Single-cell genomics will change the world

March 17, 2013   

In the future, you will know exactly which strain of influenza, Hepatitis C, or HIV infected you, and if there are any other parasites floating around in your blood. If you’re not sure about the origins of your meat, you could sequence it to check for pathogens, the biodiversity of the cows it came from, and its environment to make sure it was truly grass-fed. When you get your hair dyed or permed, you’ll also get a scalp treatment which changes the genetics of your hair so it conforms to whatever change you’re getting. Bioterrorism officials will be able to detect virulent threats at the most minuscule amount.

All this sounds very science-fiction, but I believe we are hurtling towards an exciting future in which biology will play an unprecedented role, due to the current research in single-cell genomics.

Single cell genomics is an exploding field right now, due to DNA amplification techniques introduced in 2001 improved upon in 2012, and novel single-molecule sequencing methods which require no amplification at all. For most high-throughput sequencing, the genome-wide sequencing you may have heard about through large efforts such as the Personal Genome Project, the ENCODE project, or The Cancer Genome Atlas, you need a large amount of genetic starting material. This means that to get any usable results, you need to take a large population of cells (~100,000), grind them up, make thousands of copies of the DNA, then send the DNA for sequencing.

Right now we are treating tissues as if they are an entire country like the United States, making stereotypes about everyone that lives here based off a few interactions. But the US is composed of people, individuals who work hard and make tough decisions every day. We simply cannot assume everyone is exactly the same.

The advent of single-cell genomics completely changes this paradigm that we need thousands of cells to understand biology. Instead of treating a heterogenous soup of cells such as a tissue as a homogenous population, for example, assuming every cell in the heart or liver or kidney or cancer tumor is exactly the same (which we know from physiology to be completely false), we can study individual cells and their solo struggles.

From single-cell research, we can finally study tiny amounts of cells. And soon, technology will be good enough that individuals can afford their own sequencers. The Illumina MiSeq is the closest thing we have right now, but it’s still too expensive and the bioinformatics isn’t developed enough for a blood sample –> ??? –> profit!-type experience. In the future, we can sequence individual cells in your blood to predict your current viral load, a key component of health in someone living with HIV. You’ll be able to perform your own quality control of the food in your home, even checking which farm those “heirloom” tomatoes came from, or using an advanced protocol to check for environmental effects (pesticides, soil quality, etc) via epigenetics such as bisulfite methylation sequencing of DNA, histone modifications or methylated RNA (high-throughput methods not yet invented!). When you get your hair treated, you’ll provide your genome sequence and the hair technician will match your desired hair genes with your current genes, and use that to create a gene therapy so that you don’t have to come in for root touch-ups - your roots will already be the correct color or level of curliness! Finally, we’ll be able to detect any smidgen of genetic material lying around, and halt any bioterrorism threat in its tracks.

Single-cell genomics will change the world.

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