your own genome are looking better every day.

President Kennedy famously put the US on track to win the space race by setting the goal, “… of landing a man on the moon and returning him safely to the earth.” Whole genome sequencing is now entering a similar race, with similar bold statements by prominent companies. Yet no one seems certain as to where the moon is, metaphorically speaking. Complete Genomics has announced it will sequence a million genomes in the next five years. GATC has its 100k genome goal set around the same time frame. Which of these is the important landmark? Does it really matter if either one succeeds?

Globally, the number of human genomes that have been sequenced is still in the low hundreds. With such a small data set, the number of things we can learn from a genome is still fairly limited. As we mentioned before, it has been 10 years since the first human genome was sequenced and we still haven’t had a revolution in genetics. How many genomes will it take before we get there? We may have major breakthroughs by the time we sequence a few thousand genomes, or it may take us two or three million before we find the connections needed to make big breakthroughs in genetics. Those leaps in understanding are going to be more meaningful than hitting some arbitrary mark (1 million or 100,000) in the number of genomes sequenced.

The real saving grace of all this competition to sequence the most genomes quickest is that it is driving prices down rapidly. Illumina’s HiSeq2000 and other instruments are drastically reducing the reagents costs needed for each genome. Complete Genomics is already looking to offer genomes at less than $10,000 USD this year. With service groups like GATC getting into things, we’ll hopefully see prices plummet in the next five years. That will help research teams, in the pharma industry or academia, find those major breakthroughs in genetics we’ve been waiting for. It will also mean that millions of people around the world would be able to afford to get access to their own sequence, especially if prices fall below the $1000 mark. In the end, I’m not terribly thrilled that GATC is aiming to hit the 100k genome goal by 2014, but I am enthusiastic to see what kind of changes in genetics their efforts might enable.

[image credits: GATC Biotech]
[source: GATC Biotech Press Release]

Meet the Wests, first family of recreational whole genome sequencing.

John West is very familiar with whole genome sequencing (WGS). He was a general manager with Illumina after they acquired Solexa, where he had been CEO. So it’s no surprise that John West hired Illumina to sequence him, or even that his wife Judy followed suit. What has caught attention is that he asked his daughter Anne (17), and his son Paul (14) to be sequenced as well and they agreed. This marks the first time that an entire family has publicly undergone WGS without any pressing reason to do so (such as researching a genetic disease). While some may view this as “recreational sequencing” I think that John West is simply ahead of the game. Could the West kids learn something unpleasant about their genes? Sure, but knowing your genome is going to pay big dividends in the years to come. Ethical concerns about having children sequenced are understandable now, but in the future it may be considered unethical not to sequence your children as early as possible.

According to the Times Online, West paid something close to Illumina’s retail price for the sequencing service, that’s nearly $50k a piece or $200k all together. There are relatively few people able or willing to pay that much to peer into the DNA of their families. Complete Genomics, who we see as Illumina’s chief rival, is on the road to providing WGS at a much cheaper rate -$10k or less. Both companies are aiming to hit a $1000 price tag as soon as possible. What few could do at $200k, many will be able to afford at $4k and so, from an economic perspective at least, it seems very likely that we’ll be able to sequence our families soon.

Will we want to? Understanding one’s DNA is the key to benefiting from the growing body of research about genetics. Genetic testing can give you early warnings about devastating illnesses like Parkinson’s, diabetes, and heart disease. We may also need WGS if we are ever to take advantage of certain forms of gene therapy. Those are good reasons for every individual to get sequenced, but there are benefits for families sequencing together as well. As West points out in the Illumina press release, sequencing an entire family lets you explore the importance of variations in the same gene on opposing chromosome copies (compound heterozygote), and may provide insight into medical conditions.

For now, the possible benefits from genetic testing are relatively small, but they are likely to grow with every year. Is the same true for risks of genetic testing as well? Let me be clear here, there is no physical risk to being sequenced – DNA is simply extracted from a saliva or blood sample. The ‘risk’ is how the information provided by WGS could affect one’s life. If you had a large disposition to Alzheimer’s would you want to know? Would learning about it depress you irrevocably? In that case, maybe ignorance would be bliss.

