Based upon the successful development and testing and anticipated evolution of our
laboratory techniques and data analysis methods in homogeneous DNA analysis, we
forsee several opportunities for direct commercialization of the technology in the coming
years.
Among these are an online DNA analysis software and service company, being launched
in the coming year, and in the longer term, a laboratory which would apply homogeneous
DNA analysis to perform fast, accurate, and economical clinical assays, specializing in
SNP and dinucleotide typing.
The software and service enterprise, DNAwizards.com, will serve research, clinical, and
commercial users both by providing analysis services and distributing analysis software
and educational materials for clients to use themselves.
The software we have developed thusfar and continue to improve and expand may be
divided into several integrated types. These include sequence DNA sequence
manipulation and primer optimization, DNA melting temperature modeling, melting
curve normalization, melting curve classification, and amplification curve quantification.
The concepts of each are described below along with examples for which invention
disclosures have been submitted to the University of Utah's Technology Transfer Office.
An example of primer design and optimization software is SNPWizard (UUTTO, U- ),
developed during the first year of the COE for genotyping of single nucleotide
polymorphisms by high resolution melting analysis of small amplicons. A publication by
this title [] has been recently been submitted and refers to a website where this and other
programs to be run and distributed by DNAWizards.com may be remotely beta-tested by
referees and readers requiring reproducibility, and other potential users of the software
and other services. The primers designed by SNPWizard proved superior to those
obtained by other methods in performing the necessary amplification and differentiation
of high resolution melting curves for the successful genotyping demonstrated in the
paper. SNPWizard and other DNAWizards projects are written in the Labview (National
Instruments) platform, popular in many scientific laboratories, and thus interfaces easily
with several other useful and effective DNA amplification and homogeneous analysis
programs.
Another, potentially even more useful, primer design package is ExonWizard (UUTTO,
U- ), which designs effective PCR primers which result in amplicons consisting of the
exon and splicing regions of target DNA in which functional mutations may occur. This
can maximize the ability to detect, identify, and quantify the DNA involving these
mutations, which has numerous practical and commercial applications in both research,
clinical, and industrial settings. Like SNPWizard, the primers designed by ExonWizard
have consistently led to successful amplifications and analyses where those provided by
other means have failed.
In conjunction with these and other sequence analysis needs, we have developed
numerous convenient and integrated utilities for such tasks as stand-alone misprime
checking, subsequence location, interactive mutation and primer editing, and sequence
input, display, and recording.
We plan to increase the advantages in effectiveness of our software even further with the
incorporation of an indexed genomic database in the coming year. Other projected
research in this area for the coming year includes exon-weighted multiple alignment to
complement and improve upon the hugely popular and useful public domain Clustal
software.
These programs and utilities which are not currently available to a sizeable market of
potential users, could be purchased from DNAWizards, or if the client prefers, company
experts can run analyses for them. This provides another unique opportunity for
commercial integration with the Utah companies which deliver the actual DNA primers.
DNAWizards, in collaboration with such a company, can not only determine the most
effective primers, but have them delivered to the customer the next day, benefitting all
parties involved.
Central to many of these functions is the accurate modeling of annealing and melting
temperatures and issues affecting the more detailed prediction of high-resolution melting
curves such as melting domains, base specificity, and other properties of fluorescent dyes
and probes.
We have already made improvements upon existing models with parameters to more
accurately reflect realistic analytical PCR conditions, and are currently pursuing
significant improvements to incorporate additional factors present in these reactions.
User-friendly melting temperature modeling software as well as `fee per use' prediction
service will be available from DNAWizards in the same manner as primer design
software and service.
Another program we have delivered in accomplishing a proposed goal for the first year of
this COE automates the heretofore slow and costly subjective methods of DNA melting
curve normalization and classification. Autocall (UUTTO, U- ) takes 3-4 minutes to
perform the normalization and classification steps for 216 blinded studies which take a
human expert several hours to accomplish with comparable accuracy. These steps involve
numerous artificial intelligence `pattern recognition' capabilities such as identifying the
best segments of the melting curves to extract and upon which to base normalization and
temperature shifting transformations. This is followed by the final automated
classification of melting curves as wild-type or mutant.
The remaining category of is based like the others upon an effective combination of
biochemistry and mathematics. Quantitative PCR, or qPCR, involves estimation of the
number of copies of a specific target DNA sequence from the detailed features of the
fluorescence curve through their amplification by PCR. Many diagnostics used in
molecular classification by gene expression pattern in research, clinical, and forensic
medicine settings, as well industrial process quality control are based upon these
techniques. (There is a special session during a March 2004 qPCR conference in Munich
on qPCR and brewery quality control!) We are pursuing research and software
(UUTTO), U- ) which can improve the accuracy of these methods by basing the
quantification upon mathematical models more consistent with the amplification curve
features being measured.
Education brownie points:
The beneficial synthesis of mathematics and molecular biology apparent in these
developments has been noticed by these departments at the university, and the
mathematics community in general. The annual Josiah Willard Gibbs keynote address in
applied mathematics at the recent 2004 Joint National Mathematics meeting in Phoenix,
was entitled `Biology as Information', and highlighted many of the very same problems
we are addressing. In light of this, the chair of the mathematics department,
(Distinguished Professor) Graeme Milton, has invited Dr. Palais to develop a new course
curriculum around the mathematics of DNA analysis.
In addition to direct commercialization of our DNA analysis software, the future
development of faster, more accurate and economical homogeneous DNA analysis
technology will promote the generation of jobs in clinical testing laboratories specializing
in SNP and dinucleotide typing, such as HLA identity testing for organ transplant
compatibility. It is also worth noting that improvements in diagnostics inevitably lead to
improvements in therapy.
RELEVANT CLIPS FROM THE COE HOMEPAGE
The COEP office strongly encourages collaboration between centers. We believe
interaction occurs more easily when individual directors know one another and have had
opportunity to discuss their various programs. Combining the complementary strengths
of multiple centers greatly enhances the opportunities for scientific advancement and the
ultimate commercialization of Center technologies.
The primary objective of the Centers of Excellence Program from its inception has been
to encourage the commercialization of leading edge technologies developed at Utah's
universities and colleges. This commercialization, accomplished through licensing
patented technologies and by creating new companies, impacts Utah's economic
development by the creation of jobs, the flow of licensing royalties, the expansion of the
tax base, and the leveraged use of matching fund dollars to strengthen research and
development at Utah's institutions of higher learning.
Generally centers can be funded upon an annual review for a period of five years. In the
first 1-2 years of funding, awards are granted based on the commercial potential
perceived in each center. In later years, subsequent review and approval of funding
becomes increasingly competitive and depends on the specific accomplishment of
milestones and deliverables.