Ingenuity Variant Analysis™

Category Cross-Omics>Next Generation Sequence Analysis/Tools and Genomics>Genetic Data Analysis/Tools

Abstract Ingenuity Variant Analysis™ is a web application that helps researchers studying human disease to identify causal variants from human resequencing data in just minutes.

Ingenuity Variant Analysis combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based both upon published biological evidence and your own knowledge of disease biology.

With Variant Analysis, you can interrogate your variants from multiple biological perspectives, explore different biological hypotheses, and identify the most promising variants for follow-up.

Ingenuity Variant Analysis Highlights –

1) Leverage a single application that accesses multiple sources of content to rapidly and comprehensively prioritize variants [including Single Nucleotide Variants (SNVs), indels, structural, and Copy Number Variants (CNVs)];

2) Rapidly identify variants across the genome that is known to be deleterious based upon literature evidence (Not just predictions);

3) Choose promising variants for follow-up based on detailed annotations and facts from the literature about implications of known variants and genes containing novel variants on disease biology;

4) Use knowledge of causal regulation relationships to discover compelling hypotheses for the impact of variants on disease progression;

5) Integrate your own data (such as RNA-Seq isoform expression data or epigenetic genome coordinate data) to refine your variant analysis;

6) Leverage disease models that include symptoms, signaling pathways, cellular processes, established disease genes and efficacious drug targets to rapidly identify disease driver mutations;

7) Integrate pharmaceutically relevant content (drug targets and variants implicated in drug response, metabolism, and toxicity) to more rapidly prioritize variants based on pharmacogenomics; and

8) Use hereditary relationships and inheritance patterns to identify variants that contribute to disease progression across multiple samples, ranging from a few, to hundreds all at once.

Ingenuity Variant Analysis Capabilities --

1) Interactive Filtering To Rapidly Prioritize Variants -

Variant Analysis uses a series of filters that you can apply to quickly exclude common variants (based on the 1000 Genomes project) and non-deleterious variants (those predicted to have No effect on protein function or expression), and then relate variants to relevant biology.

You can easily ask biological questions to identify variants that impact symptoms, pathways, processes, or genes implicated in disease progression or drug response, based on your expertise and the Ingenuity® Knowledge Base of millions of findings from the biomedical literature.

This filtering allows you to go from thousands of variants to a few compelling ones in just minutes, using a simple interface that works at a variety of biological levels (for example, symptoms or physiological information, mutations, pathways, etc.).

No data is ever lost; it is possible to view all variants included or excluded at each filter step, and change filter settings at any time - each adjustment immediately updates the variants that satisfy each step.

2) Integrated and Accurate Evidence for Faster Results -

The biological filtering in Variant Analysis is made possible by the rich biological content in the Ingenuity Knowledge Base, plus additional sources of variant-level content.

Variant Analysis uses millions of accurate biomedical findings curated by experts from the literature and a commonly used 3rd party databases, plus additional content about the effects of mutations on human disease and abnormal phenotypes.

This content is quality controlled for accurate results, and structured into a single, comprehensive database (the Ingenuity Knowledge Base) that leverages up-to-date information on pathways, biological processes, and disease models, plus findings about drugs, diseases, genes, and mutations.

Published findings about each variant of interest can be reviewed to assess the likely strength of it effect. Regulatory diagrams of how each variant may impact disease progression with literature supports are readily accessible.

When a select number of variants have been identified for follow-up, Variant Analysis provides a report of putative causal variants with a customizable table of annotations about the compelling variants.

Additionally, filtering strategies can be shared and reproduced to facilitate collaboration and publication.

3) Content Sources -

Variant Analysis uses primary literature on a large inventory of human germ-line mutations found in patients with particular diseases or abnormal phenotypes with an emphasis on those relevant to cancer.

It also incorporates content about somatic mutations found in human tumor samples from the Catalogue of Somatic Mutations in Cancer (COSMIC) database. This includes the specific somatic mutation and the type of tumor and number of samples in which it was found.

Variant Analysis also uses information from the Online Mendelian Inheritance in Man (OMIM) database about hereditary mutations involved in a wide variety of human disease, plus additional information curated from the literature about the effect of genes and mutations on drug response.

These mutations are mapped to genome coordinates, so they can be compared to variants from resequencing datasets.

Information about the frequency of each variant in the population and predictions as to the effect of the mutation on protein function can be used to help enrich, for the most compelling variants.

Information about the cellular process and signaling pathways associated with some common cancers are available, allowing you to identify the genes associated with these processes as candidates to be involved in disease progression.

Mouse knock-out phenotypes from “Jackson Labs” are also included to help understand the likely phenotypic consequences of loss-of-function mutations in genes of interest.

A wide variety of content types integrated into one place allows you to ask many kinds of questions:

System Requirements

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Manufacturer Web Site Ingenuity Variant Analysis

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G6G Abstract Number 20698

G6G Manufacturer Number 101440