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Exclusive: Complete Genomics To Sequence A Million Genomes – CEO

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by Keith Kleiner on January 26th, 2010

“We Are A Data Company” Cliff Reid, CEO Complete Genomics

Dr. Cliff Reid, CEO Complete Genomics, Has A Master Plan To Sequence 1 Million Genomes!

Without a doubt the hottest company in the genomics sector right now is gene sequencing powerhouse Complete Genomics. In just the last four years the company has come out of nowhere to dominate the market for low cost sequencing of human genomes in large quantities. Although Complete Genomics is now slated to sequence an incredible 5,000 human genomes in 2010, this is nothing compared to what the company has in store for the years ahead.  Just days ago, in a Singularity Hub exclusive interview with Complete Genomics CEO Dr. Cliff Reid, we have learned that the company is now hoping to sequence 50,000 genomes in 2011 and a whopping 1 million genomes by 2014. Considering that by the end of 2009 only about 100 or so human genomes had ever been sequenced, most of them by – you guessed it – Complete Genomics, this represents an enormous shift in the industry. In the rest of this post I will share with you the juicy details from the interview, followed by the full video of our conversation at the end.

Although companies like 23andme or Illumina have been hogging much of the headlines in genomics recently, the real story may be that Complete Genomics is about to rewrite the game for the entire industry. Simply put, Complete Genomics is the first company to realize that sequencing human genomes is a brute force computational problem that is best overcome through large scale centralization.

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IBM Hypes DNA Transistor, Genomes for Less than $1000

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by Aaron Saenz on October 13th, 2009
The IBM device would read single strands of DNA as they passed through layers of a microchip.

The IBM device would read single strands of DNA as they passed through layers of a microchip.

Sequencing your genome is going to be such big business that everyone wants to get in on it, even if they aren’t ready. In a recent press release, IBM announced that it is working to create a microchip that will sequence DNA by running it through tiny ‘nanopores’. The DNA Transistor will be able to sequence the entire genome rapidly and for less than $1000. While a working prototype of the chip won’t be created for three more years, IBM thinks that the theory and computation behind the concept is sound. If ultimately successful, the computer giant would launch itself to the forefront of the genome sequencing field. For now though, the company is just pushing an idea, not a product. I love it when companies compete in a field, but IBM’s got years of hard work before it could be a genome sequencing competitor. A fact that makes their press release seem premature at best. Still, you should check out the admittedly cool PR video after the break.

The first human genome cost around three billion dollars to sequence. Today, Illumina is offering to do the same for $50,000 and Complete Genomics is looking to a $5000 price tag under certain conditions by the end of next year. But the big hurdle is $1000. At that point, sequencing a genome will become accessible to almost anyone, and could see wide spread adoption in health and medicine. Using genetic information, doctors could provide personalized health care that would target illnesses and choose treatments which best suit your body. Knowing more, we could live much longer.
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23andMe Leading Way to Democratized Disease Research

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by Aaron Saenz on August 17th, 2009

Here’s a riddle: What do you get when you mix American Idol with genetic testing for disease? The 23andMe research revolution. The same company that brought you affordable testing for common genetic markers has begun a new initiative to lend insight into genetic causes for common illnesses. Starting this summer, 23andMe members can vote for which diseases they think should be researched, and submit their genetic information as patients for the studies. Co-founders Linda Avey and Anne Wojcicki want you to join, vote, and send in your spit to help find cures. Watch their video after the break.

news_pd23andMe is a personal genetics firm that allows individuals to test their genome for key genetic markers. These markers take the form of SNPs (pronounced ’snips’), single nucleotide polymorphisms. A standard test that grants you access to information about ancestry, health, and traits costs you about $399. A research version is available for just $99. Basically all you do for either option is spit in a special tube and then mail it to the company.

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MIT is Organizing New Genetic Parts

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by Aaron Saenz on July 22nd, 2009

If you want to check out a book you go to the library. If you want to get a copy of the latest DNA, you go to MIT’s Registry of Standard Biological Parts. Started in 2003, the Registry has developed from a few stored genes to a collection of more than 3000 genetic parts that can be spliced into DNA to modify an existing organism. Need your bacteria to glow in the dark? Want yeast to produce a banana smell? The Registry might have what you need. It’s a candy shop for synthetic biologists and it’s changing what genetic engineering can accomplish.

MIT is helping synthetic biologists by providing the Registry of Standard biological Parts.

MIT is helping synthetic biologists by providing the Registry of Standard biological Parts.

While there are some costs associated with getting genes from the Registry, it’s not really a store. The registered segments of DNA are stored and shipped on a looser “get some, give some” exchange. Those users who request and utilize these biological parts are expected to share some of their results and innovations with everyone else. Sort of the biological equivalent of the take-a-penny-leave-a-penny tray at the corner store.

Before you start sending your genetic requests to MIT, I should point out that the Registry is for established scientists only. Do-it-yourself biologists need not apply. Most of those who receive parts are from academic labs, and/or forming a team to participate in iGEM, MIT’s annual genetic engineering competition. Still, the wide range of users gives this registry a scope that promises to catapult synthetic biology into its next phase of evolution.

