Identify causal variants from human sequencing data in just minutes

Ingenuity IPA Interpret Biological Meaning Graphic

Rapidly Identify and Prioritize Variants

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.

Rapidly Indentify Variants Graphic - Ingenuity Variant Analysis

Variant Analysis used in NCI-60 Interpretation of Genomic Variants

The NCI-60 Data Set offers tremendous promise in the development and prescription of cancer drugs

NCI-60 Data Set Screen

Ingenuity Variant Analysis scores high marks for ease of use

97% of surveyed researchers are satisfied with the ease of use of Ingenuity Variant Analysis and we are honored that they chose to share the data through our Publish tool.

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"Being a bioinformatician, I appreciated the speed and the complexity of analysis. Without Variant Analysis, I couldn't have completed the analysis of 700 exomes in such a short time .... I found Variant Analysis very intuitive and easy to use."

Francesco Lescai, Senior Research Associate in Genome Analysis, University College of London.

Picture of Francesco Lescai, Senior Research Associate in Genome Analysis, University College of London
Fast
Fast
Identify causal variants in hours instead of months.
Knowledge Driven
Knowledge-driven
Apply a knowledge-driven approach to identifying causal variants using millions of computable, expert-curated findings from the peer reviewed biomedical literature.
User Friendly
User friendly
Easily analyze your data with the application, without the need for bioinformatics experience or support.
Scalable and Secure
Scalable and Secure
Scale from small tumor or hereditary experiments up to large association studies within a secure web application.
Easy to Purchase
Easy to purchase
Purchase analysis on a priced-per-sample basis.
Scalable and Secure
Easy to implement
Implement web-based analysis without the need for software infrastructure or integration.

Interactive filtering with integrated and accurate evidence to rapidly prioritize data for faster results

Multi-family Pedigree Support
Multi-family pedigree support
Select for variants consistent with Mendelian inheritance.
Disease ID
Disease identification
Find diseases consistent with clinical features and deleterious variants in medical genomes.
Statistical burden testing
Statistical burden testing
Find genes or pathways that have significantly more deleterious variants in one group than another.

The Ingenuity Knowledge Base

knowledge base graphic

All of Ingenuity’s solutions leverage the Ingenuity Knowledge Base, a repository of expertly curated biological interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. These modeled relationships, or Findings, include rich details, links to the original article, and are reviewed for accuracy by PhD scientists. The curated content in the Knowledge Base is structured into an Ontology that allows for contextual information, computation by the applications, and synonym resolution to ensure consistency across concepts. These features make the Ingenuity Knowledge Base distinctive and unparalleled to any other database.

Variant Analysis has a broad Set of Features that allow you to quickly understand and visualize your data

Intuitive, user-friendly interface

No bioinformatics skills needed. Easy to learn and use in your own workspace. No waiting for additional resources to get started.

Interactive Filter Cascade

Eliminate common and non-deleterious variants with a basic set of filters, quickly reducing the number of variants significantly. Apply additional filters based on your knowledge of disease, to further reduce the number of variants allowing you to go from millions to hundreds of interesting variants for follow on studies.

Iterative analysis

Variant Analysis mirrors the investigative process, allowing rapid application of a hypothesis, visualization and evaluation of results and re-iteration of the hypothesis for immediate results that speed discovery.

Sharing and Publication Tools

Easily collaborate with colleagues and peers. Export data and graphics to aid in manuscript preparation and publications.

Knowledge driven algorithms and analytics- Genetics, Functional Prediction, PLUS Biology

Keyword search within the Ingenuity ontology provides identification and prioritization of compelling variants using both your knowledge of disease, phenotypes, processes, and pathways, as well as the deep pathway information available in the Ingenuity Knowledge Base.

Causal Network Analytics

Identify variant in genes within 1- or 2- network “hops” of upstream or downstream genes. Understand not only known relationships, but also variants in genes that have relationships or interactions with those genes known to be associated.

Curated up to date content at your fingertips

No need to go search for publications on your own. Utilize a knowledge base containing millions of biomedical finding and mutations, accurate, updated and curated by experts, from the literature and public databases. Access up-to-date pathways, processes, models, genetic, drug and disease findings seamlessly, within a single easy to use interface.

Scalable processing capacity

Variant Analysis has been demonstrated to support study sizes ranging from individuals and trios to thousands of samples in a single analysis. Analyze thousands of samples simultaneously.

Explore Our Webinars and see how the scientific community has used Variant Analysis to create novel discoveries

John A. Martignetti Headshot
Garry Nolan Ph.D. Headshot

Realizing the promise of genomics through rapid innovation in biological analysis and interpretation


Presenter: John A. Martignetti, M.D., Ph.D. and Garry Nolan Ph.D.
Original Broadcast Date:Thursday, March 13, 2014

Discover how intuitive web-based applications can help scientists quickly analyze and accurately interpret the biological meaning in their genomic data.

In the last few years, researchers and clinicians have been faced with the challenge of how to effectively sort through and accurately understand the biological meaning from their genomic data. Now, web-based applications such as QIAGEN's Ingenuity Platform can be used to better comprehend complex biological systems, answer questions, analyze and interpret data.

In this webinar, the audience will discover how Ingenuity Pathway Analysis (IPA) and Ingenuity Variant Analysis softwares can be used to provide new insight into and quick interpretation of their scientific findings.

The speakers, John Martignetti and Garry Nolan, will discuss how these software solutions were applied to their respective research areas to more effectively search, explore, visualize, analyze and interpret biological findings related to genes, proteins and small molecules.


