Sequoia-backed Whole Biome wants to heal your gut with medical-grade probiotics

This post is by Sarah Buhr from TechCrunch

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Whole Biome has pulled in $35 million in Series B financing from a list of investing titans, including Sequoia, Khosla, True Ventures, the Mayo Foundation and AME Ventues — just to name a few. The goal? to heal what ails you using microscopic bugs.

Medical science has caught on in the last few years about the importance of gut health using these bugs (also known as probiotics). Now startups are pitching in using venture money to come up with new and novel ideas.

“We’re at a unique point in time as the field of microbiome biology converges with enabling cutting-edge technologies and bioinformatics that will open up a whole new world of innovative health products,” said Colleen Cutcliffe, Whole Biome’s co-founder and chief executive officer.

Cutliffe, who hails from DNA sequencing company Pacific Biosciences, along with her partners Jim Bullard and John Eid, built a platform able to compute information

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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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Sophia Genetics bags $77M Series E, with 850+ hospitals signed up to its “data-driven medicine”

This post is by Natasha Lomas from TechCrunch

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Another sizeable cash injection for big data biotech: Sophia Genetics has announced a $77M Series E funding round, bringing its total raised to $140M since the business was founded back in 2011.

The company, which applies AI to DNA sequencing to enable what it dubs “data-driven medicine”, last closed a $30M Series D in fall 2017.

The Series E was led by Generation Investment Management . Also investing: European private equity firm, Idinvest Partners. Existing investors, including Balderton Capital and Alychlo, also participated in the round.

When we last spoke to Sophia Genetics it had around 350 hospitals linked via its SaaS platform, and was then adding around 10 new hospitals per month.

Now it says its Sophia AI platform is being used by more than 850 hospitals across 77 countries, and it claims to have supported the diagnosis of more than 300,000 patients.

The basic idea is to improve diagnoses by

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23andMe might soon offer a more comprehensive $749 DNA service

This post is by Sarah Buhr from TechCrunch

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23andMe is testing a $749 “premium” service for deeper health insights, according to several customers who saw a test page for the new product and posted about it on Reddit.

First spotted by CNBC, the company served up a test web page to several customers telling them about a service that would allow them to look at their “whole genome data.” However, when they clicked on the link provided, nothing happened. A few Redditors even posited the notification may have been a mistake as the link led nowhere.

But, according to the company, there’s no error here. 23andMe later confirmed to TechCrunch it sent out a test page to some customers to “gauge interest” in such a product. However, there’s “nothing planned” at this time for such a service, according to a 23andMe spokesperson.

The consumer DNA company charges $299 for its highest package right now, and

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Guardant Health takes another $50M for ‘liquid biopsy’ cancer test

This post is by Mark Sullivan from VentureBeat

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Above: Guardant co-founders Michael Wiley, Helmy Eltoukhy and Amir Ali Talasaz (L-R)

Health care is just now starting to effectively use information from the human genome to diagnose and treat disease. Nowhere is this more crucial than in the treatment of cancer, from which 7.6 million people in the U.S. die each year, and for which we spend $87 billion a year on treatment.

One of the reasons cancer is so difficult to treat is that current testing methods often don’t help doctors match specific cancers with effective drug treatments. And it’s a moving target — cancer cells are constantly changing, mutating.

Biopsy tests are crucial for showing the look and makeup of a tumor, but less good at giving doctors clues about which drugs the cancer might respond to. Biopsies are usually performed at the initial diagnosis, then often abandoned because of risk of infection and cost.

Enter Foster City, Calif.-based Guardant Health, which has developed a blood test that can detect changes in the genetic structure of cancer cells over time. The test has become known as a “liquid biopsy” because it requires no tissue excision, just a couple of teaspoons of blood from the patient.

The test captures dead genetic material that has sloughed off living cancer cells and entered the blood stream. Sequencing the DNA from that material can provide vital clues to the current state of the cancer, and to which drug therapies to try.

After an oncologist orders a test, Guardant sends out a small kit for taking the blood from the patient.

