Personalized Medicine Draws Closer With Cheap and Accurate DNA Sequencer

Biologically engineered nanopore membrane offers cheap and accurate DNA sequencing

2 min read
Mirkó Palla (left) and P. Benjamin Stranges (right) who performed the work at the Wyss Institute
Photo: Wyss Institute/Harvard University

Sequencing-by-synthesis (SBS) technology currently dominates the gene sequencing market. The process involves dividing a DNA molecule into many pieces of single-stranded templates that are put into millions of tiny wells on a substrate inside a machine that washes them through millions of cycles. Even though prices have dropped five orders of magnitude in the last decade for this technology, it’s still complicated and expensive. 

Many experts thought the key to cheaper DNA sequencers was going to be performing the SBS process in nanopore-based DNA sequencers. Here, the strands of the DNA are pulled through nanometer-scale pores in a membrane and the electric field variations of the four nucleic acids—A, C, G, T—are measured. While a number of companies have launched businesses around this technology, it remains costly enough to delay the revolution in medical care known as personalized medicine.

Now researchers at Wyss Institute for Biologically Inspired Engineering at Harvard University believe that they have developed a way to make these nanopore-SBS DNA sequencers fast, accurate, and, most importantly, cheaper than what is currently on the market. The trick was to biologically engineer the nanopore structure. If they can further develop the technology, they could enable doctors to quickly discern changes in your specific DNA sequence signaling a disease.

One big obstacle to overcome in nanopore-SBS sequencers: The DNA strands are synthesized so close to the nanopores that they interfere with the electrical signal of those strands passing through the pore. The Harvard researchers solved this problem by developing an entirely new approach to the sequencing engine involving a protein-based method for engineering the nanopores.

“We have now engineered a new sequencing engine that gives robust and reliable sequencing results, can be loaded with different DNA templates, and can be highly multiplexed in a chip composed of hundreds nanopores individually addressable by electrodes," said P. Benjamin Stranges, a researcher at the Wyss Institute and one of the two first authors of the study, in a press release.

In research described in the journal Proceedings of the National Academy of Sciences, the scientists built the sequencing engine out of seven protein subunits that create a nanopore complex that prevents a synthesized strand from interfering with the nanopores. 

The resulting device can analyze multiple DNA sequences electronically on the same chip simultaneously. That’s a big change from conventional sequencing procedures that require expensive reagents and machines.

"We are able to identify the correct nucleotide between 79%-99% of the time and only found background events classified as true captures less than 1.2% of the time," said Mirkó Palla, the second first author of the study and a Research Fellow at the Wyss Institute. "This presents a remarkable advance over previous nanopore-SBS systems."

With research coming out just two weeks ago in which a DNA sequencer was built around molybdenum disulfide membrane that could detect different nucleotides based on motion rather than just an electric signal, it will be interesting to see which of these technologies holds the most promise for realizing cheap and ubiquitous DNA sequencers.

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This CAD Program Can Design New Organisms

Genetic engineers have a powerful new tool to write and edit DNA code

11 min read
A photo showing machinery in a lab

Foundries such as the Edinburgh Genome Foundry assemble fragments of synthetic DNA and send them to labs for testing in cells.

Edinburgh Genome Foundry, University of Edinburgh

In the next decade, medical science may finally advance cures for some of the most complex diseases that plague humanity. Many diseases are caused by mutations in the human genome, which can either be inherited from our parents (such as in cystic fibrosis), or acquired during life, such as most types of cancer. For some of these conditions, medical researchers have identified the exact mutations that lead to disease; but in many more, they're still seeking answers. And without understanding the cause of a problem, it's pretty tough to find a cure.

We believe that a key enabling technology in this quest is a computer-aided design (CAD) program for genome editing, which our organization is launching this week at the Genome Project-write (GP-write) conference.

With this CAD program, medical researchers will be able to quickly design hundreds of different genomes with any combination of mutations and send the genetic code to a company that manufactures strings of DNA. Those fragments of synthesized DNA can then be sent to a foundry for assembly, and finally to a lab where the designed genomes can be tested in cells. Based on how the cells grow, researchers can use the CAD program to iterate with a new batch of redesigned genomes, sharing data for collaborative efforts. Enabling fast redesign of thousands of variants can only be achieved through automation; at that scale, researchers just might identify the combinations of mutations that are causing genetic diseases. This is the first critical R&D step toward finding cures.

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