2017: This Was Your Year, Part II
In part one, we relived the excitement of January – June 2017. We saw the world go crazy for, about, and with CRISPR, and we started to get a glimpse into some of the big decisions we’ll have to contend with as genomic technology begins to have significant impact on the kinds of decisions patients will have to face. How did the year progress through the summer stretch and into the festive period? Read on to find out…
This has to be one of my favourite stories of the year. It’s a neat study, but more importantly it highlights how much we don’t know. We look back fondly to the Victoria era as an age of innovation and ingenuity. The very same thing can be said about this era. We’re coming up with real solutions to move away from fossil fuels, starting to talk seriously about colonising extra-terrestrially, and exploring deeper and deeper into our own biology. This story shows how unknown the universe we still have to explore in our DNA might still be.
This isn’t the first instance of long-reads having a significant effect on a diagnosis, but it offers a great case study as to why it’s so important. Short reads are great. The sequencing by synthesis chemistry that Illumina have continued to develop over the years is responsible for so much progress, but it does have its limitations. Fortunately, there are other NGS technologies out there that cover those limitations. PacBio occupy a very important niche in the sequencing market. There’s also a reason why you hardly ever hear any of their customers complain about them. It’s still kind of pricey, but for the right applications the price is easily justified!
This was the story that the FDA was considering the approval of the first-ever gene therapy in the US. It’s a first as it expanded the use of gene therapy beyond the treatment of cancer to the treatment of vision loss, and was an important milestone. The approval itself was eventually granted in late December with FDA Commissioner, Scott Gottlieb, stating “I believe gene therapy will become a mainstay in treating, and maybe curing, many of our most devastating and intractable illnesses.” I hope so!
For a story that dominated the national media, it might come as a surprise to see this sitting in the number 2 position instead of number 1. You’ll see why in a second… This is a story that so many people connected with on a deep emotional level. That’s really at the crux of why it was so hard to have a clear opinion on. I can’t imagine how tough it must have been for everyone directly involved and affected.
Amidst the boom in consumer genetics companies, one stood head and shoulders above the rest. YesOrNoGenomics.com . Were they’re offering you the key to unlocking your ‘Soccer Genes’? Were they’re giving you crucial information on the consistency of your ear wax? No. They were committed to giving you the facts. And for once, everyone agreed that it was brilliant.
How much of our genome is functional?
5.26% Around 25%
5.26% Around 80%
31.58% No one knows yet
57.89% Depends on how you define functional
Do you agree with the court ruling on the Charlie Gard case?
Imagine waking up one morning and finding out that you have horrible fishy body odour. That’s the dystopian future, Intel’s Chief Medical Officer, John Sotos proposed in August. His fear is that hackers will be able to exploit the human genome, as it is an open source system open to digital attacks. To be fair, he was just proposing a potential worst case ‘what if’ scenario. The point he was trying to make was that we need strong legislation to protect genetic information.
We hit on another great roundtable feature with this one. Single Cell sequencing is causing a lot of excitement for a whole host of reasons; it’s high throughput and it’s a new order of magnitude of information. If you’re still one of the few people out there that don’t know why this is all so exciting – it’s never too late to catch up. We were extra happy with this roundtable as it gave us another chance to feature Iain Macaulay, one of the nicest guys on the planet! G&T-seq anyone?
Another great Short Read here. This one stood out for two reasons in particular: 1) Bluebee are a pretty popular group of people, and 2) Hans is the CEO of a company in the process of scaling up. It all makes for insightful and fascinating reading. As someone who has worked in other industries his view on just where the genomics market really is, is particularly useful. Spoiler alert, this isn’t the only time Bluebee appear on this list!
A story that you can use to teach people about genetics, particularly why polygamy in a small closed community may not be the best idea. This story unsettles me a little bit, in that it doesn’t really say what happened next. Did it go down the Sigmund Freud route of considering it ‘job done’ once you’ve identified the problem, or did it go down the Carl Jung route of trying to help people get better?
The potential for liquid biopsies is huge. 2017 is the year that saw the first liquid biopsy test approved, and August brought more good news from Dennis Lo’s team in Hong Kong. There’s still a lot of work to be done, but the impact broad early detection of cancer is enormous. From a reporting side of things, it’s a tough balance we need to strike; each success really is huge news, but at the same time we have the responsibility, not to over-hype things. That’s tough to do when it really is very exciting indeed!
What do you think will have the biggest positive impact on healthcare?
51.35% Liquid Biopsy
27.03% Artificial Intelligence
10.81% Human Cell Atlas
Thinking of the broader public’s awareness of genomics, what level of understanding do you think people have?
7.32% Very good
24.39% Some Understanding
63.41% Have heard the term but have little understanding of what it means
4.88% Have not heard the term
And so came September, and the month that just wouldn’t give Craig Venter a moment’s rest. One of the biggest names in genomics, one of the most pressing social injustices that are afflicting so many industries – it’s no wonder people were hungrily clicking away on this one.