Nonsense.

I’m not a big fan of ignorance, and I can’t see it getting any more appealing in the years ahead. Yes, there is always an emotional weight to learning about a medical condition. That knowledge, however, can often be put to good use, helping us seek treatment that is needed. Even if you have a genetic disposition to a disease with no known cure or associated therapy, wouldn’t you at least want to know that before you start having children?

It all comes back to the kids. When Anne and Paul West agreed to be sequenced, they set an interesting precedent: non-adults consenting to genetic testing. They had, a few years earlier, agreed to a more basic SNP test from 23andMe. More qualified ethicists than I can debate whether a non-adult has to (or even can) consent to a medical procedure. What interests me is whether or not there is any downside to knowing your DNA. There is a concern that once someone’s DNA is on file insurance companies, employers, and potential mates would all rifle through that data looking for reasons to treat you poorly. Who knows, maybe they would, but I doubt we will let it get to that point. All around the world nations are taking steps to outlaw genetic discrimination (including GINA in the US). We won’t have to viciously protect our DNA from being searched, and even if we wanted to, we probably wouldn’t be able. $1000 WGS will eventually get even cheaper (years down the line) and DNA is easy to come by. Unless you’re going to guard your precious bodily fluids every second of every day, someone would eventually be able to spy on your genes.

In other words, I don’t think there was much legal/social risk to what Anne and Paul agreed to, and any risk they did expose themselves to the rest of us will soon be exposed to anyway as well. And for the record, while at least one of the West parents submitted their genome to the NCBI database neither of the children’s DNA was made public at this time. They’ll be able to make that decision for themselves when they turn 21.

So if you’re like John West or I, you probably see WGS for the family as a net-positive. Good chance for improving your own medical care, little risk of being ostracized from society for being a genetic leper. If more people take that view it’s likely that the age at which we will want to genetically test our children is going to get lower. Already there are preconception and prenatal genetic tests to help parents decide to have (or prepare for) children with a chance for genetic illness. Such testing effectively helped eradicate Tay-Sachs from the Jewish community. When it costs less than $1000 to sequence someone, it seems very likely that many parents will opt for the test immediately after (or perhaps even before) birth.

That could lead to unprecedented healthcare opportunities. Right now, our understanding of how DNA relates to disease susceptibilities is based on handfuls of SNPs and small groups of genes. This understanding will seem primitive in a decade. There is so much to learn, so many interactions between genes to trace, so many medical histories to explore and tie in with genetics. We are going to know a lot more in the years ahead and taking advantage of what we know is going to necessitate sequencing at some level. Why not get your child’s WGS done as soon as possible so that you can maximize the possible benefits?

Instead of asking if it is ethical to genetically test children, let’s imagine a time when not testing a child could be seen as a health risk. There are many illnesses in childhood which may have a strong genetic component (various cancers, diabetes, etc). Many of these diseases can be treated better with advanced warning. If you were a parent, wouldn’t you want that warning? If everyone got their children tested for these diseases, it may eventually seem negligent if your child wasn’t sequenced. I think we will be entering such a time sooner than we think. In that case, John and Judy West’s decision to get their children sequenced (and their children’s consent to the WGS) isn’t ethically questionable, it’s demonstrating laudable foresight.

For those wishing to read more about the ethical concerns surrounding the West family’s sequencing adventures I recommend Marc Henderson’s article in the Times Online. Genetic Future author Daniel MacArthur’s analysis of that article is also great reading. In the end, I think the debate centers as much on the fear of changing humanity as anything else. Genetic screening before conception is not such a long jump from making designer babies, and we recoil from the idea of breeding humans the way we breed livestock. Still, parents may reconsider their prejudices against such concepts when they are presented with the ability to help their children be smarter, healthier, and happier. Even if we completely outlaw all genetic selection for embryos, WGS will still be a valuable tool for understanding and dealing with the genes we receive naturally. DNA is data, and sequencing gives us access to that information. It’s hard to argue against knowledge and those that do rarely have the final say in how technology develops.

