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.
| Moore, Barry; Hu, Hao; Singleton, Marc et al. (2011) Global analysis of disease-related DNA sequence variation in 10 healthy individuals: implications for whole genome-based clinical diagnostics. Genet Med 13:210-7 |
| Reese, Martin G; Moore, Barry; Batchelor, Colin et al. (2010) A standard variation file format for human genome sequences. Genome Biol 11:R88 |
| McKernan, Kevin Judd; Peckham, Heather E; Costa, Gina L et al. (2009) Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res 19:1527-41 |
| Yandell, Mark; Moore, Barry; Salas, Fidel et al. (2008) Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins. PLoS Comput Biol 4:e1000218 |
