Backyard science: Aphids under a USB microscope

Just some random summertime backyard science here. The linden tree near my home is covered in aphids, so I took a few pictures with this USB microscope.



Can anyone confirm whether this cluster of eggs belongs to aphids or something else altogether?

The FDA, 23andMe, and selling less for more

Back in 2013 and at the beginning of the FDA vs 23andMe story, I wrote this:

Personal genetics will elicit a huge change in medicine, [but] actually doing that requires knowledge of how a person's genetics impacts their health.  For many genes, like BRCA1/2 which are the oft cited breast cancer risk markers in the media, the links between genetics and disease are established.

But for many others, a lot of work still needs to be done: clinical trials based on experiments need to be designed; experiments based on hypotheses need to be run; hypotheses flowing from data analyses need to be identified; and analyses need data sets to start from.  Fuzzy data is better than no data at all.

I expect that's where 23andMe is going to graciously come into play.  If the FDA actually winds up killing the company's main data collection channel, the company already has about 400,000 people genotyped and has built up enough traction to run for a while without having to sell another $99 test for a long time.

It took four years, but as of a few months ago, the FDA has reversed it's decision against 23andMe allowing the company to resume DTC marketing. The catch, however, is that the company will now offer tests for 36 conditions (instead of 254) for $199 (instead of $99). Gizmodo correctly points out that though this means that people are getting "less info for more money" (more on that in another post). Technically, that may be true, but if that information is more accurate or at least less irrelevant it counts for some of that value.

PCR's Next Wave

On BioTechniques:

PCR amplification of DNA is arguably one of the most important technology developments in the history of molecular biology, because without PCR, many commonly employed lab techniques would not be possible. It’s both robust and simple. Yet, there are still parts of the method that could be further refined—especially when it comes to sensitivity and error rate.

For researchers working in the cancer field, locating extremely rare variants from complicated mixtures of DNA, proteins, RNA, and other biomolecules is often a daily task. But identifying ultra-rare variants of these molecules presents a huge challenge—it’s like finding a needle in a haystack, a process that can be confounded further by PCR errors. This is another area where developers are finding fertile ground for improving PCR methods and protocols.

Anders Stahlberg from the University of Gothenburg in Sweden, along with colleagues from Boston University School of Medicine and the Ontario Institute for Cancer Research, recently described a new multiplex PCR-based barcoding strategy that can be used for the detection of ultra-rare mutations by next-generation sequencing.

This article is a nice review of the previously described SiMSenSeq paper.

Do European Research Council applications foreshadow what may happen with the NIH?

It looks like Brexit is having repercussions on UK science funding from the European Research Council, according to David Lomas:

Applications to EU funds are usually made by consortiums of researchers from a variety of EU countries. Britain has a strong track record of taking the lead in these groupings. 

Britain also has a leading position in applications for individual research grants made under the European Research Council, the ERC. 

“Previously having a British member would help you in your application to get funding … Now you are less than an asset, so we have had academics removed from grant applications,” Lomas said.

One has to wonder whether US funded research organisations, like the NIH, will be forced to "Buy American" in the future and prevent spending on research activities in foreign countries.

I get the whole populist sentiment around trade deficits and job losses, etc., but the fact of the matter is that the US can't just cut out part of international trade and partnerships without impacting the productivity of US-based initiatives. For example, groups in Toronto can offer US scientists many different kinds of scientific services on a fee-for-service or collaborative basis on very competitive terms, mostly due to the favourable USD/CAD exchange rate.

So why cut out that part of the value chain?

What's really up with Roche and PacBio?

You're probably aware that Roche recently severed its 2013 partnership with PacBio and decided to go it alone without access to long read SMRT technology. Neil Gunn, Roche's head of sequencing R&D explains that Roche will now 'focus more intently on its internal R&D efforts to "drive our long term strategy, which is to be a leader in clinical diagnostic sequencing."'. This wouldn't have anything to do with the 2014 acquisition of Genia, would it?

Keith Robison at Omics! Omics! has already speculated about various reasons for Roche's break up, but I think that the developments around Genia are the primary reason for this parting of way. As Robison explains:

The obvious culprit would be Genia, the nanopore sequencing technology which Roche purchased. ... Genia has twice reported this year technical success, first with their nucleotide chemistry and then their protein engineering.