[image credit: College Hill Life Sciences]
[source: Illumina Press Release, Times Online, Genetic Future]

Illumina recently unveiled it's new sequencer, which shows some significant improvements.

The ongoing race to become the household name for whole genome sequencing is speeding up. Industry giants Illumina (ILMN) and Complete Genomics have both made recent announcements which demonstrate how serious this competition really is. The most recent battleground is the JP Morgan Healthcare Conference in San Francisco where thousands of investors and billions of dollars are at stake. Illumina unveiled a new sequencing machine, the HiSeq 2000, which has 30x coverage and 2×100 base pair read length. Importantly, it only requires $10k in materials to process each sample and can sequence two entire genomes over a period of about 8 days. Complete Genomics has countered with some impressive news of their own. This fall they announced the sequencing of 3 individual genomes at an average materials price of just $4400, and future whole genome sequencing (WGS) will be sold at just $20k per sample with large price breaks as order sizes increase. According to their twitter feed, CG told investors at JP Morgan this week that they have delivered 50 genomes and plan to complete a whopping 5000 more in 2010. We’ll get a chance to learn more about Complete Genomics plans for this year when we interview CEO Cliff Reid at PMWC next week. It’s a fierce battle between these two genetic giants, but the war is likely to lead to some amazing benefits to you and I.

As WGS becomes cheaper, we’ll see gains in research, diagnosis, and genetic treatments. What constitutes “cheap” is really at the heart of this competition. Certainly genome prices are falling and will continue to do so. Singularity Hub believes, as many do, that the magic sales tag reads around $1000. At that cost, most individuals in industrialized nations will be able to afford WGS (or pressure their insurance providers to cover it). We would see nearly universal sequencing among those interested in harvesting the benefits of genetic research.

Both companies have a ways to go. Illumina’s price per sequencing is still hovering near $10k or above with the HiSeq 2000, though this is about one fifth the price of their first personal genome studies (~$48k). The new sequencing machine, however, does have some major promise at becoming a definitive tool in the market. The Beijing Genomics Institute has shown interest in purchasing 128 machines! At $690k a piece, that’s a major investment.

Complete Genomics is shooting for the $1000 price line by focusing exclusively on human genomes and economies of scale. Hopefully Singularity Hub will be able to tour their new (and large) facilities in Silicon Valley soon. CG’s commitment to 5000 genomes in 2010 is both promising and concerning. It’s remarkable that the genetics company is following a seemingly exponential ramp up in production going into the new year. Unfortunately, CG had originally promised 10,000 genomes to be completed in this time frame. I’m actually okay with the factor of two discrepancy. As long as CG sequencing is in the thousands, and not hundreds, I think we can be very hopeful for reaching the $1000 benchmark in the next few years.

I should mention that this isn’t a two-horse race. Not really. While Illumina and Complete Genomics are dominating the media feeds and the production benchmarks, there are other genetic sequencing companies. And, it’s still very early in the formation of the WGS industry. We could see a dark horse candidate arrive and become the new household name for sequencing. Genetic expertise isn’t limited to the US and we should all keep an eye out for companies in Europe, China, and India preparing to jump ahead in the race.

As always when dealing with genetics, I find the writing at Genetic Future to be of enormous help in putting new developments in perspective. Along with the Genomics Law Report, GF provided a well reasoned view on the recent developments at Illumina. I would also encourage interested readers to check out CG’s twitter feed, as they put some really juicy news in there on occasion. Hopefully between these sources (and Singularity Hub of course) we’ll be able to keep you abreast of all that is going on in the genetic sequencing industry. This is exciting stuff, folks. Starting now, genetic research is being accelerated by the lowered costs of WGS and we can hope to reap the benefits of those studies in the next five to ten years. In that same time frame you may see personal genomics fall into your budget. That’s going to change our healthcare, the way we plan our lives, and maybe even how we think of ourselves. The genetic revolution is coming.