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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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The Gigaom interview: Why synthetic biology and the Netflix model are the future of medicine

This post is by Signe Brewster from Gigaom

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Look inside nearly any medicine cabinet in the U.S. and there will be a few bottles of prescription pills. They might be blue, white, round or square, but their development has followed the same pattern for decades: One of the few gigantic pharmaceutical companies that have come to dominate the industry pours millions, or even billions, of dollars into designing and getting a drug approved. Then the same pill is prescribed to every single person.

Molecular biologist and futurist Andrew Hessel doesn’t see that model lasting for much longer. He envisions a world in which every individual receives pharmaceutical drugs perfectly formulated to their genetic and medical needs for a fraction of what treatment would currently cost.

Photo courtesy of Andrew Hessel.

Photo courtesy of Andrew Hessel.

That future is on its way. Companies like Cambrian Genomics are making it possible for anyone to print strands of DNA. Autodesk’s bio/nano/programmable matter group, where Hessel is a distinguished researcher, is building design software known as “Project Cyborg” that will allow individuals to make 3D models of living matter. With the price of genetic sequencing dropping every year, he believes it won’t be long before anyone who wants to will be able to create with the building blocks that make up life itself. The future of health belongs to any startup that wants in on it, instead of just the Genentechs of the world.

“By learning to read and better understand the molecular world and self-assembling world, we have the opportunity to create really novel things using the same machinery that creates a plant or a cat, which is kind of fun,” Hessel said. “The genetic language is like the internet protocol: open, and so it’s a really fascinating language to learn. You learn one language and you can basically speak all of life, which is really cool. It’s my favorite programming language.”

What follows is an edited transcription of our conversation.

Signe Brewster: Why do you think individuals should have that kind of power?

Andrew Hessel: Every time I hear of a big challenge for the world, whether it’s, oh, how do you cure cancer or reduce our dependence on fossil fuels or clean up water or create anything sustainable, for me, it’s these technologies that are going to apply. If we can democratize their use and keep them open and transparent and make better tools for people to do the work, then we’re going to change the world in ways that are positive.

What would the pharmaceutical industry look like if the big companies were not in charge?

I’m driven by the idea that one day anyone with cancer, no matter what or where, (can get) a cheap genetic screen and some sort of molecular pathology … and have a computer generated medicine generated in hours. It’s not sold to them, it’s just available on subscription. Have you seen Dallas Buyers Club? Don’t sell the medicine, sell the subscription. The biggest change here is that you can make medicines for one person, so the blockbuster model no longer applies.

Autodesk's Project Cyborg will make it possible to use software to design 3D models of cells and other living matter. Photo courtesy of Autodesk.

Autodesk’s Project Cyborg will make it possible to use software to design 3D models of cells and other living matter. Photo courtesy of Autodesk.

Right now, that idea of having kind of a subscription model, a Netflix model, for drug making is really kind of mind blowing to the pharmaceutical companies, but I think its precisely where I would hope a design company like Autodesk would be positioned moving forward. We’re not trying to make tools that we’re going to sell to the 30 or 40 big (pharmaceutical companies) in the world. We’d like to make tools that allow everyone to start to create designs that truly solve some of the challenges in therapeutics and biotechnology in general.

What would it cost to make personalized medicine?

So you essentially have design tools and a printer for biological things. Like 3D printing, where you pay really just based on the amount of plastic you use, with biology, it’s essentially free. The real value is in the design.

The software tools have been improving over the years. The printers have gotten exponentially better in terms of making DNA. But I’m still limited and I still pay per base pair (a unit of DNA). Today it’s about 20 cents, but when I started it was about $20. But, again, if you write 10,000 base pairs, it’s still going to be a $2,000 synthesis. That’ll drop very quickly in time if Cambrian Genomics gets their laser printed DNA up to market. They say it’ll cost about $1.50. Ten years from now, it’s a fraction of a penny.

Cambrian Genomics wants to make it 10,000 times cheaper to synthesize DNA with a laser-based system. Photo courtesy of Cambrian Genomics.

Cambrian Genomics wants to make it 10,000 times cheaper to synthesize DNA with a laser-based system. Photo courtesy of Cambrian Genomics.

What can be accomplished at the current price?