If we were to make a ranking of service/solution providers based on how many good things are said about them, Edico and DNAnexus would be pretty high up on that list. The work that Edico have done with DRAGEN is simply sensational. They have a great approach to identifying bottlenecks, and finding solutions to make them go away. Not only do they have a superb technology, not only do they all seem to be incredibly nice, but they also picked out the best venue out of all the ASHG receptions this year. I’m also looking forward to seeing what Guinness World Record they break next. Keep up the good work Edico! In fact, I’m going to plug them even further. Looking up at our content calendar, it looks like we’ve got a webinar running with them on February 21st – check it out!
I remember interviewing Stephen Scherer last year; it was a real eye-opener on the complexity of untangling autism. There’s some phenomenal science going on in this field that really highlights the progress new tools are allowing us to take. As the basic science improves, the translational effect will start to follow. For the time being, just being able to diagnose and explain already makes a world of difference. This story from September adds to that growing pool of knowledge.
A strange one, this. Human Longevity took some heat, as it was felt that they just weren’t delivering on their promises. With national scale projects up and running, it’ll be interesting to see how HLI continue to develop their proposition. The Health Nucleus package is what it is. I think the company is much more than that. It’s the partnerships it’s forming around the industry that are of real interest!
And here it is. The story that starting the Venter finger pointing in September. Data privacy is a big issue for the public, so Venter coming out and saying that data anonymity is a “false promise”, probably wasn’t great. Have a look at the story, then have a look at the images. I’m pretty unconvinced….I’m not the only one either.
Craig Venter took some heat in September. What’s your take?
8.33% He’s an easy target due to what he’s achieved
36.11% The criticisms are fair
5.56% The criticism is overdue
19.44% People forget how much he’s done to constantly raise the bar of innovation
25% I honestly couldn’t care less
Is anonymity something you can guarantee to participants of genetic studies?
33.33% As long as your data security program is up to standard, yes
61.54% No, any system is vulnerable to attack
5.13% No, you can build an image of someone’s face from their genome
After the month of Venter, it was nice to get back to normality. And what better way to do that, than with a Short Read from one of the world’s great lovers of cat pictures? He also gave some of the best advice we’ve had in the Short Read yet: “I’m a bit of a perfectionist, and I wish someone had taught me earlier in my training to have a more constructive relationship with failure. Perfection and success can be the enemy of innovation, as failure is often a necessary prerequisite for invention and discovery.” Very good words to live by!
Oxford Nanopore Technologies. Two things come to mind when you hear the name; mouth-wateringly cool tech, and one of the busiest legal teams in the business. Both Illumina and PacBio have gone after them through the legal system. These stories always do well as they involve drama between companies we all know extremely well.
‘George Church’ and ‘start up’, that’s all you need to say to get people interested. Much like Venter, Church is one of the true superstars of the field. If he’s involved, you know it’s going to be the very leading edge of technology and a very cool application. No different here with GRO Biosciences.
GTEx (Genotype-Tissue Expression Consortium) are doing some very exciting work. This is the kind of story I really love. There are lot of groups working together through GTEx to bring this whole project together. That kind of collaboration and effort towards a common goal is always inspiring to see, and is motivating to find ways to work together in other areas. As with many other people out there, I’m really excited to see the positive effect this will have on our understanding of ourselves and our diseases.
This article is actually from 2016. It saw a massive resurgence this year as it became increasingly relevant. It’s a nice commentary challenging how we do science. We are trained to build a hypothesis, and then attack it until we’re satisfied that we can’t disprove it. It’s a good system, but in the era of ‘big data’, it does have its limitations. So the big question remains – is the currently accepted scientific method wrong?
Do we need to abandon hypothesis-driven research to get the most out of big data?
5.13% Yes, as we don’t know what we’re looking for
7.69% No, otherwise we’ll get caught up in noise and insignificant results
87.18% We need to find a balance. Listen to what the data is telling us, but still test hypotheses we develop as a result.
How much data would you donate for research purposes?
60% My genome
52.5% Healthcare records
55% Lifestyle data
And here he is again, one of Genomics’ favourite sons, George Church. The ethical debate around whether or not we should be tinkering with the human germline, is one that won’t go away anytime soon. It’s a fine line between preparing ourselves responsibly and stalling – but which one represents the greater risk?
How many times have you heard people ask an audience, “how many of you would want to know if you were going to get Alzheimer’s?” It’s a poster disease to highlight the tough decisions we have to make around genetic testing. Alzheimer’s is the acknowledged boogie man that looms in our minds, so good news to help fight the disease is always welcome news!
Originally published in April, this blog post had a late resurgence as 2017 came to an end. Our staff writer, Frances Addison, wrote this off the back of a discussion at the office. It’s a very personal story, and one that reminds us to think carefully about the terms we use and how we use them.
