Only 2% of genomic material available for research comes from Africa, 54gene wants to change that


This post is by Jonathan Shieber from TechCrunch


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New advances in genetic mapping and manipulation hold the promise of reshaping medical treatments in the 21st century, but thanks to a lack of sufficient infrastructure and apparent scientific disregard, an entire continent is at risk of being left out.

Only 2% of genetic material used for pharmaceutical research comes from the African continent, while genetic data on caucasians makes up 90% of the data and samples available. This is despite the fact that Africans and people of African ancestry are more genetically diverse than all of the other populations in the world combined.

At the beginning of the last century the American sociologist and scholar W. E. B. Dubois wrote, “the problem of the Twentieth Century is the problem of the color-line”, and as the twenty first century dawns, Abasi Ene-Obong, the founder of 54gene, is trying to make sure that the color line doesn’t circumscribe the ability

Abasi and team

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A new lawsuit involving Stanford and Sequoia Capital highlights fights to come over cell-free DNA testing


This post is by Connie Loizos from TechCrunch


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This morning, a publicly traded transplant diagnostics company called CareDx, along with Stanford University, sued another publicly traded genetic testing company, Natera, for patent infringement.

Much appears to be at stake and it all centers on cell-free DNA testing, a type of technology that has already been at the crux of numerous lawsuits and looks poised to play center stage again in future corporate battles.

Loosely defined, cell-free DNA (or cfDNA) technology involves blood tests that enables physicians to understand what’s happening in someone’s body. They’re not looking at his or her red or white blood cells (thus the “cell free” part) but at plasma, which carries pieces of broken-up DNA, among other things.

Companies like newly public Guardant Health are using it to try to ensure that cancer patients receive the right drugs and ultimately, they hope, detect cancer earlier than before. Prenatal cfDNA screening has meanwhile

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XGenomes is bringing DNA sequencing to the masses


This post is by Jonathan Shieber from TechCrunch


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As healthcare moves toward genetically tailored treatments, one of the biggest hurdles to truly personalized medicine is the lack of fast, low-cost genetic testing.

And few people are more familiar with the problems of today’s genetic diagnostics tools than Kalim Mir, the 52-year-old founder of XGenomes, who has spent his entire professional career studying the human genome.

Ultimately genomics is going to be the foundation for healthcare,” says Mir. “For that we need to move toward a sequencing of populations.” And population-scale gene sequencing is something that current techniques are unable to achieve. 

“If we’re talking about population scale sequencing with millions of people we just don’t have the throughput,” Mir says.

That’s why he started XGenomes, which is presenting as part of the latest batch of Y Combinator companies next week.

A visiting scientist in Harvard Medical School’s Department of Genetics, Mir worked with the

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Nutrigene wants to personalize your vitamins using your genetic code


This post is by Sarah Buhr from TechCrunch


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Vitamins are proving to be a lucrative industry in the United States. Just last year vitamin sales pulled in roughly $37 billion for the U.S. economy. That’s up from $28 billion in 2010. To cash in on this growing market, several startups have popped up in the last few years — including Nutrigene, a startup combining the vitamin business with another lucrative avenue of revenue in consumer DNA analysis.

Nutrigene believes your genes may hold the secret to what you might be missing in your diet. The company will send you tailor-made liquid vitamin supplements based on a lifestyle quiz and your DNA. You get your analysis by filling out an assessment on the startup’s website, choosing a recommended package such as “essentials,” “improve performance” or “optimize gut health.” After that you can also choose to upload your DNA profile from 23andMe, then Nutrigene will send you

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Figuring out what comes after gene sequencing in China


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biotech-ardent-biomed-daan-gene-wondfo-illumina-3 In recent years, a crop of companies have emerged that are using genomic sequencing to detect diseases in order to prevent the negative outcome of those diseases. It’s led to a budding ecosystem of startups that are crunching the data, as well as the cost of that sequencing coming down. But while we’re at the stage of getting the cost of genomic sequencing down and making it… Read More

Trace Genomics launches a 23andMe for farms, raises $4 million to improve the world’s food supply


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farms A San Francisco startup called Trace Genomics wants to help farmers diagnose and improve the health of the soil where they want to raise crops before it’s harvest time and too late to change course.
So the startup has developed a soil testing kit and “pathogen panel,” that tells the growers of high-value crops, like berries or lettuce, whether or not their soil has harmful… Read More

Genomic sequencing could help cure cancer, but first we must manage the data


This post is by Kif Leswing from Gigaom


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The field of genomics is on the precipice of bringing real, tangible benefits to people worldwide, but we need to figure out how to handle all the data it produces, said Francis deSouza, president of Illumina, at Gigaom’s Structure conference in San Francisco on Thursday.

