Technology

Cornerstone Technology - SIGEX

Vitruvius Biosciences has discovered a new method for analyzing genetic information across whole genomes allowing researchers in the life sciences to gain valuable insights into the molecular basis for the differentiation between individuals, organisms, and cell types at the genome (DNA) and transcriptome (mRNA) level. The acronym coined for this new method is SIGEX, which stands for Sequence-Independent Genetic Exploration. SIGEX represents a completely new generation of whole genome or transcriptome microarray scanning technology based on the properties of intelligently designed sets of hybridization probes to rapidly characterize target nucleic acid populations at the DNA or RNA level without prior knowledge of the sequence being analyzed.

SIGEX differs from classical DNA analysis using basic hybridization principles primarily in the design of the DNA probe molecules (oligonucleotides) used to “fish” for specific DNA sequences. Conventional DNA probe design requires prior DNA sequence information to design and synthesize a probe to capture a specific DNA or RNA sequence. Vitruvius Biosciences’ approach is radically different from all current microarray-based probe design technology in that specific genetic sequence information is neither necessary nor required prior to the design of the DNA probe set. A proprietary computational process (patent pending) generates probe set sequences that are designed to be maximally informative in describing unknown genetic systems. A microarray presenting the derived set is used to generate specific hybridization patterns from target samples that can characterize and differentiate individual genomes or transcriptomes. Since the probe set is not tailored to any specific genome and is independent of sequence content, it can be considered “universal” in that a single microarray probe set can differentiate and uniquely define the genetic material being scanned.

The SIGEX process of using a single, intelligently designed finite probe set to characterize genetic variations is remarkably similar to the mechanism by which humans and (to a greater degree) animals sense different smells. The sense of olfaction uses a combinatorial approach to recognize and process odors. Instead of dedicating an individual odor receptor to a specific odor, the olfactory system uses an “alphabet” of receptors to create a specific smell response within the brain. As in language (or music), the olfactory system appears to use combinations of receptors (analogous to words or musical notes) to greatly reduce the number of actual receptor types required to convey a broad range of odors.

The SIGEX approach to genetic analysis employs the same type of combinatorial processing as the olfactory system. The alphabet of receptors is an arrayed set of DNA probes in which each probe is not designed to bind a specific target sequence, but participates in a system in which combinations of outputs convey a genetic “sense”. Thus, both SIGEX and the mechanics of the sense of smell generate meaningful information from a collection of receptors or probes in which no single receptor is specifically tailored to any individual molecule, and only provides useful information content in conjunction with all other receptors (probes) in the system.

Vitruvius Biosciences is initially focusing this technology on the development of DNA microarray probe sets to identify and differentiate microbial genomes. Since only approximately 100 microbial genomes have been completely sequenced (sequencing one genome may take upwards of a year and is incredibly labor intensive and expensive), this technology becomes extremely valuable because it does not rely on specific sequence information. Vitruvius Biosciences has been awarded a Phase I Small Business Innovative Research grant (SBIR) from the U.S. Department of Defense to begin development of the technology in support the national initiative for biodefense. As a large part of Phase I work has been successfully completed, Vitruvius Biosciences has been invited and has submitted a significantly larger Phase II proposal to finance additional research and engineering to drive the technology toward commercialization.

Vitruvius Biosciences has also begun the application of SIGEX technology in further characterization of more complex genomes and transcriptomes (such as the human genome with 3.2 billion bases or “letters of the genetic alphabet” in its script). Although the primary sequence of at least a small number of individuals has been mostly completed, our knowledge of the number of genes actually represented in the genome is not known with certainty (predictions range from 30,000 to 120,000), and even less is known about their complex interactions in biological processes. It is becoming clear that there is not a one-to-one relationship between individual genes and overall cellular functions. As an example, consider the fact that it is believed that 60% of all human transcripts (mRNAs) are alternately spliced. That is, different coding regions called exons are differentially put together or “spliced” to create new combinations of the same gene. Within this 60%, on average, each transcript has 5 isoforms or variants. In one instance, scientists have identified a human gene called dsCAM (a homolog of a Drosophila spinal motor gene) that has about 18 to 20 exons but (and here is the catch) some of these exons have up to 16 variants each. Other exons in this gene have 6 variants. When all the combinatorial splicing variants are calculated for this gene it comes out to 38,000 different splice variants for this gene alone! Now, this is not to say that all genes will have thousands of variants but some other human genes may. Thus, it is very difficult to use conventional expression array for all these variants, as well as other differentially expressed but unknown genes, because it requires a priori knowledge or a hypothesis about each of those individual events.

It is clear that the relationship between genotype and phenotype is complex and highly nonlinear and cannot be predicted by simply cataloging and assigning gene functions to genes found in a genome. If genomics is truly going to pave the way toward new drug targets, pharmaceuticals, personalized medicine and the like, it will have to be studied in a manner that addresses it at the level of biological complexity at which it operates. Vitruvius Biosciences technology directly addresses this complexity problem by providing a method for characterizing nucleic acid populations as whole systems instead of a collection of individual hybridization events. As in the analogy cited above, we are interested in studying the organization of the entire “song”, not just a hit-or-miss analysis of what “notes” seem to be present. Although no single technique, including this one, will be 100% efficient in completely characterizing complex genetic populations, it is envisioned that the SIGEX technology will provide a tool that can uncover unknown and uncharacterized genetic associations, not accessible by any current methodology.

For these reasons, Vitruvius Biosciences SIGEX technology is extremely attractive as a future generation genetic tool, because it allows the interrogation of complex genetic systems in which an almost infinite number of outcomes or events may be analyzed with a finite element probe set.