[image credit: Illumina]

A new genetic test is going to increase milk production in cows and yield big profits.

While it may take years before widespread genetic testing changes humanity, animals are experiencing a difference today. According to Forbes, a single genetic test for breeding dairy cattle has almost completely replaced older pedigree tests in less than two years. Developed by Curtis Van Tessell at the USDA and performed by Illumina, this test costs only $250, replacing the previous system’s $50,000 price tag! The cheaper testing allows smaller dairy farmers to enter into the profitable business of selling cattle eggs and sperm. Using genetic testing, milk producers predict that the annual increase in US milk production will double to 5%. We’re talking about millions of dollars of increased profit in the United States alone. Van Tessell’s new test demonstrates that the age of widespread genetic evaluation has already started.

When it comes to human genetic testing, Illumina is one of the biggest names in the business. It and competitors like Complete Genomics are aiming to bring whole genome sequencing into the price range of most individuals. Right now, more affordable genetic evaluation can focus on key genes in human DNA. These single nucleotide polymorphisms (SNPs) are cheaper to test – companies like 23andMe use them exclusively to great avail. In Van Tessell’s test, SNP tests are used to keep track of 38,000 key differences that the USDA team discovered were important in dairy cattle breeding. One wonders how whole genome sequencing will affect animal husbandry. The bovine genome was recently mapped in 2009. Could we see even more profitable breeding? Maybe greater acceptance of germline genetic engineering? The reverse also could be interesting: how will attitudes about human genome testing change when genetic evaluation becomes a staple on the farm?

Funny enough, Illumina wasn’t really interested in getting into the animal testing business. Van Tessell was originally working with Solexa when that company was acquired by Illumina. He had to work tirelessly to convince the new company that his cattle evaluation was a worthwhile endeavor. Finally, Illumina developed a chip (snp 50) to use in Van Tessell’s test. It paid off for everyone. Illumina generates about $50 million a year, 8% of its revenue, through agricultural genetics, of which the cattle testing is a major contributor.

What exactly is the Van Tessell test looking at? A long history of milk production. The USDA Animal Improvement Programs Lab evaluates genetic fitness by examining milk records and certain cells in the udder. This helped the USDA and Van Tessell determine which 38,000 genetic markers would correspond to animals that not only had the best genes for milk production, but were actually passing those genes on to offspring. The last century of pedigrees were only about 30% accurate in finding good dairy cows. No pedigree can be better than 50% (due to uncertainty in which parent will pass on a particular gene). The new genetic test is about 70% accurate in predicting milk production. And again, it costs just $250!

With genetic benefits, however, come genetic concerns. In the past thirty years selective breeding has lead to a 8% increase in milk production per Hollstein cow. It has also generated a system by which only 500 bulls are used to inseminate nearly 9 million heifers. The new test has allowed smaller farms to enter into the sperm and eggs market, finding better breeding stock in previously unevaluated cattle. Yet of the 3000 bulls tested under the new system last year, only 130 qualified for breeding. It seems like the male side of the gene pool is going to stay pretty shallow. I worry about any living product (animal or plant) with a narrow family tree. It opens the way for a small genetic predisposition to a new disease to devastate an entire industry.

That won’t likely be a problem with humans however, and the genetic testing of cattle has some important implications for our own species. A single test is going to double the increase in production, and yield untold profits for milk farmers. What kind of parallel benefits might humans enjoy as genetic evaluation becomes more available? We’ve already seen how SNP testing can help tell you about your susceptibility to certain diseases. The real changes in humans, as with cattle, may come when genetic sequencing starts to affect breeding. People are already clamoring to evaluate their kids, and many may want to start the evaluation process earlier. Would you pay $250 to see if your prospective mate had a genome clear of defects? Some would. Some will. And while public discrimination based on genetics in now illegal in the US (and has been in other nations for some time), private discrimination is still to be determined. Are we going to pay a social/moral price for the profits of genetics? Van Tessell’s work with cows make those profits seem very high. In the next few years humanity may follow the herd.