DeSouza pointed out cancer as a problem area where genomic research could lead to big jumps in treatment efficacy. “We classify cancer by where it shows up, instead of the genetic profile of the cancer,”  deSouza said. “That is a primitive approach to the problem.”

DeSouza would recommend a full sequence of both the tumor and the patient as a first step to anyone unlucky enough to be diagnosed with cancer in 2014. A genomic researcher at Washington University in St. Louis, Lukas Wartman, did just that a few years ago when he discovered an off-label use for an existing drug which helped push his acute lymphoblastic leukemia into remission.

These advances are becoming possible because of the rapid decrease in cost associated with sequencing. When the first human genome was sequenced in 2003, the total cost was close to $3 billion. Now a full sequence is as inexpensive as $1000. There’s a lot of technological innovation that has helped drive that price down — advances in molecular biology, optics and semiconductors among others — but as prices decrease, it leads to a lot of data that needs to be secured and aggregated. “One gram of DNA contains two petabytes of info. Just massive, massive amounts of data,” deSouza said.

Not only is there a lot of data, but that data needs to be secured. Currently, the hospital or foundation that does the sequencing owns it. This brings up important questions: Who is encrypting it? Who is protecting it?  “I should own my own genomic data, I feel,” deSouza said. “You want it anonymized, but available.”

But allowing patients to lock down their own data could end up being a tragedy: genomic data is most useful in aggregate, as to pick out trends in certain populations and demographics. Currently, when a study slightly changes its scope, it often has to ask for consent from all the providers of data once again, which ends up being a headache. “We need a consent infrastructure allowing the use of this data,” deSouza said. “Currently consent is very specifically granted, and new studies might need to regain consent.”

If genomics figures out its massive data problems, it could lead to a major revolution in the way we treat cancer.

Photo by Jakub Mosur

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Want the latest on what’s hot in IT (and IoT) infrastructure? Listen up.


This post is by Barb Darrow from Gigaom


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What are Twitter and Facebook doing to build the infrastructure they’ll need for their next-generation services? What sort of foundations are Amazon, Microsoft, Google designing to support the startups of the future? And, finally, what does the current flock of promising new companies like Illumina, which proposes to bring genome processing to the masses, and Dropcam, which ingests more video per minute than YouTube, need to see in infrastructure to fuel their ambitions?

Speakers: Jean Yang - Ph.D. Candidate, MIT CSAIL

Speakers:<br />Jean Yang – Ph.D. Candidate, MIT CSAIL

That’s what Stacey Higginbotham, Derrick Harris and I discuss on this week’s show as we preview Structure which kicks off next Wednesday  and where executives from all those companies will be on hand to talk aobut how tomorrow’s infrastructure needs to grow and evolve to support the massive workloads generated by the Internet of Things.

So take a listen and remember to check out the big show in San Francisco next week.

 

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IBM’s Lance Crosby: to glimpse the future of cloud, check out the banking industry 

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Heroku CEO on why two PaaSes are better than one. No really!

OpenStack must be growing up if we’re talking indemnification for goodness sake

 

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Computer vision and genomes: Exploring next-generation cloud workloads


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Dropcam, the Wi-Fi connected video camera, ingests more video per minute than YouTube according to CEO Greg Duffy, whose startup hosts all that content on Amazon’s cloud. That’s a lot of movies starring empty homes, but video in the cloud may be soon overtaken by genomic data if Francis DeSouza, the president of Illumina is to be believed. Both men will be speaking at our Structure conference June 18 and 19 about what cloud providers and equipment vendors need to do to prep the cloud for next generation workloads.

Greg Duffy, CEO of Dropcam

Greg Duffy, CEO of Dropcam

Duffy, who still codes for his site and is responsible for architecting the Dropcam cloud service, isn’t just hosting video in AWS. He’s also running computer visualization algorithms to support an upcoming product that will recognize the people in customer videos. It will handle the analysis in real-time, requiring access to both compute, data and storage in a scenario that Duffy will explain in depth onstage before the providers of the top public clouds.

Francis DeSouza, president at Illumina

Francis DeSouza, president at Illumina

If online video doesn’t inspire you, DeSouza’s talk about how lowering the cost of decoding the humane genome to $1,000 is going to change the world of medicine. As the former head of products at Symantec De Souza has a foot in both genomic and tech worlds. He believes the ease of translating genomes not only can offer customized medicine and possibly cures for cancers, but will also create a lot of data. That, in turn, will require new computational models to store and parse all that data. DeSouza believes that data will be stored in the cloud, and he has some ideas on how providers need to think about their offerings to make genomics an economical workload.

