Frog, while it is true that there is a clear inference that the competitive advantage is directly related to the amount of time that the information could be kept from publication, you cannot suppose that the eventual presentation of the details will necessarily eliminate the competitive advantage. Notwithstanding the fact that at least some of the "competitive advantage" relates to the elapsed time between the filing of the provisional/utility patent applications and the details becoming publicly visible, there are questions about how usable the details would be to the competition – especially in terms of being able to utilize the details to perform a method which would not clearly violate the patent. There is also the issue that the company has patented all of the components of the ADMIXMAP platform, and we should therefore not be solely concerned with the AIMs patent, even though it is potentially the most important.
It is, as you infer from Tony Frudakis’s statement, fair to assume that the competition can extract meaningful and helpful information from the patent. A key issue here is to what extent can they use that information "outside of the protection provided by the patent"? We are hampered somewhat in that we do not ourselves know the details of this particular patent, or know with certainty the "phenomena" that the company believes it has uniquely discovered (i.e. we may suppose, but do not yet know, that these are solely concerned with population structure).
In the absence of being able to provide a comprehensive answer to this point, let me reproduce some relevant material that at least gives us some context – and which I base my own opinions on.
From the December 9, 2002 press release (“DNAPrint Launches Revolutionary Pan-Genome Screening Platform Based on Ancestral Admixture Mapping”):
DNAPrint genomics, Inc. (OTC Bulletin Board: DNAP - News; the "Company"), unveiled a new whole-genome screening platform (ADMIXMAP) that promises to rapidly change the landscape of disease and drug response gene hunting. The new platform is revolutionary because it represents the first yet developed for cost-effective whole-genome scanning in large, heterogeneous populations. It taps into sequence differences among the world's various continental population groups to increase the power and efficiency of pan-genome disease gene screening.
ADMIXMAP will allow DNAPrint to identify new disease and drug response genes 10 times faster and 1,000-times less expensively than others who use existing methods. Dr. Tony Frudakis, CEO, informally announced the introduction of ADMIXMAP to attendees at the invitation-only IBM Life Science Solution Developer Conference in Boca Raton, FL, and proclaimed the Company's intent to partner collaborative services based on the platform to pharma, biotech and academia.
The development of ADMIXMAP was a culmination of years of research into population genomics structure and human ancestry conducted with Dr. Mark Shriver of the Pennsylvania State University. The primary focus of the work was to create an original type of human genome map based on validated and characterized Ancestry Informative Markers. snAIMs are Single Nucleotide Polymorphsims (SNPs) of significant allele frequency differences between the world's various continental population groups; prior to DNAPrint's work, such a map had not existed. This map is combined with other compositions and new, highly specialized analytical algorithms to constitute the ADMIXMAP platform. The platform functions by allowing a fine appreciation of population genomics structure relevant for solving complex human conditions, and it is based on a process called Mapping by Admixture Linkage Disequilibrium (MALD) or Admixture Mapping (AM).
DNA exists in a block like state, and hypothesis-free genome screens aim to inspect each of several hundred thousand of these blocks for sequence correlation with disease or drug response. A genome-wide study usually queries hundreds of genomes. Because each genotype costs about $0.50 and hundreds of thousands of genotypes need be created per genome, a typical genome study costs several tens of millions of dollars.
On the other hand, Mapping by Admixture Linkage Disequilibrium (MALD) or Admixture Mapping (AM) takes advantage of the fact that in recently admixed populations (i.e. Hispanics or African Americans, among many others), the block-like structure of DNA extends for MegaBases rather than kilobases (Chakraborty and Weiss, 1988; Stephens et al., 1994, McKeigue 1998, McKeigue et al., 2000). Because the DNA is made of a relatively small number of very large blocks, pan-genome coverage can be obtained with as few as 1,500 markers at a cost of only $1-2K per sample or a couple hundred thousand dollars per study.
MALD and AM can only be accomplished using Ancestry Informative Markers (AIMs) and to its knowledge, the Company is the only to yet mine the human genome to produce a pan-genome map of validated snAIMs. In addition to a validated AIM map, the MALD/AM methods also require the determination of individual ancestry admixture proportions and DNAPrint was the first to reduce the determination of individual admixture proportions using AIMs to commercial practice (see www.ancestrybydna.com). As a result, DNAPrint believes it is the only company in the world capable of practicing the MALD and AM methods.
