Friday, June 19, 2015

Genomics England picks these smaller names to crunch UK100K Genomes Project data

The most stunning news is delivered in the opener of Nick Paul Taylor's report on FierceBiotechIT:
Genomics England has named the four companies it wants to work with on the interpretation of the first 8,000 genomes from its massive sequencing effort. The list of successful bidders is lacking some big-name applicants, notably Illumina which Genomics England asked not to tender for the contract.
Though it's shocking that Illumina's BaseSpace wasn't a contender, in reading Genomics England's news release there's no mention of Illumina being asked not to tender, rather they were simply not asked to tender, a much less damning conclusion than what's mentioned above implies, which is that Illumina's analyses were so bad that no one in the UK ever wanted to see them again.  Sadly, there was no mention of DNAnexus or Ingenuity either, but I suspect they were in the running as well.

But that's beside the point.  Starting in August, Omicia, NantHealth, WuXi NextCODE, and Congenica will each provide reports on 2,500 patients from within Genomics England's data centers.  Some of these shortlisted companies are not too surprising; for example Omicia is the primary licensor of the VAAST mutation analysis software (which is pretty good at analyzing family mutation patterns that I expect the UK100K genomes project contains a ton of), while Congenica is partnered with Genomics England to begin with, making them a natural fit.

WuXi NextCODE is a spinout of deCODE genetics (which was a hot company at one point) and has become an interesting arm of WuXi AppTec, a large Chinese CRO that's listed on the NYSE and has a $3B market cap. I'd like dig deeper into their business models in future posts.

However, the most enigmatic company of the set is NantHealth.  This company, led by Patrick Soon-Shiong, has been trying to make a huge splash into the genomics market, mostly by building systems for hospitals to crunch genomic big data and present treatment propositions for patients, according to Matthew Herper at Forbes.  This is the same Dr. Soon-Shiong that brought the world Abraxane, so he has credibility (which I admit was slightly reduced when I saw him holding a Circos plot on a BlackBerry Passport).  If you read other stories by Herper you get the sense that there's a good dose of hyperbole coming from Soon-Shiong and NantHealth, so how that translates into results with the UK 100K Genomes Project is up in the air.

We'll have to wait until next year when the four companies complete the pilot phase of the study, and hopefully one will be an obvious winner to crunch the rest of the data.

Friday, June 12, 2015

Noninvasive Prenatal Tests detect cancer at a very low rate

Noninvasive Prenatal Tests (NIPT) has enjoyed a surge in growth due to their reliance on a simple blood draw to be able to detect fetal chromosomal anomalies, and is one of many tests available during pregnancy.  Over 800,000 women in the US alone had a NIPT last year, according to Eric Topol at the Scripps Translational Science Institute when interviewed by BuzzFeed.

The neat thing reported at the Future of Genomic Medicine conference back in March was that NIPT tests detected 26 cancers in pregnant women, presumably out of the 400,000 MaterniT21 tests that were described at the time, for an overall rate of about 0.01%.  It's impossible to figure what this number should be without looking into Sequenom's data further, but I think it's safe to say that this is way into the range of being incidental. 

However, another new report has just come out of JAMA Oncology, showing that NIPT is able to catch early pre-symptomatic cancers in pregnant women, at a considerably higher rate that is still only about 0.1% (3 in about 4000, according to the paper).

The neat thing about JAMA's study is that they look at whole genome sequencing instead of what Sequenom's MaterniT21 test does, which is to only look for chromosomal count changes in a handful of chromosomes.  The actual paper shows MRIs from these three women, as well as genome wide representation plots (basically, plots of DNA copy numbers) of cells from each patient, which are quite obviously abnormal to anyone working in the cancer genomics field.

What does this mean for those electing for NIPT tests?  You probably don't need to worry about a surprise cancer diagnosis, but that non-invasive genetic tests can be easily adapted (or reinterpreted) for new purposes as time goes on.

Thursday, June 11, 2015

Mammalian limbs can be regrown from cells

I remember the first time someone told me that salamanders can regrow their tails.  Now, it looks like regrowing mammalian limbs is possible. Andy Coghlan, writing for New Scientist, says:
The technique behind the rat forelimb – dubbed "decel/recel" – has previously been used to build hearts, lungs and kidneys in the lab. ...