But good publications do not a commercial instrument make, and there has been no signal that a launch is imminent.  Perhaps we will hear a lot more at JP Morgan or AGBT, but Genia has burned a lot of credibility in the past with premature announcements.

This may be true, but consumers in the genomics space have been pretty forgiving:

Many of complained that ONT announced vaporware at 2012, but they've delivered devices to customers since mid-2014.  

And as of now there are a lot of working ONT devices in the field.

But back to Roche/Genia. It's tempting to speculate that Roche is building a competing platform to Oxford Nanopore's technology, which on the surface may look like what it is. However, the technologies and the way sequence is read from them is different.  On one hand, ONT's nanopores detect electrical signals generated by DNA kmers traveling through the pore, and in comparison Genia's technology reads DNA by having a polymerase send engineered tags through their pore.

How will Oxford Nanopore's MinION compare with Roche's Genia?

At this point, they look like competing technologies in the nanopore sequencing space, but without more information on the Genia it's hard to make a call. However, since the Genia relies on proprietary modified bases called NanoTags read by a nanopore, I'm going to speculate and assume that the Genia will have a higher consumable cost as result; potentially a big drawback for the Roche platform. Nevertheless, here's how they compare across a two key value drivers.

Read accuracy is a big deal. At the moment, it looks like Genia might have a hand up due to their NanoTag read system. I suspect that it easier to calling bases directly using engineered NanoTags that it is to infer bases from electrical signals generated by DNA going through a pore, as is the case with ONT. If Roche can make up the additional cost of NanoTag reagents by offering a higher read accuracy, the Genia might be worth it, particularly if the flow cell cost is kept below that of ONT's.

Cost. There are two major categories of cost sequencing teams are concerned with; operating costs and capital costs. The nice innovation that ONT has brought to the genomics field is the idea of zero (or nearly zero) upfront capital costs. You buy a flow cell for <$1000 and start sequencing.  The capital cost of a Genia is an unknown, but if it's anywhere near that of PacBio or Illumina equipment it'll be an obstacle to adoption in the field. Unfortunately, without a target purchase price (and other assumptions about the Genia's longevity) it's impossible to come up with a cost model and estimated $/gigabase.

Some guidance from Roche is needed here both in terms of cost and accuracy. I haven't even touched read length as a dimension of performance, but given ONT's extreme read lengths (up to 200kb, more commonly ~50kb), Genia needs to easily hit >30-50kb even to be considered as competition.

Why you should be wary of companies hiding everything for 'intellectual property reasons'

Think of Theranos. I remember reading this article when it came out, thinking 'what can they possibly be protecting?':

The technical details about Theranos' seemingly revolutionary tests are hard to come by, and the company is known for its secrecy about its founder's invention.

There's one fundamental question, one that in some ways is unanswerable without revealing information that Theranos wants to keep confidential: How, exactly, does what Holmes invented work? ... [The company] hasn't published peer-reviewed studies comparing its tests to traditional ones, and the company hasn't allowed independent experts to publicly assess its labs, citing the need to protect its intellectual property.

IP comes in many flavours: patents, designs, trade secrets, and business processes, to name a few. Not all intellectual property can be protected like a patent, but some of it can, and that means that not all intellectual property needs to stay secret.

When a company like Theranos doesn't even let independent experts in to check out the technology and say 'Yes, I've seen what they do and it works', which they could conceivably do under an NDA, it raises a red flag that something isn't right. Most medical device/diagnostic companies have at least something that can go through the patent prosecution process, which allows experts to understand how the new widget works and whether it will eventually provide value in a business model.

Sometimes the best strategy is to show everyone that at least part of your firm is not just smoke and mirrors.

Scientists' perennial problem: The Brexit Effect

I've spent the last week or so thinking about the effect a Brexit would have on U.K. science, as have many other folks on the 'net. Having lived through the Canadian War on Science (2006-2015), there are lots of parallels to draw between policies and strategies that try to cut out basic research and what scientists seem to be freaking out over with regards to the Brexit (which by the way isn't a done deal after the key leaders bailed on the movement).

In my experience, three things related to changing science policy hit a nerve with researchers: funding cuts, restricted mobility of people, and general political instability. All of these aren't unique to the kind-of-hypothetical Brexit Effect; they're just brought to top of mind by it.

Funding cuts. It's no doubt that money and resources are the lifeblood of a research group - any group, for that matter - and whenever there's less money to go around it's an uncomfortable time, by definition.