[photo credit: ESPN]

The race to provide you with access to your genome is really heating up. Industry leader Illumina (NASDAQ: ILMN) has completed its first genome sequencing service for an individual at the low-low price of $48,000. That’s almost ten times what Complete Genomics plans to charge, but Illumina is offering the service directly to private individuals, not research groups. In fact, this is the first time any one person has had their genome sequenced for less than $50k. Illumina’s performance shows that it is still one of the forces to be reckoned with in whole human genome sequencing.

What are we to make of Illumina’s successful personalized genome sequencing service? It stacks up well against Knome’s KnomeCOMPLETE™ service which is perhaps the only other successful individual genome sequencing service on the market at the moment. Knome is trying hard to remain a contender in the field, but at $99.5k, it’s more than double Illumnia’s price.  With comparable capabilities and results, price becomes the real determining factor between those two companies.

Of course, it’s hard to take either seriously as a contender against Complete Genomics. $99,500 versus $48,000 versus $5000, which price would you want to pay? Of course, CG is only offering that low price to orders of 40+ genomes. In orders of 8+, they’ll be charging $20,000 (see our earlier article for more). The price for a single solitary genome could be even higher. But it’s actually unclear whether Illumina or Complete Genomics is really after the individual customer market. We know people who are after the individual market, and may be offering it at only $1000, and we’ll get that story published soonish. (It seems like we mention this mystery company every other day. Sheesh)

While CEO of Illumina, Jay Flatley was the first to get his genome sequenced under the new system, the first official customer was Herman Hauser of Amadeus Capital Partners. According to the Illumina website, both men intend to place their genomes in the public domain (potentially doubling the number of such genomes) in order to facilitate understanding and research. The next two customers on the docket are preeminent scholar of African American studies, Henry Louis “Skip” Gates, Jr. and his father, Henry Louis Gates, Sr. As Skip Gates hosted and produced two TV specials on African American heritage that featured DNA tests, I anticipate his genome results will facilitate the production of a third show.

There are two broad approaches to the task of analyzing the entirety of your DNA. You can specialize as much as possible, and in doing so reduce costs, or you can keep your range of applications wide, but sacrifice in economic efficiency. Complete Genomics represents the first approach, Illumina the second. Illumina can sequence DNA and RNA and not just from humans. Their sequencing services are broad, rigorous, and perhaps the most trusted in the industry.

So that’s how I view Illumina’s latest success: just another feather in a well-feathered cap. Unless Illumina drastically brings the costs down, Complete Genomics, or another company like them, will dominate the human genome sequencing market. If Illumina does cut the price, they certainly will enjoy a large share of the market. They have broad respect in a variety of DNA testing fields and they are working with 23andMe, Knome, deCODE Genetics, and Navigenics in secondary data analysis.

Knowledge of your genome is likely to be one of your strongest assets in the decades to come. Current uses and understanding of genetics tend to focus on relatively few genes – single nucleotide polymorphisms or SNPs. Companies like 23andME help you determine ancestry, risks for diseases, and important trait information just by using SNPs (and some short sequences of DNA). That’s why services from those companies are so cheap. As research into genetic traits continue, the range of ‘interesting’ DNA segments will increase. Whole genome sequencing has the potential to tell you about every inherited aspect of your body. In that light, sequencing your complete genome is likely to change from novelty to necessity.

Anyone who’s read my posts before probably knows that I love when businesses compete. The only thing that makes me happier than knowing someone is trying to provide wide-range access to genome sequencing, is knowing that someone else is trying to do it even cheaper. The public needs that access sooner rather than later. Today, knowing your genome just gives you a little more information for you and your doctor to use when planning your healthcare. Tomorrow, understanding your genome could help you extend your life by 30 years, increase your intelligence, or make you glow in the dark. It all starts with sequencing, and thankfully no one has a monopoly on that. Yet.

