TECHNOLOGY

Beyond 1000

As the genomics community pushes toward the $1,000 genome, Genia is looking beyond, to the $100 genome, bringing the benefits of genome sequencing out of the lab and into the everyday world.

Biological Nanopores: Structure-Based Sequencing of Single DNA Molecules

Genia’s technology reduces the price of sequencing and increases speed, accuracy, and sensitivity by moving away from complex sample preparation and optical detection. The heart of Genia’s technology is the biological nanopore, a protein pore embedded in a lipid bilayer membrane. Our planar electronic sensor technology enables highly efficient nanopore-membrane assembly and accuracy of current readings, overcoming many of the limitations faced by earlier nanopore sequencing efforts.

Genia’s NanoTag sequencing approach, developed in collaboration with Columbia and Harvard University, uses a DNA replication enzyme to sequence a template strand with single base precision as base-specific engineered tags cleaved by the enzyme are captured by the nanopore. As the cleaved tags travel through the pore, they attenuate the current flow across the membrane in a sequence-dependent manner (Figure 1).

 


Figure 1.
Schematic of a single molecule DNA sequencing by a nanopore with phosphate tagged nucleotides. Genia’s NanoTag sequencing approach identifies DNA sequences not by detecting the nucleotides themselves with the nanopore, but by measuring the current changes caused by the passage of each of four different tags that are released from the incorporated nucleotide during the polymerase reaction.

 

Electrochemically, each of the four tag-types interact with the nanopore recognition site differently, partially blocking the ion current by a characteristic amount which results in a tag-specific electronic signature (Figure 2). DNA sequences are computed from the residual currents of the cleaved tags that flow through the nanopore/DNA complex. Because of the sensitivity of Genia’s analog circuitry underneath each sensor, Genia’s platform is ideal for sequencing single DNA molecules.

Figure 2. Example using unique current blockade signatures from engineered electronic tags to identify individual nucleotides. Scientific Reports (Nature Publications group), “PEG-Labeled Nucleotides and Nanopore Detection for Single Molecule DNA Sequencing by Synthesis” (2, 684;DOI:10.1038/srep00684)

 

Standardized Semiconductor Technology Reduces Costs and Complexity 

The brains of Genia’s technology lies in our electronics. Unlike the majority of today’s sequencing platforms, which rely on specialized, expensive optical sensors, Genia’s technology measures changes in electrical currents. These changes are readily detected by the same inexpensive semiconductors that are present in consumer electronic devices such as cell phones, computers, and handheld devices. Because of the well-developed fabrication processes and abundance of manufacturers, bringing semiconductor technology to DNA sequencing will greatly reduce the cost of Genia’s sequencer, making the $100 genome a reality.