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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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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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Super Babies Reveal the Key to Strength Gene

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by Aaron Saenz on June 30th, 2009

It’s known as myostatin, but it might as well be called kryptonite, because it’s what keeps each of us feeling like Clark Kent. This protein tells your muscles when to stop growing, and in the last few years we’ve seen two babies born with a mutant gene that prevents them from producing enough myostatin. The result? Super Babies. And like any amazing mutation, scientists are studying it to see if, and how, we could all become as muscle bound as these tots.

Two super babies have the gene for rapid muscle growth.

Can a baby unlock the gene for strength?

The first super baby was born in Germany in 2004. Though his name was never released, pictures demonstrated that his young physique contained almost twice as much muscle as other infants. Look ahead to fall 2005 in Michigan, Mr. and Mrs. Hoekstra adopt a young boy named Liam. Soon he is growing muscle at an astounding rate. Hanging on rings in an iron cross position by 5 months, pull-ups by 9 months, Liam is the second super baby. His condition, now known as myostatin-related muscle hypertrophy, makes him hungry, lean, and strong. Check out his pic after the break.

With Liam, scientists had further proof that a genetic mutation could exist that causes a human to naturally build muscle. Without even trying, Liam has little to no body fat, can lift seven pound weights arms extended (he only weighs 30 lbs himself) and has a six-pack. Now nearly four, Liam is taking gymnastic lessons, but this is more of an outlet for his energy than an explanation for his physique. No doubts, it’s the lack of myostatin that’s helping him get ripped.

super-strength-babies

The Protein to End All Proteins

Blocking myostatin has been shown to have drastic effects in animals besides humans. Myostatin tests in labs have pumped up mice to Schwarzenegger proportions.

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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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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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Complete Genomics – New Information About the Hottest Company in Genetic Sequencing

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by Keith Kleiner on February 10th, 2009

Daniel MacArthur has once again delivered some of the best information on the net about Complete Genomics, the company that is lighting a fire in the genomics community with its claim that it will sequence human genomes for $5,000 apiece in the middle of 2009.  Nature News also has a revealing article with further information.  Daniel spoke directly with Complete’s CEO Clifford Reid and CSO Rade Drmanac as a followup to the Complete Genomics presentation given at AGBT last week.  Daniel’s report is highly technical, so here is a summary for those that don’t want to sift through the myriad details:

Complete Genomics uses a sequencing technology called “short read”, which means that they decode the DNA in small segments and then stitch all of these small segments together to make the whole sequence.  This same technique is used by many of Complete’s competitors, and is plagued with the problem that errors are sometimes introduced into the sequence during the stitching process.  MacArthur notes that Complete Genomics’ current error rate of 0.1%, which is reasonable by current industry standards, would result in 300,000 errors in a 3 billion base pair whole human genome.

So what does this mean?  It means that although Complete Genomics’ ability to accurately decode genomes seems to be within the range of its competitors, it falls short of the 100% accuracy that is ultimately desired.  The upshot is that the coming revolution in genomics in the next few years will be somewhat limited by sequencing that is not 100% accurate.  There is still a great deal of work that can be done on genomes that are 99.9% accurate and great scientific progress will undoubtedly result.  Ideally though, in the next ten years the technology will improve to true 100% accuracy, at which point further doors will be opened in the field of genetic analysis.

MacArthur reminds us that Complete Genomics is committed to only sequencing human genomes, even though genomes of monkeys and other organisms could easily be performed.  The reason:

“focusing only on large-scale human -omics will allow Complete to avoid the worst complexities of the service model (i.e. receiving many types of sample that require processing in many different ways), but still focus on the area where the market is the strongest.”

“Reid says that the goal of Complete is to create “a stream-lined factory” producing complete human genomes; by focusing on just one application (unlike any other genome facility) they can hone this process down to the point that they can do it cheaper and better than anyone else.”

Our interpretation: Complete Genomics is smart!  These guys are carving out the position as the company to go to for human genomic sequencing.  The genomics field is competitive and wide.  By narrowing their focus to human only genome sequencing, Complete Genomics is simplifying their business model and further solidifying their position in the lucrative market for human genome sequencing.

Image: source

Complete Genomics Stuns Genomics Community, Confirms Industry Shattering Capability

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by Keith Kleiner on February 6th, 2009

Daniel MacArthur at Genetic Future has just completed his post covering the Advances in Genome Biology and Technology (AGBT) conference, where an intense battle is taking place as genetic sequencing companies seek to position themselves in the race to bring fast, cheap genetic sequencing to the masses.  The verdict: Complete Genomics has stunned the genomics community by confirming it is on track to blow past the competition.

When reading Daniel’s post you can feel the intensity at the conference as companies at AGBT fight for top bragging rights to deliver the fastest and cheapest genome sequencing capability to the world.  The stakes are extremely high: literally billions of dollars in sales await the company that can dominate in the delivery of affordable, rapid, whole genome sequencing to every human on the planet.

The intensity at the conference reached a climax when Clifford Reid, the CEO of Complete Genomics, delivered his much anticipated presentation to confirm whether or not the company’s industry shattering claim of $5000 sequencing of a whole human genome by mid-2009 was really true.  According to MacArthur, Complete Genomics did not disappoint, and hence a company that nobody had even heard of until it came out of stealth mode in October 2008 now appears to have cemented its position solidly at the front of this high stakes race.