There's a wonderful post at the London School of Economics' BrexitVote blog that goes into extensive detail about how the UK science funding may change. Specifically on how whatever gains won by leaving the EU are overshadowed by the general loss of economic activity if the UK were to go through with the plan:

Importantly, even the more optimistic assessments of the UK’s economic performance following a Brexit ,.. model an immediate loss in GDP for the transition years following a Brexit. The size of that loss is substantially larger than the current net contribution of the UK to the EU budget. ...

Therefore the attempt to financially gain in the short term via a Brexit is akin to killing the goose that lays the golden egg. It is a sure-fire short term loss, wiping any free money for Research & Innovation investment until at least a decade down the line – according to the most optimistic scenarios. This strongly counters any claim that voting to leave the EU provides immediate funds for a shot in the arm of national science. The extra money simply will not be there for science as the UK economy is hit by huge transition costs. 

Other parts of the post go on to explain how Switzerland manages to get along with science just fine without being an EU member.

Now you might point out that the above scenario explains what would happen to global research funding (similar to a US-style Sequestration effect), and ask what about cuts to specific programs or areas of research? This, sadly, is sometimes needed. Just as in any other business, as the needs of the 'market' move on, science needs to adapt to ask new questions, use new technologies, and re-train people.

This process of creative destruction has been accepted by mainstream business people and spawned so many different bestsellers (including the classic ones by Eric Topol and Rotman Professor Sarah Kaplan). It really should be one of those things that's accepted as a given by grant funded researchers, not fought against.

Next post, Mobility of People.

Is your business idea unscalable?

Jon Westenberg:

There’s a lot of pressure put on young entrepreneurs. It’s the pressure to only build scalable startups, rather than focusing their efforts on any other type of business. You can see this almost everywhere. If you’re not building high growth software or platforms, you’re seen as wasting your time.

It’s snobbish. And it’s dangerous. It relies on the idea that there are businesses that are inherently better than others. And they’re only the businesses that have room to become $100,000,000 companies.

Lots of business ideas aren't scalable, but they can still make a ton of money for the founders.

On Transgenic Zika-Proof Mosquitoes

Reinaldo Jose Lopes:

Even if [Oxitec's] transgenic mosquitoes can be proven to reduce dengue or Zika infections, it is possible that natural selection could reduce their effectiveness. Females could develop a preference for wild-type A. aegypti males — stopping the company's currently furthest-developed lineage of GM insects (called OX513A) from spreading in the wild.

At best this means a lot of money for Oxitec and little value for the payors. At worst, Zika virus adapts and the mosquitoes become useless.

Someone once said that "Life... finds a way".

Really, PubMed?:"Diverse biological effects of electromagnetic-treated water"

Really? Oh yes, if it's published it must be true:

The effects of water treated with an electromagnetic field (EMF) were investigated on two biological systems, humans and plants. Purified de-ionised water was treated by (1) boiling, (2) exposure to microwave radiation, and (3) low frequency electromagnetic oscillation molecular resonance effect technology (MRET), before being used to prepare media for culturing human peripheral blood mononuclear cells (PBMC) from three healthy females. Our results indicated that PBMC culture in MRET-activated medium showed significantly less oxidative metabolism when compared to media prepared from other types of water. As for the effects on soybean, our results indicated that both MRET- and microwave-treated water greatly enhanced the length of the root. These results suggested that electromagnetic-treated water can have diverse biological effects on both animal and plant cells. Since these effects are related to the ‘Memory of Water’, hypothesis which has been suggested as an explanation of the action of high homeopathic dilutions, our finding warrant a further investigation on the mechanisms of various types of physically conditioned water on specific cellular activities.

Issues with this paper:

1. No controls.
2. Apparently no ethics review for using healthy human volunteers.
3. A paywall. An Elsevier paywall.
4. Because of the paywall, there's no idea what the n of soy plants is.
5. Homeopathy.
6. The "Memory of Water" hypothesis is based on two PubMed citations. Hey, at least it's more than one.

Gene editing in human embryos gains traction

Nature has a short update on where human gene editing research is going:

China's lead

Fan’s team began its experiments in early 2014 and originally submitted the paper to Cell Stem Cell, Fan says. By the time the manuscript ended up on the desk of David Albertini, editor-in-chief of the Journal of Assisted Reproduction and Genetics, a different Guanghzou-based team had become the first to report human-embryo-editing experiments. That paper, which tried to correct a mutation that causes a blood disease, fed into a firestorm over the ethics of modifying human reproductive cells (or ‘germline’ modification). Some researchers called for a moratorium even on proof-of-principle research in non-viable embryos. ...

