SBIR-STTR Award

Omicia, Inc. intends to deliver genomic information services to individuals that allow them to make use of current genetic and clinical research better to manage their health. The motivation behind this SBIR grant is to solve the problem of integrating existing clinical databases with the most current genomic data, in a system that is maintainable and extensible. As part of this Phase I program, 0micia intends to develop new "mapping" methods to annotate Mendelian mutations as tabulated in the Online Mendelian Inheritance in Man ("OMIM") database within the current human genome sequence. Specifically, there now exists in the public domain two distinct information resources and neither is as valuable as it potentially could be because current research efforts require their integration. A key aspect of research in genetics is the association of sequence variation with disease genes and phenotypes. Sequence variation data is currently available from OMIM, HGMD and others, both of which provide phenotypic information and describe amino acid variation. Unfortunately, in most cases these variation references do not provide sufficient information to support their direct mapping onto current genomic sequences and the associated annotated genes. Single nucleotide polymorphism (SNP) data is held in dbSNP and other publicly accessible databases. While these databases contain millions of entries each including the position of the SNP on the genome, they do not provide significant phenotypic information about the SNPs. The specific aim of this Phase I program is to build a prototype computer system that precisely and uniquely identifies the exact nucleotide positions of these OMIM mutations within the annotated gene of the latest human genome sequence assembly as published by the NIH. This system will include automated mapping capabilities and, in addition, will include an annotation workstation to support manual annotation efforts. The prototype system will be tested and validated by annotating 100 highly important disease genes, to show that the system is capable of supporting the breadth of mapping issues that we anticipate. As part of this effort, these mutations will be categorized using extensions of existing gene ontologies ("GO") and phenotype classification schemes ("MeSH"). The deliverables from this project will be enhanced and refined during Phase II, and will become an integral part of Omicia's ongoing business of delivering broad-based, personalized genetic profile information to individuals

Omicia, Inc. intends to deliver genomic information services to individuals that allows them to make use of current genetic and clinical research better to manage their health. The motivation behind Phase II of this SBIR grant is to finalize the mapping and annotation of Mendelian mutations as tabulated in the Online Mendelian Inheritance in Man ("OMIM") database within the current human genome sequence assembly. In addition, modified mapping methods are also used to include individual mutations from the Human Genome Mutation Database ("HGMD"), as well as polymorphisms from databases such as dbSNP. A key aspect of research in genetics is the association of sequence variation with disease genes and phenotypes. Sequence variation data is currently available from OMIM, HGMD and others, both of which provide phenotypic information and describe amino acid variation. Unfortunately, in most cases these variation references do not provide sufficient information to support their direct mapping onto current genomic sequences and the associated annotated genes. Single nucleotide polymorphism (SNP) data is held in dbSNP and other publicly accessible databases. While these databases contain millions of entries each including the position of the SNP on the genome, they do not provide significant phenotypic information about the SNPs. In order to use these databases to deliver accurate and reliable genomic information to individuals, these gaps must be resolved. The specific aims of this Phase II program are: first, to finalize the implementation from Phase I of a software system to support the mutation mapping and annotation from various databases; second, to map uniquely and accurately the positions of mutations associated with a human phenotype onto the human genome assembly using a computer-assisted expert driven manual approach; third, and finally, to capture the mutation-disease associations for each of these markers in a meaningful and electronically tractable way using links to the MeSH disease ontology. An initial selected set of 97 disease genes, developed during Phase I, will be used to validate each software development step. The goal of the project is to map and clinically annotate a very comprehensive set of disease genes estimated to be between 2,000 - 3,000 genes. The deliverables from this project will become integral components of Omicia's business of delivering broad-based, personalized, genetic profile information to its customers. Furthermore, Omicia expects to license its genotype-phenotype database and Biofinormatics infrastructure to interested commercial entities in biotechnology and Pharma. An initial collaboration project with a small biotechnology company, Human Genetic Signatures Pty. Ltd., has already started.

Thesaurus Terms:
bioinformatics, computational biology, computer program /software, computer system design /evaluation, gene mutation, genetic mapping, genetic marker, genetic susceptibility Internet, information retrieval, molecular biology information system, nucleic acid sequence, phenotype, single nucleotide polymorphism, vocabulary development for information system biotechnology, human data