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Another Step in the March Towards Designer Babies

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by Keith Kleiner on January 10th, 2009

pgd genetic screeningThe Herald and other major outlets are reporting that the “UK’s first genetically selected baby has been born.”

This sensational claim is misleading since the practice of genetically screening embryos, as was done in this case, has been commonplace for over a decade now.  Such screening, called PGD,  is almost exclusively used to look for debilitating characteristics in the embryo, such as cystic fibrosis.  What is unique about this particular baby is that the embryo was screened not for a true debilitating disease, but rather for a gene that could potentially be harmful later in the child’s life.  The gene, called BRCA1, increases the risk of breast cancer in females by as much as seven times.

This genetically screened baby represents a decisive step down the slippery slope of screening embryos not only for genetic defects that are seriously debilitating, but also for genetic traits that are simply risky or undesirable.  Future “parents to be” in the UK and elsewhere may use this as a precedent to support the screening of all sorts of other traits.  Screening for genes that are completely unrelated to disease, such as height or intelligence, is therefore a step closer to reality.  Selection of the sex of an embryo has long been a widespread practice, serving as another precedent for more relaxed limitations on embryo screening.

For those that want to know more about the field of pre-screening embryos a detailed explanation follows:

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Archon X Prize Offers $10 million to Revolutionize Gene Sequencing

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by Keith Kleiner on July 25th, 2008

Many people have heard of the original X Prize, which was a $10 million prize given to the first company that could build a spacecraft capable of carrying three people to 100 kilometers above the earth’s surface, twice within two weeks. Many people are unaware that this original X Prize has since spawned an entire family of other $10 million X Prize challenges that are ongoing today.

The Archon X Prize is offering $10 million “to the first Team that can build a device and use it to sequence 100
human genomes within 10 days or less, with an accuracy of no more than
one error in every 100,000 bases sequenced, with sequences accurately
covering at least 98% of the genome, and at a recurring cost of no more
than $10,000 per genome.”

The Archon X Prize will accelerate mankind’s efforts to achieve affordable and fast sequencing and analysis of the DNA for every individual on the planet. Once this capability is a reality it will unleash a revolution in our ability to make people healthier, fight disease, and even improve people beyond their original genetic and biological bodies.

Picture from Archon X Prize Website

deCODEme video tour

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by Keith Kleiner on July 23rd, 2008

deCODEme offers an excellent video tour on their website that demonstrates what they can do with your dna. This video will be enlightening for those who are new to genetics and the amazing power that personalized dna analysis will offer all of us in the coming years. deCODEme offers four distinct tools for analyzing dna:

1. Risk analysis for various diseases based on your genes

2. Assessment of physical attributes such as hair color

3. Detailed assessment of ancestory (did your grandparents really come from New Zealand

4. Comparison of your DNA to other people in the database, such as family members or famous people

Personal Genome Project (PGP) Highlighted by Wired

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by Keith Kleiner on July 23rd, 2008

Wired came out with a pretty nice article on the Personal Genome Project (PGP) with a focus on the project’s founder, George Church. The PGP will be collecting and analyzing the DNA of 100,000 volunteers. Each volunteer must fill out an exhaustive survey that will tally information about them such as head circumference, ability to roll heir tongues, exposure to power lines, dietary preferences, medical history, and much more. This data will be entered into a database along with their genetic data, creating a vast trove of data that can be cross referenced in countless ways. From the article:

“This phenotype data will be integrated with a volunteer’s genomic
information, then combined with statistics from all the other subjects
to create a potent database ripe for interrogation. In contrast to the
heavy lifting that genetic research requires now — each study starts
from scratch with a new hypothesis and a fresh crop of subjects,
consent forms, and tissue samples — the PGP will automate the research
process. Scientists will simply choose a category of phenotype and a
possible genetic correlation, and statistically significant
associations should flow out of the data like honey from a hive. A
genetic predisposition for colon cancer, for instance, might be found
to lead to disease only in connection with a diet high in barbecued
foods, or a certain form of heart disease might be associated with a
particular gene and exposure to a particular virus. Genomic discovery
won’t be a research problem anymore. It’ll be a search function. (This
helps explain why Google, among others, has donated to the project).“

One of the fantastic features of the PGP is that all of the data will be completely open to the public. By opening the data to the public researchers across the globe will be empowered to sift through the data and further advance the field of genetics for all of humanity. From the article:

“If the PGP were simply an exercise in breaking down 100,000 individuals
into data streams, it would be ambitious enough. But the project takes
one further, truly radical step: In accordance with Church’s principle
of openness, all the material will be accessible to any researcher (or
lurker) who wants to plunder thousands of details from people’s lives.
Even the tissue banks will be largely accessible. After Church’s lab
transforms the skin into stem cells, those new cell lines — which have
been in notoriously short supply despite their scientific promise —
will be open to outside researchers. This is a significant divergence
from most biobanks, which typically guard their materials like holy
relics and severely restrict access.”

If you want to be a volunteer to donate your genetic information (I did!) to the project all you have to do is sign up at the PGP website here.

Picture from the wired article

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