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The Genetically Modified Food You Eat

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by Drew Halley on July 15th, 2009

Would you eat food that was genetically modified? You probably already have.

gmfood-leadpicScientists have been tinkering with the DNA of commercial food for nearly two decades, and they’ve covered most of the food pyramid. Modern soybeans, cotton, tomatoes, potatoes, corn, rice, and sugarcane have all had their genomes tweaked to serve the human species. Most of the genetically modified (GM) food in the world sprouts on American soil, but the practice is growing in Argentina, Canada, Brazil, and China, to name just a few.

Maybe the strangest part of GM food is that most people have no idea they eat it. The majority of Americans don’t know how it’s done, why it’s done, how it’s regulated, or why they should care. The Grocery Manufacturers of America estimates that 70-75% of all processed foods in your local grocery store contain ingredients from GM plants. Genetically modified food: it’s what’s for dinner.

Harder, Faster, Better, Stronger

So why remix food genomes? It depends. Some GM food is designed to resist diseases, insect attacks, or herbicides regularly used in modern industrial agriculture. Plants can be made hardier and more tolerant to environmental stress such as drought or irregular weather. Crops can be made to mature faster (decreasing their growing time) and rot slower (increasing shelf-life). GM food can also produce higher crop yields, and be engineered to lack unwanted toxins (such as allergens).

But that’s not all. Genetic modification is giving a new meaning to the phrase “super food”. Crops are being engineered to produce more nutrients, vitamins, and all that healthy stuff. Work is also underway to turn plants into little pharmaceutical factories, pumping out desired drugs… is “Pfizer Farm” trademarked yet? And (of course) GM foods are specially tweaked to please your taste buds, engineered to make every edible on your plate that much more appetizing.

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Artificial Life on the Horizon

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by Drew Halley on June 24th, 2009

Admit it: you wouldn’t mind winning a Nobel Prize. Well here’s a science project for you: reverse global warming, solve the world’s energy crisis, and pave the way for breakthrough antibiotics and vaccines… all in one fell swoop. The modest task before you? Create the world’s first synthetic life form, and make it dance.

creation-of-adamNow for the bad news. You’ve got competition. Some of the best scientists across the globe are chasing the holy grail of biology, and they’re making some serious headway. The prospect of man-made life is becoming less a question of if, and more a question of when. But can gene engineering really save the world? Can it destroy it?

Welcome to the wonderful world of synthetic genomics.

The Idea

The first step to cooking up your own life form is to understand the language it’s written in: DNA. The genetic revolution of the past few decades has allowed scientists to sequence whole genomes, from fruit flies and rats to our very own species. Once the genomes are mapped, the task becomes making a synthetic copy, A by T by C by G. DNA gets stitched together using a combination of different lab techniques, with the final goal of building a whole genome. Different research teams have taken different approaches, and the race is on to see who succeeds first.

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Google, Papa Brin Step In For 23andme

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by Keith Kleiner on June 19th, 2009

23andme-brin-googleBoth Google and Sergey Brin have made an investment in personal genetics company 23andme in a series B funding round.  This comes on top of a previous investment from both Google and Brin in the series A round in 2007.  On the one hand, this is pretty sketchy.  It is a serious conflict of interest, as Brin is married to 23andme co-founder Anne Wojcicki.  On the other hand, you gotta hand it to Google and Brin for sinking their hands into yet another initiative that is trying to make the world a better place.  Overall though, I wish they had found a less controversial way of doing so.

Brin appears to have sunk $10 million into this series B round, while Google has put in $2.6 million.  As if the financial investments weren’t controversial enough, apparently Google and 23andme have entered into some sort of leasing agreement, though the details of this agreement are not available.

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Another Step in Genetic Engineering: Glowing Primates

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by Andrew Kessel on June 3rd, 2009

The primate family tree seems to have gotten a bit brighter lately.  Earlier, Singularity Hub reported on Ruby Puppy, the genetically engineered glowing dog, and now the puppy has been one-upped by a team of Japanese scientists who have created a gaggle of glowing marmosets.  Monkeys are just steps away from humans on the evolutionary ladder.  Does that mean that we’ll soon be glowing too?

Glowing Primates: Terrible at Flashlight Tag

Glowing Primates: Terrible at Flashlight Tag (credit Erika Sasaki - Hideyuki Okano / AP)

The marmosets were given the glowing gene in much the same way as Ruby Puppy but, instead of glowing red like the transgenic dog, the primates glow green.  The genetic mutation of these marmosets holds many of the same implications as a glowing dog, including the potential study of many human diseases as well as the ethical dilemmas that come with the territory.  The marmoset itself was targeted for study because it reaches sexual maturity faster and has more offspring, allowing experiments to take less time from breeding to data collection.

