Ivan Karabaliev, with Eagle Genomics located at the Babraham Research Centre in Cambridge, UK, for more than two years has been discovering the essence of bioinformatics. Coming from a business marketing background, Ivan likes to explain the complex world of bioinformatics, and to look out for the latest updates in the industry. His posts can be seen on the company's blog. Follow him on twitter @ivanhk100 for biotech updates and marketing tips. Follow on Twitter @ivanhk100.
The era of the $1000 genome, which is all but upon us already, is a new era of predictive and personalized medicine during which the cost of full genome sequencing for an individual or patient drops to roughly $1,000.
Think about what personalized medicine can do: having access to your own genome information will open the doors to dozens of men and women wishing to find out if they have gene variants associated with Alzheimer’s, diabetes, heart disease or cancer. In some circumstances this genome map will also help your doctor determine which drugs you should consider taking and at what dosage, which if accurate enough would be much more efficient than the current approach. Sounds great doesn’t it?
You probably heard something like this back in 2000 when Bill Clinton mentioned the completion of the Human Genome Project in a speech and suggested that humanity can cure any disease and reveal the secrets of our evolution. Well, back then we didn’t have a clue what this 3 billion letter code would bring upon us in terms of storing and handling it and properly analysing it. Only the most savvy IT experts and bioinformaticians foresaw what the technical impact would be, and the side effect of the ensuing flood of data certainly didn’t make revealing the secrets of evolution particularly easy.
Twelve years on, the target users of the $1000 genome are scientists at R&D companies and academic institutions, and the occasional wealthy businessman or celebrity such as Ozzy Ozbourne. But so far they’ve all paid much more than $1000. Steve Jobs, for example paid $100,000 for his genome to be sequenced and analyzed,when he was fighting with cancer. Admittedly the higher price was a year or so ago, so with the continuing decline in sequencing costs you may well now get a number closer to the $1000 if it is just for sequencing, but without analysis.
If some analysis needs to be done, have a look at this article in Forbes which describes a $4000 genome scan but only covering a fraction – 0.02% – of the full genome. This type of sequencing is often used for sequencing targeted areas of cancer tissues in order to find the mutations which triggered the cancer.
The $1000 genome figure refers to a full genome scan, much more than what is covered in the Forbes example. Whole genome sequencing covers the complete genome, all 3 billion bases of it, 99.9% of which is identical to every other human, and indeed 99%identical to chimpanzees and bonobos.
Life Technologies announced this year that they can already scan the full genome for $1000, and another company called Geniachip claims to go beyond this and deliver the same results for just $100. It will be interesting to see how good the quality of this $100 genome is!
Given that 99.9% of the genome is identical in all individuals, full genome sequencing is largely unnecessary – at least, if we believe that we are sure that all the information we need is in the remaining 0.1%. The recently published ENCODE project found some individually unique traits within that supposedly constant 99.9% genetic sequence which means that we definitely do not know as much about what makes each genome individual as we might have previously thought.
Exome sequencing is a lighter option which will cover only the 1% of your genome that is coding sequence – i.e. translated into proteins within your body. This type of sequence will still not include the features that the ENCODE project suggests might exist in the non-coding regions, but it is suited well to current knowledge about the individual variations that can be found in humans. It is offered to the general public by 23andMe and other similar companies and can cost as little as $299 when offered as a commercial service.
To sequence the genome is just the start. Storing it and analysing it can turn out quite pricey. To store only the basic sequence data (no quality scores or ambiguous results) from your fully sequenced human genome you will need roughly 780MB. This can easily be stored on a DVD, which is not expensive at all, but for companies sequencing many human genomes, and certainly for any research where the quality information is as important as the sequence itself, they will need much bigger storage than a single DVD. In-house data centers are the default choice, but the growth in data is outpacing the growth in storage available in these facilities. That is why many of them have embraced the power of the cloud technologies, such as Amazon Web Services.
Analysing genome data includes comparing it to the reference genome to see how different you are from the others. This requires powerful computers working together and running your DNA through some relatively complex analysis pipelines. More advanced analysis to obtain detailed information or to answer very specific questions comes with a complexity (and cost) that depends on the expected outcomes. As mentioned above, Steve Jobs paid $100,000 for his genome to be sequenced and compared to the reference genome to find the mutations which triggered the cancer – only a fraction of this would have been the actual sequencing cost.
The science community has the technology to read and assemble the human genome, to efficiently store it, and run suitable analyses. But to achieve a broader embrace of the $1000 genome, the public itself will need more education on the mechanics and benefits of personalized medicine. Limited or incorrect information can cause dangerous misunderstandings and illogical fear or bias against the technology amongst the public, and poor interpretation of the results by amateur geneticists might have serious negative side effects on health. Governments will have to incorporate into the current medical system ways to educate both health practitioners and patients with knowledge on how to interpret the results and be sure that they act appropriately upon them.
There is a very good scenario of a moment in the near future, mentioned in a Forbes blog post by Jim Golden: “The challenge for the clinical oncologist (GP) is the informed patient who says “I want to have my genome sequenced so we can pick the best drug. Here’s $1000.” It is worth a read.
If Jim’s patient had got their genome sequenced directly, then despite all the disclaimers provided by the supplier they may still misinterpret the information without understanding that it is far from sufficient for what is required to know, for example, that there is a 95% chance they will have Alzheimer’s disease. In their position, even if you could rely on this disease prediction, what would you actually do about it? Is it better to know but be unable to treat it, or not know and never worry about something you couldn’t treat anyway?
Bottom line is, scientists are ready for the $1000 genome, but the governments, the medical system, doctors, and the general public are almost certainly not.
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