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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Healthcare by 2028 will be doctor-directed, patient-owned and powered by visual technologies


This post is by Jonathan Shieber from TechCrunch


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Visual assessment is critical to healthcare – whether that is a doctor peering down your throat as you say “ahhh” or an MRI of your brain. Since the X-ray was invented in 1895, medical imaging has evolved into many modalities that empower clinicians to see into and assess the human body.  Recent advances in visual sensors, computer vision and compute power are currently powering a new wave of innovation in legacy visual technologies(like the X-Ray and MRI) and sparking entirely new realms of medical practice, such as genomics.

Over the next 10 years, healthcare workflows will become mostly digitized, with wide swaths of personal data captured and computer vision, along with artificial

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


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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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George Church’s genetics on the blockchain startup just raised $4.3 million from Khosla


This post is by Sarah Buhr from TechCrunch


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Nebula Genomics, the startup that wants to put your whole genome on the blockchain, has announced the raise of $4.3 million in Series A from Khosla Ventures and other leading tech VC’s such as Arch Venture Partners, Fenbushi Capital, Mayfield, F-Prime Capital Partners, Great Point Ventures, Windham Venture Partners, Hemi Ventures, Mirae Asset, Hikma Ventures and Heartbeat Labs.

Nebula has also has forged a partnership with genome sequencing company Veritas Genetics.

Veritas was one of the first companies to sequence the entire human genome for less than $1,000 in 2015, later adding all that info to the touch of a button on your smartphone. Both Nebula and Veritas were cofounded by MIT professor and “godfather” of the Human Genome Project, George Church.

The partnership between the two companies will allow the Nebula marketplace, or the place where those consenting to share their genetic data can earn Nebula’s cryptocurrency called “Nebula

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Is America’s national security Facebook and Google’s problem?


This post is by Jonathan Shieber from TechCrunch


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Outrage that Facebook made the private data of over 87 million of its U.S. users available to the Trump campaign has stoked fears of big US-based technology companies are tracking our every move and misusing our personal data to manipulate us without adequate transparency, oversight, or regulation.

These legitimate concerns about the privacy threat these companies potentially pose must be

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Human sequencing pioneer George Church wants to give you the power to sell your DNA on the blockchain


This post is by Sarah Buhr from TechCrunch


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 The blockchain is the buzziest thing on the internet these days and now MIT professor and godfather of the Human Genome Project George Church wants to put your genes on it. His new startup Nebula Genomics plans to sequence your genome for less than $1,000 and then add your data to the blockchain through the purchase of a “Nebula Token.” Read More

The genomics intelligence revolution


This post is by Mahni Ghorashi,Gaurav Garg from TechCrunch


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Image: PASIEKA/SCIENCE PHOTO LIBRARY/Getty Images We’ve entered a new phase in the history of whole-genome sequencing; it has opened the door to understanding our entire world at the molecular level. With this intelligence, we’ll be able to understand, influence and optimize the way we interact with ourselves and our natural world. The promise of genomics is just beginning — we are at the leading edge of an intelligence… Read More

Genetics startup Genos wants to pay you for your DNA data


This post is by Sarah Buhr from TechCrunch


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DNA The first whole human genome sequencing cost a whopping $2.7 billion. That didn’t bode well for making any breakthroughs on genetic disorders. Luckily, the cost has dropped dramatically since then, leading to a new breed of consumer genetics startups taking a deeper dive into all the double helix’s that make up you
Genos is one of those startups using a next-generation… Read More

23andMe reportedly laid off the lab working on next-gen sequencing


This post is by Sarah Buhr from TechCrunch


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23andme-blimp 23andMe won’t continue with next-generation DNA sequencing and has reportedly laid off the lab working on the project. About half-a-dozen workers were laid off from the Salt Lake City, Utah-based lab, according to BuzzFeed, which first reported the news. By our own count based on LinkedIn, at least five members of the lab have been let go, including its chief medical officer, Dr.… Read More

What happens if we live to be 150?


This post is by Brian Wilcove from TechCrunch


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Vintage clocks Humans have lived for approximately 8,000 generations, but only in the past four has life expectancy taken dramatic leaps upward thanks mostly to societies addressing some of the most basic life issues. In 1907, the average human life expectancy was 46 years; in 1957, it rose to 66; in 2007, it reached 76. But I predict we won’t stop there. Read More

Rex Animal Health is using genomics to keep livestock healthy


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Rex Animal Health gives farmers "weather maps" showing illnesses impacting livestock in their area. A startup called Rex Animal Health wants to protect livestock from illnesses that can quickly turn into epidemics, and help farmers breed animals with the healthiest and most attractive traits. Today at Disrupt SF, Rex unveiled technology to help veterinarians provide clinical support at the point on the farm, and predict the genetic causes of problematic traits in their herds, and in the… Read More