Fan’s paper should help to reassure international observers about the legitimacy of human-embryo-editing research in China, says Robin Lovell-Badge, a developmental biologist at the Crick. More such embryo-editing papers are likely to be published, he adds. “I know that there are papers floating around in review,” he says.“I’d much rather everything was out in the open.” 

The public issue, in my mind, is that many opposing human cells see the next logical step as a full blown program to produce genetically engineered human. I'm very skeptical that the science is going to go that far, that fast.  To start, through CRISPR-Cas9 gene editing is pretty specific, it's known to have off-targets, and those off-target regions depend on the site being edited.

Until all the consequences of editing a specific site (including unintentional targets) are determined to be 'safe', human CRISPR experiments in embryos should remain very basic.  First things first.

Our SiMSenSeq: Simple, Multiplexed, Sensitive, DNA Sequencing paper is out

The SiMSenSeq PCR method that I've been working on for about two years has just been published in Nucleic Acids Research.  Here's the abstract:

Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast method for introduction of barcodes into DNA libraries made from 5 ng of DNA. Barcoded adapter primers are designed with an oligonucleotide hairpin structure to protect the molecular barcodes during the first rounds of polymerase chain reaction (PCR) and prevent them from participating in mis-priming events. Our approach enables high-level multiplexing and next-generation sequencing library construction with flexible library content. We show that uniform libraries of 1-, 5-, 13- and 31-plex can be generated. Utilizing the barcodes to generate consensus reads for each original DNA molecule reduces background sequencing noise and allows detection of variant alleles below 0.1% frequency in clonal cell line DNA and in cell-free plasma DNA. Thus, our approach bridges the gap between the highly sensitive but specific capabilities of digital PCR, which only allows a limited number of variants to be analyzed, with the broad target capability of next-generation sequencing which traditionally lacks the sensitivity to detect rare variants.

I'm currently packaging up the informatics pipeline used to analyze SiMSenSeq data, which will be up on GitHub pretty soon.

Working 24/7 is the cognitive equivalent of coming to work drunk

In an NPR interview about her new book, The Sleep Revolution, Arianna Huffington offered up this perfect quote on the importance of sleep and its relationship to the workplace:

We hear employees being congratulated for working 24/7, which now we know is the cognitive equivalent of coming to work drunk. But it's changing. We are now in this amazing transition period where more and more companies are beginning to realize that living like that and working like that has actually terrible consequences — not just on the health and productivity of their employees but also on their bottom line. 

Why AbbVie still has traction despite looming Humira patent expiry

Arthur Jeannerot, on Seeking Alpha:

In 2015, Humira (Adalimumab) represented 61% of AbbVie's total revenues, which could be seen as problematic since the composition of matter patent covering Humira expires in December 2016 in the U.S., and in October 2018 in the European Union. However, Humira is covered by more than 50 other patents on formulation, method of treatment, manufacturing and more. Those other patents are due to expire between 2022 and 2034, which should make it more difficult for competitors to come up with biosimilar versions of Humira.

Either way, AbbVie is going to start experiencing competition from other companies that are more than capable of producing Humira biosimilars - the technology to produce therapeutic antibodies is becoming more and more commonplace, and even large academic groups are jumping on the bandwagon. This means that, as far as technical complexity goes, making a biosimilar is within the capability of a talented PhD student.

What I think the market is over-estimating is the ability for competing biosimilars to carve out Humira market share, probably with the assumption that customers will be able to substitute one antibody for another as easily as one proprietary molecule for a generic drug in the small molecule drug space.

Unfortunately, it's not that easy. Antibodies can have a ton of idiosyncratic activities; they're bigger, and less well defined than small molecule drugs. In addition, there's going to a great deal of brand name inertia with Humira, as consumers stick with what works until a generic proves that it's as good as the original - which will take some time. This likely means that Abbvie can ride out the storm and plan a strategy to protect this drug for a little while longer.

Move over cronut burgers; the Burgerizza has arrived

In Toronto, The Ex is known for outrageous food being created for the once annual occasion.  Leave it to a baseball stadium to top Cronut Burgers, poutine balls and Krispy Kreme burgers with The Burgerizza:

Yuck. No thanks.

(Photo credit: National Post)