Sequencing
The Sequencing application will start with moderate molecule lengths, between 10,000 and 15,000 basepairs in length. Each strand will be independently labelled. Sequence will be determined directly from the images, with built-in error checking by comparing the information from the two strands.
ZSG process enables electron microscopes to “see” DNA
Parallel rows of Iodine atoms built into DNA molecules. White stripes are inter-strand spaces. Adjacent molecules have overlapping iodine atoms, as these labels are on the edges of the dsDNA.
Background
Sequencing is the most powerful form of genetic research. It provides a wealth of information that can come from no other technology. Done correctly, it is expected to unlock the mysteries of the most complex human diseases, especially the myriad forms of cancer. Unfortunately, costs are too high for widespread use. To use sequencing to develop a new class of drugs could take the equivalent of thousands of complete genomes. At the current costs of several million dollars or more per genome, the overall project would cost several billion dollars. This amount exceeds the market capitalization of all but the largest pharmaceutical companies. Even the “Next-Gen” technologies lower these costs only to the high hundreds of millions of dollars for such a project.
Sequencing costs are intimately tied to sequencing speeds; the best traditional system can process 2 million base pairs per day and requires a team of experts to prepare samples and perform intermediate steps in the process. The fastest innovator in the market claims 100 million bases per day; these “Next-Gen” Sequencers are in the early stages of product introduction. We expect to be able to perform reads of a billion base pairs per day with our early versions and many times more than that in the following generations.
Sequencing Application
The ZS Genetics Sequencing System is targeted for availability in the latter half of 2008.
With our Sequencing technology, a sample is prepared once, a picture is taken with a transmission electron microscope and the Sequence is read directly from that picture. A second picture is then taken, then another, and so on. Our approach is expected to be able to read over 1.7 billion base-pairs per day as a starting point, compared to 100 million for the leading Next-Gen competitor today. After applying a 4X over-sampling rate to address potential errors, the net rate will still be over 400 million base-pair calls per day.
The Reading System consists of:
- A modular, specially-modified, transmission electron microscope.
- A digital imaging system from the world’s leader in digital imaing systems for electron microscopes.
- Image analysis software reading sequence, cross-checking base-pair identities, genome reassembly and data export.
- This system is completely modular, protecting users from obsolescence. Regular system upgrades will be available from ZSG (likely from competitors as well) to keep users at the forefront of their fields.
Reaction Kit:
- Custom substrate configured for de novo sequencing. This will incorporate microfluidics and surface chemistry needed to attach and align molecules for sequencing.
- All the reagents (buffers, labeled dNTP’s, primers, enzymes) needed for labeling a sample, fixing and aligning molecules on the substrate.
Advantages
Our comparative advantages give us the potential for the lowest cost sequences:
- Our method requires 5 or fewer cycles of PCR; eliminating most of the chemistry and most of the error that PCR induces.
- Our unique contrast-atom labels are much smaller than fluorescent labels, and therefore easier to incorporate.
- Our Reading System is a modified version, focusing on automated imaging, of an instrument already commercially available and fully developed. It is not a new machine that requires extensive custom development.
- Read lengths should start at 10,000 base-pairs and quickly move to 20,000 or more depending on availability of effective isothermal methods.
On top of these advantages, our system is expected to be amazingly fast with on-going improvements driven by two large, dynamic industries; semiconductors (which drives electron microscope innovation) and digital imaging (which is following Moore’s Law). ZSG believes it will be hard for other innovators to beat 10 cycles of wet chemistry (instead of billions) followed by direct digitization of over 1.7 billion base-pair reads per day and rising.