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Oakland, CA, United States

Yandell M.,University of Utah | Huff C.,University of Utah | Hu H.,University of Utah | Singleton M.,University of Utah | And 4 more authors.
Genome Research | Year: 2011

VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds on existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-touse fashion. VAAST can score both coding and noncoding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any existing methodology. Here we demonstrate its ability to identify damaged genes using small cohorts (n = 3) of unrelated individuals, wherein no two share the same deleterious variants, and for common, multigenic diseases using as few as 150 cases. © 2011 by Cold Spring Harbor Laboratory Press. Source


Disclosed is a method for determining whether an individual has an enhanced, diminished, or average probability of exhibiting one or more phenotypic attributes and related methods of selecting a set of genetic markers; for providing relevant genetic information to an individual; of evaluating the probability that progeny of two individuals of the opposite sex will exhibit one or more phenotypic attributes; and for determining the genomic ethnicity of an individual.


Patent
Omicia Inc. | Date: 2011-09-09

Disclosed are methods for detecting and/or prioritizing phenotype-causing genomic variants and related software tools. The methods include genomic feature based analysis and can combine variant frequency information with sequence characteristics such as amino acid substation. The methods disclosed are useful in any genomics study; for example, rare and common disease gene discovery, tumor growth mutation detection, personalized medicine, agricultural analysis, and centennial analysis.


Disclosed is a method for determining whether an individual has an enhanced, diminished, or average probability of exhibiting one or more phenotypic attributes and related methods of selecting a set of genetic markers; for providing relevant genetic information to an individual; of evaluating the probability that progeny of two individuals of the opposite sex will exhibit one or more phenotypic attributes; and for determining the genomic ethnicity of an individual.


Grant
Agency: Department of Health and Human Services | Branch: | Program: SBIR | Phase: Phase I | Award Amount: 149.17K | Year: 2010

DESCRIPTION (provided by applicant): High-throughput sequencing technologies are beginning to deliver complete individual genome sequences. However, significant barriers still obstruct the use of these data for basic research and in clinical evaluation for personalized medicine. One major barrier is the absence of tools for variant annotation with respect to disease. Our goal is to overcome this barrier by creating for sequence variants a suite of tools similar to those that exist for gene annotation. Although disease, gene and sequence ontolgies already exist, systematically interrelating (harmonizing) them to one another in a manner that will support effective variant annotation is a major task. We will use state of the art protocol for biomedical ontology development, ensuring interoperability and usability to achieve this goal. The research proposed in this application has three aims. In Phase I we will harmonize and interrelate existing ontologies for variant and disease annotation, with a specific focus on cardiovascular disease (CVD). In Aim 2 we will curate an existing CVD gene collection compiled at Omicia Inc. consisting of 336 CVD disease genes to the harmonized ontology. In Aim 3 we will annotate the variants and implications of each variation for ten personal genomes. Our plan is to begin with a proof-of-concept project to develop an ontology for annotating personal sequence variants in genes implicated in CVD. In phase II we intend to expand the ontology to a broader coverage of disease, utilizing the lessons we learn from phase I. This firm logical foundation will allow us to build a suite of commercial strength software for variant annotation to provide a much needed tool for personal genomics. PUBLIC HEALTH RELEVANCE: This project will produce a modular, harmonized ontology for the description of personal genomic sequence variants with respect to cardiovascular disease (CVD). This will in turn provide a means to generate detailed, clinically relevant genetic-signature reports. This work will be preformed in partnership with Omicia Incorporated. Omicia's goal is to provide content and analysis tools for molecular diagnostic tests using personal genome sequences. The tools produced by this project will promote better public health and provide significant commercial opportunities.

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