In the first, decel step – short for decellularisation – organs from dead donors are treated with detergents that strip off the soft tissue, leaving just the "scaffold" of the organ, built mainly from the inert protein collagen. This retains all the intricate architecture of the original organ. In the case of the rat forearm, this included the collagen structures that make up blood vessels, tendons, muscles and bones.

In the second recel step the flesh of the organ is recellularised by seeding the scaffold with the relevant cells from the recipient. The scaffold is then nourished in a bioreactor, enabling new tissue to grow and colonize the scaffold.
So the catch is that you still need a donor limb to provide a collagen scaffold. Since 3D printers have become so popular why not just print one?

Friday, May 29, 2015

Pieter van Rooyen on startups and resilience

Pieter van Rooyen, CEO of Edico Genome, tells a compelling story to Bioentrepreneur about his experiences with failure while building companies:
For example, when I started Zyray Wireless, I was the only employee that was based in the US; the rest of the team was in South Africa. We wanted to move the core team from South Africa to San Diego, but first I needed to raise money. This was not easy. What US investor would put money into a bunch of people who were not even in the US? I was rejected by almost all the initial investors I pitched to. I will never forget the words of one of these investors: “Pieter, you have nothing—go home and don't quit your teaching position at university.” That was a very hard blow, but as the saying goes—if you are going through hell, keep on going. To his credit, however, that investor was the first person to congratulate me when Zyray was acquired by Broadcom.
Another great example of persistence occurred when we were pitching the idea of ecoATM. We approached 52 venture capitalists and every single one gave us a definitive no. But the 53rd venture capitalist said yes, and we never looked back.
Rejection.  It's an event that many people actively try to avoid, because of experiences like the ones where someone's reply is: "You have nothing."  It's a message that invalidates a lot of the work that went into that concept that an entrepreneur-scientist is pitching to everyone that is willing to hear.

But van Rooyen's ecoATM example provides a glimpse into a more unbiased view of what's actually going on.  ecoATM, in being rejected 52 times, wasn't necessarily told that it had nothing to pitch.  I read this example as one of 52 people finding that ecoATM didn't fit their requirements, expectations, expertise, or the like, and they weren't willing to partner with a company unless they knew that something positive would come out of the relationship.

There are two sides to every deal.

Friday, May 1, 2015

Ontario law to schools: Let asthmatic kids keep their inhalers.

Good job.  Keep up the good work.  This seems like an obvious thing to do, at least to me.

The National Post writes that the law was proposed after a 12 year old boy died in 2012 because his school locked up his inhaler.  Here's the draft of Ryan's Law.

Monday, April 27, 2015

Inventors: Don't overly rely on your own searches

Mark Nowotarski, on self-directed invention searches:
Some inventors consider doing the search of the Patent Office on their own, but there are several downsides to this plan. Their emotional attachment to the invention will cloud their judgment, and they will steer away from finding other products that are similar. Although chances are they have already identified a few other competitors, searching the U.S. Patent Office is a more intense process.  From my experience with clients who have done their own search, they have ignored similar products that have already been patented because they don’t want to know that their idea isn’t as unique as they once thought it was.

However, finding additional similar products does not mean that all is lost. The strategy changes to comparing the proposed invention with the patented one, and discussing ways to improve it and make it patentable. A good patent agent or attorney will provide objective insight at this phase. The process is to take the invention, ignore the parts that have already been incorporated into another patent or patents, and the remainder is a patentable invention.
He goes on to point out that Thomas Edison did not actually invent the lightbulb.

There's a certain strategy to figure out what specific part of an invention is patentable (and of value to anyone), and without some experience or guidance in mapping out exactly how the patent landscape looks, you might overlook the best direction which to apply your effort.

Thursday, April 23, 2015

Canadian budget pushes applied research (again)

Yes, the Canadian federal government is still directing money to applied research.

I'm not saying that it's good or bad; just that it's nothing new or unpredictable.

A phrase you hoped to never hear: "Human induced seismic hazards"

Alexandra Witze, at Nature, writes:
Fifteen quakes of magnitude 4 or greater struck in 2014 — packing more than a century’s worth of normal seismic activity for the state into a single year. Oklahoma had twice as many earthquakes last year as California — a seismic hotspot — and researchers are racing to understand why before the next major one strikes.

Whatever they learn will apply to seismic hazards worldwide. Oklahoma’s quakes have been linked to underground wells where oil and gas operations dispose of waste water, but mining, geothermal energy and other underground explorations have triggered earthquakes from South Africa to Switzerland.
This map, from the article sums it all up: