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?