Just when you thought CRISPR couldn’t get any more exciting, its efficacy improves. There comes a point every year, when I assume people are saturated by CRISPR stories, then something downright cool comes along to bring it back to life. Although the story we’re all dying to see some progress on is this shocker from 2016.
Was this a watershed moment? Is injecting yourself with CRISPR live on facebook the new stage selfie? Science history is littered with examples of people experimenting on themselves, so this isn’t necessarily something new. It certainly scores high on shock value though. Suppose the self-injection was a success? Suppose it’s been a horrible failure? Which would be worse? Those of you following this list, will already be familiar with Josiah Zayner; you certainly can’t question his determination and belief.
Are bans against germline editing unnecessarily slowing down progress?
This year we were treated to live streams of biohackers injecting themselves with CRISPR solutions. What is the lasting effect going to be?
36.67% Prompting others to take a more active interest in genetic technologies that might be available to them
13.33% Force traditional therapeutic research to take risks
50% Nothing. It’s already forgotten
Experimental drug successfully treating a disease for the first time – what’s not to love? Before we get too carried away, it’s important to note that this isn’t a cure. It’s groundbreaking, which means there’s still a lot of work to be done. That being said, it was still very exciting news!
An interesting story, here. One that goes to show that even the very best can make mistakes. To his credit, Szostak handled the situation pretty well explaining what went wrong. This also highlights one of the central pillars of science – stating something as fact is exceptionally difficult. Our interpretation of results, is just that – an interpretation. Our theories are based on our best understanding and explanation of what we see. We should never take things for granted, and always remember to question everything!
We had the pleasure of meeting Variantyx CEO, Haim Neerman, at ASHG in 2017. We had a great chat about the future of sequencing in the clinic and how genetic testing is likely to change in the future. This is something I’ve been talking to a bunch of people at any show I’ve been to. Everyone seems to have a different opinion on what’s going to stay, and just how widely adopted whole genome sequencing is going to be.
This was one of my favourite stories of the year. I was very happy to see it make the December top 5. Adding two new bases to an alphabet of four; that’s huge! And this time they actually produce unnatural amino acids! Even looking back at this now, I’m still excited. What can we do with the ability to produce more amino acids? This is so exciting for science and science fiction. More of this, please. If we did an Editor’s choice for coolest piece of work – this would definitely have scooped it up for 2017. I should probably e-mail the authors and let them know?
Despite the sensational achievement of expanding on the very language of our evolution, it looks like people were more taken by Google’s release of DeepVariant. To be fair, it is still pretty cool. Google have impressive computing infrastructure and machine learning expertise, so seeing that applied to healthcare is exciting in its own right. I still think new bases is cooler though…
Will we see whole genome sequencing used as an all-in-one genetic test in the clinic?
30.77% Yes, but not in the next 10 years
41.03% Yes, within the next 5-10 years
15.38% Yes, within the next 5 years
What will be the lasting impact of Artifical Intelligence in genomics?
80% It’s going to take out time-consuming tasks so we can focus on bigger questions
17.14% It’s going to let clinicians spend more time with patients
2.86% The Matrix
So concludes our trip down memory lane. 2017, was a fascinating year full of discoveries; moments that changed the world forever; and moments that made us consider the emotional side of our advances. It’s a popular belief that some months are traditionally ‘slow news months’. That’s just not the case with genomics. Each week, let alone month, has exciting news. And that is all thanks to those of you out there building technology, doing the research, and pushing the industry forward.
So what were the top 5 stories of the year? Let’s take a look…
CRISPR doesn’t work! No wait…. Yes, the story that threatened to derail the future of CRISPR.
The desperately crushing story of the Gard family’s fight to save their son’s life.
Big news on a tiny device. Proof, as if it was needed, that people can’t get enough of the hype around ONT!
Easily the funniest thing to make headlines in 2017. It still shocks me that outside of scientific circles, there is a misconception that scientists don’t know how to have fun. They’re clearly going to the wrong parties.
Marc Hogenbirk takes home the crown for 2017. His article challenging the scientific method was the most read feature on the site. I’d recommend you give it a read, but it seems you already have!
Thank you to all of you who help make FLG a fun place to read and write about genomics! Keep talking to us by e-mailing in and letting us know what you think!
Stories for the website: Frida
Stories for the magazine: Megan
Talk about something you think is cool or Star Wars: Carl
Promotional stuff: Andrew
How awful was Star Wars: The Last Jedi?
23.53% A huge disappointment after The Force Awakens
11.76% Just thinking about all the plot holes makes me so angry
5.88% Bring back George Lucas, even The Phantom Menace wasn’t this bad
58.82% If it wasn’t part of the Star Wars franchise, no way would anyone even be talking about this movie