Working with under 10,000 base pairs limits what I can practically make. The smallest genomes that have the most utility are actually viral genomes. About 30 years ago people started investigating cancer-fighting viruses. They are called oncolytic viruses because they actually break apart the cancer cell. It turns out a lot of weak viruses have these capabilities. And people have been engineering them to make them more specific and more functional for killing various cancers. So for the last few years, I’ve been largely going and exploring the tools, the researchers that have a lot of experience with viruses and the groups that are really keen to be able to engineer viral genomes quickly.

Autodesk's Project Cyborg will make it possible to use software to design 3D models of cells and other living matter. Photo courtesy of Autodesk.

Autodesk’s Project Cyborg will make it possible to use software to design 3D models of cells and other living matter. Photo courtesy of Autodesk.

And then the last couple of years, we seem to have hit the turning point. (A geneticist) was working with Novartis and they were able to make synthetic viruses as vaccines for the latest flus that were popping up around the world. They did it a few years early as an exercise, as a proof of concept, and then last year they actually got to test it with a new flu that appeared in China and demonstrated that within four days, without ever receiving a biological isolate of the virus, just an email of the viral genome, that they were able to make a vaccine and get it into production, which was really cool.

What’s an example of a company that is already leveraging available tools?

One of the applications you may have heard of is the Glowing Plant project. The fellow that did that, Antony Evans, is a friend of mine. … He had some great science behind it so that he knew it was technically possible and then raised the money through Kickstarter. … It was remarkable because he really opened up so many minds along the way by (finding an application) that wasn’t too scary, but right on the edge. It changed the discussion of what is a bio-tech company.

An early rendering of a glowing plant. Photo courtesy of the Glowing Plant Project.

An early rendering of a glowing plant. Photo courtesy of the Glowing Plant Project.

How do you think the public would react to this kind of shift?

There is a challenge in getting people beyond the automatic fear of the word virus or the engineering thereof. Certainly, the kind of idea that anyone is going to use these tools to make Ebola or smallpox is kind of laughable. I think we’ve figured out those blocks. But, the potentials for positive engineering are so dramatic, particularly when it comes to making medicines.

I think it’s going to take a generational change in the end. Younger people aren’t afraid of these technologies in the same way that people my age typically are. They grow up learning about molecular biology in school. So, on those fronts, they’re much more comfortable with the technology and also with the idea of sharing. You know, the privacy issues are very different for younger people today than for older people.



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Craig Venter on moving at the speed of light

This post is by Ryan Bethencourt from O'Reilly Radar - Insight, analysis, and research about emerging technologies

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Last week I had the privilege of speaking with J. Craig Venter at the Hillside Club in Berkeley, as part of the Bay Area Science Festival. Dr. Venter is a pioneer in biotech, from sequencing the Human Genome to creating a synthetic organism. It was an exciting moment for me, personally, as he thinks in terms of moonshots and succeeds often (through the failures).

Dr. Venter was in Berkeley as part of his tour to promote his new book, Life at the Speed of Light, which was inspired by Erwin Schroedinger’s question in 1943, “What is Life?” That question set Dr. Venter off on a life-long quest: first, to first take life apart and then rebuild it; to test his understanding of the machinery of life; and, ultimately, prove that he and humanity could rebuild life from scratch. The machinery of life still involves a lot of mystery, even for the simplest synthetic organisms. When when they were building the first synthetic organism, they focused on the minimum number of genes needed to create a viable life form. They found that they needed to include 50 genes with unknown functions. Without these genes, they couldn’t get the organism to “boot up.” They are clearly necessary, but why? What do they do? We still don’t know.

Venter also shared his thoughts on life on Mars. He thinks it is likely that life has existed on Mars, as Earth and Mars regularly exchange large amounts of particulate matter filled with bacteria. He’s planning a project to sequence Martian DNA (which he believes exists), with a plan to send the digital DNA sequence back to Earth for re-synthesis. His ultimate aim is to rebuild Martian bacteria on Earth for further study. Venter’s joy in exploring the domain of life rang through. With the rapidly decreasing costs of genetic sequencing and the tiny fraction of bacterial species that we have sequenced, anyone can now be an explorer. In every breath of air or every clump of dirt we grab, there are a multitude of new bacterial species waiting to be discovered.