Innovation in genomics and the future of medtech 


This post is by Dr. Lavinia Ionita from TechCrunch


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DNA The field of medicine is in the process of being profoundly transformed by new technologies; much of this transformation comes from exciting advances in genomics. Although genomics is relatively unknown to the general public, innovations in the field have started to make headlines: Genetic testing startup 23andMe, the “gene editing” technology CRISPR and the ambitious 100,000… Read More

Four short links: 4 April 2016


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


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  1. Cello CAD — Verilog-like compiler that emits DNA sequences. Github repo has more, and Science paper forthcoming.
  2. Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting — crypographically preserved privacy when using cloud servers for read alignment as part of genome sequencing.
  3. How to Network in Five Easy Steps (Courtney Johnston) — aimed at arts audience, but just as relevant to early-career tech folks.
  4. Quantified BabyThe idea of self-tracking for children raises thorny questions of control and consent, Nafus said. Among hard-core practitioners, the idea has not really taken off, even as related products have started hitting the market.

You can now pull up your entire genome for under $1,000 on your smartphone


This post is by Sarah Buhr from TechCrunch


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Screen Shot 2016-03-08 at 10.53.15 AM Veritas Genetics was one of the first companies to sequence the entire human genome for under $1,000 in 2015. It’s now taken that technology a step further by delivering the results of your entire genome in an app. To put in context just how radical this is, consider the first attempt at whole human genome sequencing required $3.7 billion to produce in 2001. It wasn’t until 2007… Read More

Genomics Needs A Killer App


This post is by Mark Kaganovich from TechCrunch


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15651749447_568e71e9db_o Genomics has undergone a major shift in the last year. The drop in price in the past decade from $3B to $1K to sequence a genome is the 10X force likely to cause an inflection point in a number of health-related industries. But despite the price, right now genomics is a niche product in large part used in and promoted by academia. Read More

Genetic researchers have a new tool in API-controlled lab robots


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A Menlo Park, California, startup called Transcriptic opened a unique service to the world’s genetic researchers on Tuesday. Using a set of APIs, researchers can now command Transcriptic’s purpose-built robots to process, analyze, and store their genetic or biological samples, and receive results in days.

The high concept idea, says Founder and CEO Max Hodak, is cloud computing for life sciences — only with “robotic work cells” instead of  servers on the other end. “We see the lab in terms of the devices that make it up,” he said, meaning stuff like incubators, freezers, liquid handlers and robotic arms to replace human arms.

And although Transcriptic’s technology is complex, the process for getting work done is actually pretty simple. Researchers write code to tell the robots exactly what to do with the samples (right now, the company focuses on molecular cloning, genotyping, bacteria-growing and bio-banking), and then they send their samples to the Transcriptic lab. Alternatively, Transcriptic’s robotic infrastructure can also synthesize samples for users.

When the job is done, researchers get their results. That process can take anywhere from a day to weeks, Hodak explained, in part because the company’s operation is still pretty small and in part because “cells only grow and divide so quickly.”

Transcriptic was founded in 2012 and so far has raised $4 million in venture capital from Google Ventures and others.

The molecular cloning process with Transcriptic.

The molecular cloning process with Transcriptic.

Still, using Transcriptic’s service touts a number of advantages for scientists over doing lab work themselves. For starters, robots don’t get tired after long days and so are less prone to mistakes that could end up costing a lot of time to redo later, Hodak said. Because the process is asynchronous, scientists can start analyzing a given job whenever it suits them, and they don’t have to worry about storing the samples or the results in the meantime.

Early users have been university researchers at Caltech, Stanford, Harvard and the University of California, San Diego, but Hodak sees a bright future in the pharmaceutical industry, as well. Already, large pharmaceutical companies are trying to cut costs by by licensing the the discoveries of smaller, nimbler companies. The way he sees it, if Transcriptic can provide these smaller firms with cheap, easy access to research infrastructure, they’ll be more flexible and be able to conduct more-innovative experiments.

“Really, it’s a research problem,” he said, noting that concerns over the cost and difficulty of clinical trials might be overblown. “The resources that you have access to really change the questions you can ask,” he added.

If research labs buy into Transcriptic’s pitch, the company is ready to grow, Hodak said. It will add new services and new instructions for existing services, and has designed its physical infrastructure to scale pretty easily. The company has a dedicated hardware team that designs equipment specially designed for Transcriptic’s unique environment, and that saves the company a lot of money. Its liquid handlers, for example, cost less than 10 percent of commercially available gear and actually improved precision.

“Every time we’ve built infrastructure,” Hodak said, “we’ve saved one or two orders of magnitude on the cost.”

 

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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

Structure 2014 ticker

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