So head over to San Francisco on June 18 and 19 for Structure, not only to hear about the big shifts in infrastructure from major cloud providers, vendors and CIOs, but also to understand what you should be building next to ensure that computing keeps up with the workloads we’ll be creating in the next three to five years. I’ll see you there.

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This is real innovation: Illumina’s new machine could slash cost of sequencing your genome to $1,000


This post is by Christina Farr from VentureBeat


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This is real innovation: Illumina’s new machine could slash cost of sequencing your genome to $1,000
Illumina

The HiSeq X sequencing machine

The race for the $1,000 genome has been won.

Biotech firm Illumina sent shockwaves through the biotech industry this week by unveiling a new machine that it says can sequence a full human genome for $1,000. Until Illumina came along, it cost approximately $5,000 to sequence the human genome, a price that puts the service out of range for many patients.

Illumina’s supercomputing machine, which is a combination of ten machines working together and is called the “HiSeq X Ten,” is available to purchase at a starting price of $10 million. This is too expensive for most labs, but three of these machines have been acquired by Macrogen, The Harvard-MIT Broad Institute in Cambridge, and the Garvan Institute of Medical Research in Australia.

The HiSeq X Ten can partially sequence five human genomes per day. The company says it can completely sequence 16 human genomes within three days. According to Illumina chief executive Jay Flatley, the HiSeq X Ten can sequence human genomes accurately enough to reliably identify DNA variants 10 times faster than its predecessor.

The new machine is designed to sequence thousands of genomes each year for a $1,000 a pop. At that price, an institution could expect to recoup the cost of purchasing the HiSeq X Ten in about five years, exclusive of operating costs. That may be a reasonable proposition for providers that can afford to pay the initial purchasing fee. However, while the $10 million price tag takes into account the cost of the machines and the chemicals needed to do the sequencing, it doesn’t account for overhead, such as power, data storage, and labor.

Full-genome sequencing is much different from the DNA sequencing offered by commercial outfits like 23andMe, which focuses on identifying short genetic sequences within a person’s genome, not on sequencing the entire genome.

The first crop of customers purchasing Illumina’s machine might opt to charge patients more than $1,000. However, by keeping the price tag low, they should be able to reach a mass market who will pay out of pocket to sequence their whole genome for the purposes of medical testing.

At the J.P. Morgan Healthcare Conference, Illumina also unveiled a desktop-sized, $250,000 machine called the NextSeq 500, which is designed for the lab and can handle just one genome at a time. It can only handle some of the most common sequencing operations. The company said this machine would reach customers in March.

Outpacing Moore’s Law

Less than a decade ago, it cost over $250,000 to sequence a single human genome. The industry is moving so quickly (it has outpaced the famous Moore’s Law) that the X Prize Foundation recently cancelled its $10 million competition. X Prize organizers realized that geneticists did not require the financial incentive to innovate in the field of next generation sequencing.

cost_per_genome_apr

Source: National Human Genome Research Institute

With its new machine, Illumina has outpaced its chief rival, Life Technologies. Life announced a year ago that it would be capable of sequencing the code of a human cell for $1,000. However, this announcement proved premature, as technical glitches prevented the company from actually selling its own machine. That machine’s price was set at $149,000.

“The HiSeq X Ten should give us the ability to analyze complete genomic information from huge sample populations,” said Eric Lander, founding director of the Broad Institute and one of the world’s leading geneticists, in a statement. “Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”

Scientists have pointed out to Forbes that it will take some time before consumers can buy their genome for $1,000. Another grievance is that Illumina hasn’t factored labor costs into its price. In addition, storing raw data will set back customers tens of thousands of dollars. Computational scientist Glenn K. Lockwood estimates that the cost of being able to store four weeks worth of HiSeq X 10 output will run about $60,000 in capital (this calculation is based on the best rate for purchasing high-performance parallel storage hardware at around $0.30 per gigabyte.)

That said, industry reactions have been largely positive. Merrilyn Datta, chief commercial officer for biomedical firm Definiens and a former marketing lead for Life Technologies, said this announcement will usher us into a new era of personalized medicine.

“You need to have extensive population correlations from the genes to really drive towards personalized medicine,” she said. “To get us to the next step, we really need more people to have their genome sequenced.” Today, only about 100,000 genomes have been sequenced.

Datta is optimistic that in the ten years, millions of babies will have their genomes sequenced at birth. With this drop in price, reimbursement won’t be such an obstacle for patients. The low price of genome sequencing means that many more people can afford to pay out of pocket.

Researchers will soon have access to exponentially more data to use in their analysis of how genetic variations manifest themselves in diseases.