"The single largest problem drug and diagnostics developers currently face is the cost associated with genotyping," said Dr. Matt Thomas, DNAPrint's Chief Molecular Biologist. "Due to this cost, most whole-genome research today is restricted to isolated, homogeneous populations, which can limit the general applicability of the results obtained."
"In part, the human genome was sequenced to help us get away from a restrictive focus on homogeneous, isolated populations for drug and diagnostics design," said Zack Gaskin, DNAPrint's Chief Technician. "Because ADMIXMAP is the first platform to enable cost-effective whole genome scans in heterogeneous populations, we expect it to have a profound impact on genomics- based drug and diagnostics design and we consider its development to represent an important milestone in human genome research."
DNAPrint intends to partner this new platform with biotech, pharma and academia seeking to identify new drug targets and diagnostic tests. Using this model, partners would fund the work and the Company would retain a share of the intellectual property produced. DNAPrint hopes to use the method with partners to discover hundreds or even thousands of disease genes and to acquire a significant stake in the future of genomics-based medicine. Given the magnitude of drug and diagnostics royalties, relatively few of the discovered genes need be developed as drug targets or diagnostic tests to render the endeavor a success.
Here is a news article from November 21, 2003 that people might not have seen previously that covers the same ground more succinctly:
Genome Screening Platform Based on Ancestral Mapping Last Updated: 21 November 2003 (Medinews.com)
A new platform that allows whole-genome scanning in large heterogeneous populations will help researchers identify new disease and drug response genes much faster and less expensively.
The platform, called Admixmap, is based on years of research into population genomics structure and human ancestry conducted with Dr. Mark Shriver of Pennsylvania State University (University Park, USA). The focus of the research was to create an original type of human genome map based on validated and characterized ancestry informative markers, or snAIMS, which are single nucleotide polymorphisms (SNPs) of significant allele frequency differences among the worlds various continental population groups. This map is combined with other compositions and highly specialized analytical algorithms to constitute Admixmap. The platform is based on a process called mapping by admixture linkage disequilibrium (MALD) or admixture mapping (am).
Admixmap is the product of DNAPrint Genomics, Inc. (Sarasota, FL, USA). The company says by using Admixmap, it can identify new disease and drug response genes 10 times faster and 1,000 times less expensively than existing methods. DNAPrint intends to partner this new platform with biotechnology, pharmaceutical, and academic organizations to identify new drug targets and diagnostic tests.
Because Admixmap is the first platform to enable cost-effective whole genome scans in heterogeneous populations, we expect it to have a profound impact on genomics-based drug and diagnostics design and we consider its development to represent an important milestone in human genome research.
"The first to identify a disease causing or drug response gene variant owns it, and each variant connection can only be discovered once. Once discovered and patented, the new owner controls their use in the therapeutic and diagnostic markets. Because there are only so many genes for any disease, this means the new owner also controls a significant fraction of the therapeutic and diagnostic market for the disease itself."
"The first company to build a "disease gene discovery platform" to overcome these limitations could be the first to discover hundreds or even thousands of disease genes."
"DNAPrint exercises a virtual monopoly on this method, not only for the present because we are the only ones with the resources to perform the method, but by virtue of our patent, which effectively precludes others from performing the method efficiently."
So it would appear that ADMIXMAP (not to be willfully confused with any other things that have a similar nomenclature) provides the company with significant advantages in terms of the identification of new disease and drug response genes allowing them to develop new drug targets and diagnostic tests (not forgetting disease predisposition in addition).
Will the AIMs patent help DNAP corner the market on practical genome screening, as Tony Frudakis believes? Will other companies be able to utilize information contained in the patents in such a manner that they can circumvent our patent(s)? What has the company done with the platform in the intervening period and what else has they potentially discovered? How many other patent applications related to e.g. drug response classifiers are in preparation or have been submitted?
We do not know the answers to these questions and await developments. Like W2P though, I believe that the details of the AIMs patent will provide more insight into at least some of these questions. In the meantime, and considering the fact that nobody else seems to have developed a complex trait classifier (and we seem to have developed at least five), I am inclined to believe that the ADMIXMAP platform and the patents currently provide and will continue to provide a significant competitive advantage.
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