Aside from the usual perks of having a genetically engineered pet/lab experiment, the plethora of scientists credited with writing the report believe that this is the first time that the offspring of genetically engineered primates are able to inherit the new trait.  This was proven when three out of the four second-generation marmosets bred in the experiment were capable of glowing under ultraviolet light.  The presence of this gene in the sperm and egg cells of the marmoset could not only lower the cost of each animal, but also increase the yield.  Whereas only a few marmosets matured to adulthood from the 900 original embryos, tradition breeding could allow for a much better survival rate.

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Now Recruiting: The Personal Genome Project

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by Andrew Kessel on May 20th, 2009

Everybody has a database: staffers, bankers, law enforcers and now geneticists, too.  The PGP is not a college fraternity (rush Lambda Lambda Lambda) but a new database of mapped genomes and medical records called the Personal Genome Project.  It started with just ten people but now it is poised to turn into medical who’s-who of genetic abnormalities.  Finally, there’s a definitive way to figure out if dinner guests are diabetic without having to ask that awkward question.

dna_double_helix

More Twisted than the End of an M. Night Shyamalan Movie

The good folks at the Personal Genome Project, founded by the legendary George Church, have gotten the go-ahead from its host institution, Harvard Medical School, to expand from 10 to 100,000 participants.  As a proof of concept, the PGP began with ten people, sharing every facet of their personal information from height and weight to tissue samples and photographs, all of whom allowed the coding region of their genomes to be mapped and put on display online.  Now, the PGP is hoping that it will be able to grow their free database and that scientists will start making connections between genetic sequences and medical conditions.  Already, the genomes are available for download via BitTorrent.

The opportunity presented by the PGP to foster knowledge about the human body is enormous.  As more people become part of the database, clearer links between certain genes, activities, risks and diseases may begin to emerge.  Such a project may one day allow doctors to, in a sense, pre-qualify certain patients for risks based on their genetic coding.  If a risk is known, then it can be either regularly checked and caught early or even treated before it becomes an issue.  This could not only potentially save lives, but it could also be a way to cut healthcare costs.  One could assume that small procedures and early detection are much cheaper to both patients and hospitals than a large and in-depth operation.

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Genetically Engineered Puppies Glow In The Dark

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by Andrew Kessel on May 13th, 2009

Dog training is poised to become much more interesting.  In addition to the usual tricks (sit, lay down, heel, look adorable), “glow” may soon be added to the repertoire.  A team at Seoul National University located in South Korea has successfully created a new breed of beagle capable of fluorescing under ultraviolet light (see video at the end of this post).  It sounds odd, but it certainly is a novel way to find Sparky: if he runs off, just head for the nearest glowing shrubbery.

glow_in_the-_dark_dog_fluoresce_gene

I Can Glow Red At Night, How About You?

Although some species can naturally create light (such as fireflies and some planktons), in recent years scientists have been keen to develop the trait within animals that do not glow on their own accord.  Genetically engineered luminescence is generally regarded as the first step in gene alteration, allowing scientists a clear indication of whether or not their experiment succeeded.  Fluorescent animals have been bred in the laboratory before, but this is believed to be the first instance of a dog being given the gene.

The transgenic canine named Ruby Puppy was cloned using a technique called retrovirus-mediated gene transfer.  This allows scientists to introduce a foreign gene into the host animal’s DNA.  The gene that was introduced into Ruby Puppy’s DNA was for the creation of a fluorescent protein that, upon contact with ultraviolet light, emits a red glow.  A genetically modified virus was used to inject the new genetic code directly into a stem cell nucleus.  That nucleus was then inserted into a de-nucleated egg cell and placed in a surrogate mother.  Give it a little time and voila: an eating, sleeping, pooping, glowing (literally) puppy.

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Viruses – Batteries Now Included

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by Aaron Saenz on May 7th, 2009

next-jetsons-battery2lg

Microscopic workers of the world unite! There’s a trend floating around laboratories: designing tiny mechanisms that can build other devices from the atomic level up. The concept isn’t new, but we’re finally seeing some real progress in the field. When most people think of these tiny workers, there’s just one word on their mind: nanobots. But we’re here to tell you that the playing field is much wider than that. Biology is getting into the micro-worker game.

Virus-Built Batteries from MIT

Some could give you a cold, the Swine Flu, or Ebola, but viruses may just end up being humanity’s best tool. Researchers at MIT have created the next generation of battery assembled using special genetically engineered viruses. These batteries are close to out-performing the lithium-ion standards used today, and will soon exceed them in scale and power. Better yet, the virus built batteries are green-energy — constructed without hazardous chemicals or waste. Who knew that viruses could help save our environment?

Of course, no virus comes out of the wild willing to make batteries. You have to rewire the little guys to become happy workers.

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Exponential Trends – What Are Your Favorites?

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by Keith Kleiner on May 5th, 2009

Over at Hacker News there was a discussion about our ebay genome story that I thought was cool enough to post below.  In the first part of the thread user davidmathers is talking about the cost to sequence an entire human genome (which we have written about many times).  As user Femur later points out, there are obviously many such trends, which of course is a foundational aspect of Kurzweil’s works.  Do you know of similar trends that are your favorites?  Let us know in the comments.  Just to break the ice, I will go first.  Check the comments!

genome_pricing_trends1

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