DNAPrint genomics, Inc. Expands Proprietary SNP Database
August 28, 2000 DNAPrint genomics (Pink sheets: ‘DNAP’) announced today the addition of
the 2,000th candidate SNP to its PhenomeSM database. The PhenomeSM database contains
a high-density map of SNP and haplotypes candidates for certain human genes of
pharmacogenomic and cancer genetics value. This is believed to be one of the highest
resolution SNP maps for genes of critical import to these two fields, and will be used by the
company in conjunction with the public SNP database, as a platform upon which the
companies work will be performed. The milestone of having made the 2,000th addition to this
database allows the company the opportunity to share with its shareholders the value of the
database and to highlight the DNAPrint genomics approach.
The SNP consortium is slated to add a large collection of SNPs and corresponding
sub-population allele frequencies to the public database. The value of this database is it’s
widespread coverage of the human genome and its accessibility free of charge to researchers
all over the world. The genome wide coverage of the public SNP database make it well suited
for genome-wide linkage studies which will require a SNP, on average, every 3Kb of the human
genome. These types of systematic studies will allow workers to identify important linkage
disequilibria, or “physical relationships” between SNPs and disease/trait genes.
Targeted Scanning is an alternative to systematic genome wide scanning, and focuses on
surveying smaller number of genes in greater detail. The value of this approach can be
appreciated from the decades of research that have contributed to our understanding of human
disease. Studies of drug metabolism and cancer have shown a relatively small collection of
genes, and gene types, to be responsible for a vast majority of problems. Pharmacogenetic
studies have shown that polymorphism in xenobiotic metabolism proteins such as cytochrome
p450 genes and N-acetyltransferases, among others to be associated with aberrant drug
metabolism, resulting in some cases in hepatocellular toxicity or other “side-effects”. Work in
the field of cancer has shown that mutations in genes normally involved in these genes, as
well as other basic tasks such as cell cycle regulation and DNA repair play important roles for
this disease. Thus, certain phenotypic traits such as drug metabolism or cancer, are well
suited for a targeted scanning study design.
Notwithstanding it’s tremendous value, the pan-genome coverage of the public database
comes at the expense of individual gene resolution. Since the public SNP database will
contain relatively few SNPs for most human genes, there is and will remain a need for higher
resolution SNP maps for many of the most “important” genes of clinical value. The public
resources will contain no information on genetic haplotypes, or phase coupled genotype sets,
which have considerable power for discovering genotype-phenotype associations. Further, the
public SNP database will not be available publicly for some time. Lastly, most of the public
SNP database will have come from healthy donors used for the human genome project and
related efforts and therefore may biased against SNPs which play a role in human pathologies.
Because of these anticipated deficiencies, DNAPrint genomics has been building it’s own
candidate SNP and Haplotype database, called the PhenomeSM database. The database
focuses on many of the most “important” human drug metabolism and disease genes whose
function is compromised in certain individuals who show drug side-effects or neoplastic
disease. The database serves as a foundation for virtually any pharmacogenomic or cancer
genetic study and is derived from two main sources: the application of a proprietary and
automated set of data mining algorithms to the public (NCBI) EST/mRNA and Gene database,
and through a process called “re-sequencing” where the large regions of the genes are actually
sequenced from target patient groups. Resequencing involves obtaining long read sequences
in contrast to single base, high-throughput SNP scoring which relies on the existence of an
accurate SNP map such as the PhenomeSM or public database. Candidate SNPs are
accompanied by extensive annotation and 200bp of flanking DNA sequence that facilitates
SNP scoring study design. SNPs for over 100 “important” human genes have been discovered,
and approximately 20 high-quality candidate SNPs have been identified for each of these
genes. The density of high quality SNP candidates within these genes is higher than the
frequency of SNPs expected in the human genome from work by others (approximately 1 per
1000 base pairs). Further, the average gene in the PhenomeSM database contains over 10
times the number of candidate SNPs that are currently available in the public database. SNPs
for many of these genes have been discovered to be part of major population Haplotypes. The
company will use this proprietary database as a foundation for it’s first SNP/Haplotype
association and linkage disequilibrium studies for Pharmacogenomics and breast cancer. In
addition to providing a proprietary database resource platform not available through the public
SNP database, it enables the company to conduct detailed and high-resolution studies well in
advance of those organizations awaiting the completion of the public database.
The PhenomeSM database recently recorded it’s 2000th entry, and is scheduled to add its
5,000th entry later this year. To the companies knowledge, it is one of the first databases of
its kind to focus on resolution within “important” genes rather than across the entire genome,
and will offer the company a decided advantage in its high-throughput SNP/Haplotype scoring
studies. The company intends to copyright the database, and patent it’s components
discovered to be associated with clinical pathologies as “diagnomics” products.
About DNAPrint genomics
DNAPrint genomics, Inc. provides practitioners of genomic research and personalized medicine with a
comprehensive system for complex trait dissection and patient classification. DNAPrint genomics Inc.
was founded by a group of scientists with research and commercial experience in high-level
mathematical modeling, programming and molecular genetics. For more information about the
company, please visit www.dnaprint.com.
For scientific inquiries please contact: Dr. Tony Frudakis at (941) 351-4543. All other inquiries please
contact: Richard Craig Hall at (941) 341-0136. Except for factual statements made herein, the
information contained in this press release consists of forward-looking statements that involve risks
and uncertainties. The Company’s actual results could differ materially from those contained in such
statements. Factors that could cause or contribute to such differences include unexpected shortages
of critical components, rescheduling or cancellation of customer orders, the timing and market
acceptance of new product introductions by the Company and its competitors, and general
competition and price pressures in the marketplace
Copyright DNAprint genomics © 2000
1748 Independence Blvd. Ste D1
Sarasota, Florida 342
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