Today, scientists have only discovered a small number of positive correlations between genetic mutations and a person’s likelihood of contracting certain diseases. In the near future, biotech firms will begin developing more accurate diagnostic tests and targeted drug therapies. Datta believes that oncologists will no longer rely on a “trial and error” approach to cancer treatment.

In the coming years, Illumina intends to diversify its hardware and continue to reduce the cost of its sequencing machine. The company is also investing in analytics tools to rapidly process genetic information.

With the launch of these new platforms, Illumina shares were up $11.13 to $136.16 Friday, a record high.

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The $1,000 genome could actually be here


This post is by Signe Brewster from Gigaom


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People want to know what their genes mean for their current and future health. And researchers want more people to reveal their genome because it helps them better understand the significance of DNA anomalies, helping to improve the analytics that make sense of a gene sequence.

Given that a full sequencing generally currently costs $10,000, and gene tests can be patented, most genetic tests are currently limited to a small assortment of interesting genes, which may or may not be actual health indicators. As a result, tests like 23andMe have been scrutinized for their accuracy.

Lowering the cost of full gene sequencing could spur more people to pursue one and, as a result, provide researchers with the data they need to sort out the real interesting genes. Illumina, a San Diego life science tool developer, released a sequencing machine today that it says is capable of bringing the price down to $1,000.

Illumina gene sequencing machine

“To figure out cancer, we need to sequence hundreds of thousands of cancer genomes, and this is the way to do it,” Illumina CEO Jay Flatley said at a San Francisco investors conference today, according to Businessweek. “This will be a blockbuster product.”

Dubbed the HiSeq X, each machine can sequence tens of thousands of genomes a year by handling more data at once. The higher yield is responsible for the potential price drop. The machine costs $1 million and will ship in the first quarter of 2014. Illumina also revealed a more modest $250,000 machine meant to fit in a lab that is available now.

The genetics industry set its sights on the $1,000 sequencing when the human genome was first mapped in the early 2000s. It’s not a surprise that a company is now stating they’ve hit the milestone; last year, an X Prize meant to encourage teams to develop cheaper genomes was canceled due to the incredibly fast pace at which the price was dropping.

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Genetics field opens up with California ruling that ‘natural phenomenon’ can’t be patented


This post is by Christina Farr from VentureBeat


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Genetics field opens up with California ruling that ‘natural phenomenon’ can’t be patented
DataBeat 2013

Dec. 4 – 5, 2013
Redwood City, CA

Early Bird Tickets on Sale

In June of this year, the Supreme Court ruled that human genes should not be patented, a decision that is already having enormous impact on the future of science, technology, and medicine.

This week, a District Court judge in California upheld the landmark ruling, and struck down a patent held by a San Diego-based diagnostics company called Sequenom. Sequenom offers a non-invasive genetic test for Down’s Syndrome, which pregnant women can take as early as 10 weeks.

Sequenom plans to appeal the decision to the Federal Circuit Court of Appeals. It was highly unexpected, and has caused shockwaves of disbelief in the scientific community. The judge, Susan Illston of the United States District Court in Northern California, ruled against Sequenom after a summary judgement, citing the Supreme Court case “Association for Molecular Pathology v. Myriad Genetics, Inc., 12-398.”

In both cases, the judge ruled that a “natural phenomenon” could not be patented.

Sequenom’s stock has taken a massive tumble since the news broke. Meanwhile, the company’s rivals, Verinata, Ariosa Diagnostics, and Natera, stand to benefit from the ruling. Fighting patents is an extremely expensive process, which costs most diagnostics companies millions of dollars in legal fees each quarter.

Bryan Roberts, a health-focused investment partner at Venrock, predicts that “real innovation will be patentable and rewarded” while patents on natural phemenona will not. Roberts is a leading investor in Ariosa Diagnostics, the San Jose, Calif. based company that filed suit against Sequenom in 2011.

The ruling “raises the bar to rely on intellectual property as a business defense,” said Roberts. “It will drive prices down [and support] the product that is both high quality and efficiently priced.”

It’s an important step for the scientific community at large. For years, researchers have argued that genetic patents will stunt progress, and stifle competition in the market.

“You should be able to give patients gene sequencing information that will benefit their health,” said human geneticist and entrepreneur Dr. Dietrich Stephan in a recent interview. “Patents may prevent that.”

Sequenom’s test is an alternative to Amniocentesis, which carries a risk of inducing a miscarriage. Sequenom had licensed intellectual property that showed the presence of fetal DNA in the mother’s blood.

If Sequenom does not win its appeal, “I don’t see how you can maintain a genetic diagnostic claim anymore,” Christopher Holman, a molecular biologist and professor of law at the University of Missouri, Kansas City told Science Magazine.

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