At the end of Venter’s talk, I was able to ask him, “Where do you think the next moonshots in biotechnology will be?” His answer left me excited about the future. He said that the world’s population is rapidly rising; there are now seven billion people out there who desperately need access to medicine, food and energy. For humanity to live sustainability on this planet, we need revolutions in all of these areas, and those revolutions will be driven by new biotechnologies. His advice to any burgeoning scientist was that there is no area of human endeavor that will be left untouched by biotechnology, and all of these areas are fine areas to pursue.

As we’re all exploring, playing, biohacking DNA in front of computers, in labs, garages or at home, I look forward to the day when an innovation in biotechnology is just as likely to come from an industrial biotech lab in San Francisco as it is from the mind of a young biohacker in a home DIY Biolab. Venter left me with a sense of wonder and excitement for biotechnology and the future; I can’t wait to see what he sequences on Mars!

Using big data to cure cancer, Bina ushers in new era of medicine

This post is by Rebecca Grant from VentureBeat

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shutterstock_114067633Dr. Narges Bani Asadi says cancer is a genetic disease, and she is using technology to fight it.

Asadi is the founder and CEO of Bina, a healthcare startup working to make ‘personalized medicine’ a reality. Bina applies big data analytics to genomics, making it possible to sequence the human genome in a matter of hours rather than days or weeks.

Today, Bina launched its commercial product. The platform provides physicians, clinicians, and researchers with a detailed picture of a patient’s health. From there, they can make data-driven diagnoses and prescribe individualized courses of treatment.

“Medicine today is very experimental,” said founder and CEO Narges Bani Asadi in an interview with VentureBeat. “Before, there was a bottle neck to crunch the massive amount of genomic data. At Bina, we have created the fastest, most highly accurate, cost-efficient processing solution available in the market today. The next step is to incorporate this genomic data into medical use. Data-driven, information-based medicine is much more targeted. Personalizing therapies for different diseases means a longer and healthier quality of life for all humans.”

There are thousands of genetic disorders. In 2013, over 580,000 Americans are expected to die of cancer. One in 20 babies born in the U.S. is admitted into the neonatal intensive care unit, and 20 percent of infant deaths result from congenital or chromosomal defects. Technology can be used to curb these terrifying trends. Bina’s role is to bridge the gap between DNA sequencing technology and the diagnosticians and clinicians who can apply it to their practice.

“The study of genomics has largely been a research activity done in medical schools and universities,” said Mark Sutherland, Bina’s senior vice president of business development. “They could only look at a few samples at a time because it was too expensive or complicated to do it at scale. There is a tidal wave of data that has not been manageable or in a format physicians can understand. Now we are seeing an inflection point. Sequencing is a powerful way of looking across a broad spectrum to provide insight into the cause of certain diseases and conduct risk assessments, early detection, or predict the possibility of recurrence. It can also be used to find applicable therapies and customize treatments.”

Asadi said her team had to achieve innovations in every step of genetic processing in order to create a scaleable, marketable, effective solution. Bina’s platform includes a hardware box to collect DNA, advanced software to process the data, and applications to turn the data into actionable form. Whereas before a full genetic analysis took weeks or months and could cost thousands of dollars, Bina turns it around within hours for around $200 a sample.

The technology emerged out of Asadi’s PhD work at Stanford. She collaborated with professors from around the world to apply high performance computing and computer architecture to gain a new understanding of human health and disease. Bina was founded in 2011 by three professors from the University of California at Berkeley and Stanford. It is backed by venture funding, and pilot customers include the Stanford Genetics Department and Palo Alto Veteran Affairs Hospital.

Startups don’t often set out to cure cancer or prevent infant mortality. However, as technology continues to evolve and along with it, the healthcare industry, a medical system where diagnoses and treatments are based on hard data, where each and every individual is treated  as such, could be on the horizon.

Read a VentureBeat guest post by Dr. Asadi: The personalized medicine revolution is almost here.

[To learn more about the most transformative IT trends hitting health care, including big data, consider coming to HealthBeat, our event for health care executives and decision-makers, on May 20-21 in San Francisco.]

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