Complete Genomics is pushing down the costs of sequencing the human genome.

It’s getting progressively cheaper to sequence your entire genome. Earlier in June, Illumina announced it would provide sequencing for close to $50k, half of their original price. Not to be outdone, Complete Genomics just released on Monday that it had gathered $45 million dollars in funding. The Silicon Valley based company is planning to use that money to further develop their streamline sequencing operations so that they can offer a complete genome for just $5000 by next year. CG’s goal is to finish 10,000 sequences by years end 2010. Even though that’s later than we had hoped, it’s still a whole lot of DNA and at the cheapest price for a whole genome seen so far. The question is, can they really pull it off?

We’ve been looking for a company, any company really, to break the $1000 price mark for a complete genome sequencing sometime in the next few years. That’s about the point where retail sales of the service will explode. With their exponentially decreasing price tag, Complete Genomics might be on that path. However, we know of at least one company that is trying to reach that goal by the end of this year. Stay tuned for that story in the next few weeks.

If you’ve never heard of Complete Genomics, read our first and second story to catch up. Basically they use a common form of short read sequencing and throw in a ton of computer power to sequence a human genome. Interest in personal genomics is escalating as genetic links to diseases are discovered. 23andMe already offers some testing for such diseases and is hoping to gather samples for further clinical trials. By providing the entire genome for perusal on the cheap, CG could make it economically feasible to expand that research into many more illnesses. Already, we’ve shown you how some facilities are erroneously promising to predict a child’s aptitude based on genetic sampling. Perhaps with the cheap sequencing CG could provide, scientific research will match pace with the growing demand for such testing.

Daniel MacArthur of Genetic Future was able to pry CG head Cliff Reid to provide some details in how they hope to achieve their goals. First, Reid disclosed that the test won’t be offered directly to consumers, but rather through retail providers such as Knome and 23andMe. That means the price you or I will see could be considerably higher than $5k. Whatever the retail price, Reid promises 120 billion base pairs sequenced, 98% of the genome, with just one error in 10,000. That’s considerably better stats than what CG offered in February (92% of genome, about one error in 1,000).

Between now and year’s end 2009, Complete Genomics will focus on its dozens of customers currently in the line up. These include the Broad Institute out of MIT and Harvard which announced it was purchasing at least 5 genomes from CG in March. The Broad Institute reportedly paid $20k for each of their genomes which might be taken as the current baseline price for CG customers. If so, that’s a factor of four that the company has to make up between now and next year.

But scaling is no problem for genome sequencing. Remember that it took 15 years to sequence the first human genome, but the next 6 were done in 24 months. Now we’re talking about doing thousands a year. That’s just nuts and one of the amazing parts about sequencing that I love. Exponential growth is sexy science. And it’s supposed to be one of CG’s strengths. They just finished their first genome in the summer of 2008, and are now on schedule to finish 100 by the end of 2009. Current estimates of finishing 1000 by mid 2010, and 9000 more by the end of that year fit within the exponential growth curve. As MacArthur points out, most of these sequencing services will likely be purchased by researchers in genomic and cancer studies. So the demand is also there.

How can CG scale so quickly? By remaining inflexible but efficient. Their process doesn’t rely on making huge improvements in sequencing technology. Or finding a new sequencing technique. It comes down to streamlining the process. Stick to one task, human genome sequencing, miniaturize whenever possible, fewer reagents means lower costs, and build build build. You can bet a huge portion of that $45 million is going to expanding their facilities in Mountain View.

Who provides the cheap genomes is probably less important than the change it will create. While scientific research will undoubtedly benefit first, the public at large will likely become a dominant consumer. Genetic information is on the journey to becoming one of the most important sets of data someone can know about themselves, with insights into disease, aptitudes, and longevity. Give us the chance for cheap access to that info and you’ll never run out of customers. Just a little while longer, it’s bound to happen.