Leadership in Genomics: VarElect – Variants in Disease and UCSC Genome Technology Center | Leaders in Pharmaceutical Business Intelligence (LPBI) Group

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Leadership in Genomics: VarElect – Variants in Disease and UCSC Genome Technology Center

February 17, 2016 by 2012pharmaceutical

Leadership in Genomics: VarElect – Variants in Disease and UCSC Genome Technology Center

Reporter: Aviva Lev-Ari, PhD, RN

SOURCES

http://www.genecards.org/

https://genomics.soe.ucsc.edu/

Integrated Biomedical Knowledgebase

The Next Generation Sequencing Phenotyper – Extensive disease – gene relationship data

GeneCards^®: The Human Gene Database

GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

APPLICATIONS

Interpret next generation sequencing results
Identify & Prioritize genes and variants according to their relevance to diseases and phenotypes of interest
Explore relationships between genes and gene variants and selected diseases or phenotypes via relevant pathways, interaction networks and publications

Discover biomarkers for diseases

Rapid prioritization of variant genes based on disease/phenotype of interest

VarElect – Powerful gene-based NGS biological interpretation for revealing potential variants playing a role in disease

VarElect is a cutting edge Variant Election application for disease/phenotype-dependent gene variant prioritization. It is an effective and user friendly tool for analyzing genes with variants following Next-Generation Sequencing (“NGS”) experiments. VarElect can rapidly prioritize genes that have been found to have variants according to selected disease/phenotype – gene associations.

VarElect leverages the rich information within the LifeMap Knowledgebase of GeneCards®, the leading human gene database, MalaCards, the human disease database, LifeMap Discovery®, the regenerative medicine, and PathCards, the unified human biological pathways database.

Using VarElect you can input a list of dozens, or hundreds of genes with variants, and narrow it down to the top 1-10 genes that are potentially associated with a particular disease, phenotype, or other biological function. VarElect acts jointly on the gene list and phenotype/disease keywords, and produces a list of prioritized, scored, and contextually annotated genes and direct links to supporting evidence and further information. VarElect utilizes the deep LifeMap Knowledgebase to infer direct, as well as indirect, links between genes and phenotypes. Indirect association between genes and disease are based on shared pathways, interaction networks, paralogy relations, domain-sharing, and mutual publications.

An example of an indirect GeneCards-based inference of GeneA to Phenotype PhenX is when PhenX is found to be associated with GeneB, which in turn shares a pathway with GeneA. Such gene-to-gene relationships are also formed (among others) by interaction networks, paralogy relations, domain-sharing, and mutual publications. MalaCards, in turn, allows one to produce a comprehensive phenotype search expression by using its data about diseases, underlying symptoms, and their relationships. The degree of mutual linking is quantified via endogenous search scores. VarElect provides a robust algorithm for ranking genes within a short list, and pointing out their likelihood to be related to a disease, enabling the researcher to perform the last decision step in deep sequencing runs in a fast and objective manner.

SOURCES

http://varelect.genecards.org/about/

http://lifemapcms.azurewebsites.net/media/95773/2015-05-varelect-%E2%80%93-powerful-gene-based-ngs-biological-interpretation-white-paper.pdf

Spin-Off Companies – Research conducted by UC Santa Cruz Genomics Institute researchers has resulted in new companies:

BioStinger

Nanopipette for single-cell manipulations

DoveTail Genomics

An in vitro proximity ligation approach that simplifies genomic discovery by integrating the highest quality long-range genomic information with next-generation sequencing output.

Five3 Genomics

Genomic sequencing analysis algorithms

MagArray

Multiplex cancer biomarker detection

Maverix Biomics

Analyze, visualize, interrogate, and manage biological data

Two Pore Guys

Solid state nanopore technologies for genome sequencing and medical diagnostics

https://genomics.soe.ucsc.edu/