Vivien Sheehan Headshot

Using QIAGEN’s Ingenuity Variant Analysis in Pharmacogenomics


Presenter: Vivien Sheehan, Asst. Prof. of Pediatrics Baylor College of Medicine
Original Broadcast Date: Thursday December 5, 2013

Vivien Sheehan will be speaking about her work in pharmacogenomics. This presentation will cover sickle cell disease (SCD), specifically the genetic component to fetal hemoglobin response to hydroxyurea. Such knowledge will enhance the ability to predict drug response, improving patient care by allowing selection of individuals who will benefit most from hydroxyurea, and offer alternative therapies.

Variant Analysis Tips and Tricks[34:11 minutes]
Presented by Dr. Darryl Gietzen, Senior Field Applications Scientist, QIAGEN Redwood City (formally Ingenuity Systems, Inc.)

Whether you are a new or experienced user of Ingenuity Variant Analysis, you will benefit from attending this Tips and Tricks presentation. This presentation will walk you through several scenarios and give tips on how to work more efficiently and get more accurate scientific results. These tips come from the people who work with Variant Analysis every day: the Field Application Scientist and Customer Support teams.

In this webinar you will learn fast and efficient variant analysis design and set-up (covering several study types and sample numbers), how to quickly re-analyze the same samples with different filter settings, how to get the most from the Genetic Analysis filter module without over filtering, optimization of the filter cascade, and quickly prioritize biologically compelling variants.

Ingenuity Knowledge-Based Tools for Comprehensive Interpretation of Variant & Gene Expression Data [56:16 minutes]
Presented by Jean-Noel Billaud and Megan Laurance
Ingenuity Staff Scientists Jean-Noel Billaud and Megan Laurance present strategies for integrated analysis and interpretation of variant and gene expression data generated from cell lines representative of 2 breast cancer subtypes: Claudin-Low and Luminal. These subtypes represent different disease entities associated with specific molecular alterations and histo-clinical features. Interrogating these samples at both the variant and transcript level with Ingenuity's Variant Analysis and IPA software presents a powerful approach to drawing clear molecular paths from variants and gene expression changes to phenotypes relevant to these disease subtypes including Epithelial-to-Mesenchymal Transition and Metastasis.
Improving Single Genome Annotation by Multi-Genome Analysis [37:32 minutes]
Presented by Gustavo Glusman, Senior Research Scientist, Institute for Systems Biology
This webinar discusses the analysis of whole genome sequence data in Alternating Hemiplegia of Childhood (ACH) samples using custom workflows and Ingenuity Variant Analysis platform to improve the sensitivity and specificity of genome interpretation.
Whole Genome Sequencing for Rare Clinical and Consanguineous Familial Cases [37:16 minutes]
Presented by Christopher E. Mason, Ph.D., Assistant Professor, Department of Physiology and Biophysics and the Institute for Computational Biomedicine; Affiliate Fellow of Genomics, Ethics, and Law, ISP, Yale Law School
Learn how to use Ingenuity® Variant Analysis™ to analyze whole genome sequencing data. Chris Mason, Ph.D., presents a case study where Variant Analysis was used to analyze data from rare clinical cases with extreme phenotypes from the NIH's Undiagnosed Disease program and a consanguineous family with neural-tube defects. You will learn how to pinpoint likely genes causing disease phenotypes and see how an integrated systems biology approach that leverages biological analysis can contribute to advancements in personalized medicine.
Ingenuity Knowledge-Based Tools for Comprehensive Interpretation of Variant & Gene Expression Data [56:16 minutes]
Presented by Jean-Noel Billaud and Megan Laurance, QIAGEN Redwood City
This Case study presents strategies for integrated analysis and interpretation of variant and gene expression data generated from cell lines representative of 2 breast cancer subtypes: Claudin-Low and Luminal. These subtypes represent different disease entities associated with specific molecular alterations and histo-clinical features. Interrogating these samples at both the variant and transcript level with Ingenuity's Variant Analysis and IPA software presents a powerful approach to drawing clear molecular paths from variants and gene expression changes to phenotypes relevant to these disease subtypes including Epithelial-to-Mesenchymal Transition and Metastasis.
Rapid biological interpretation of human NGS data: Ingenuity Variant Analysis [59:14 minutes]
Presented by QIAGEN Redwood City
Biological interpretation of thousands of potentially deleterious variants is a bottleneck in extracting valuable insights from DNA resequencing studies, often requiring months of effort after completion of the reference genome alignment and variant calling steps. Ingenuity Variant Analysis is a fast, easy-to-use application that leverages an extensive knowledge base of millions of expert-curated mutation and biomedical findings from the literature to empower real-time interactive filtering and rapid prioritization of variants, enabling clinical researchers to quickly zero in on the few that are most compelling for follow-up. Using a combination of causal analytics, genetic analysis at the variant, gene, and pathway levels, and the ability to visualize how variants impact disease progression, we will demonstrate the application of a context-rich knowledge base to discover cancer driver variants and novel causal variants for human genetic disease.

A diverse group of researchers are using Variant Analysis to identify causal variants faster. Meet a few and learn more about how they are using Variant Analysis in their research.

"Being a bioinformatician, I appreciated the speed and the complexity of analysis. Without Variant Analysis, I couldn't have completed the analysis of 700 exomes in such a short time .... I found Variant Analysis very intuitive and easy to use."

Francesco Lescai, Senior Research Associate in Genome Analysis, University College of London.

Picture of Francesco Lescai, Senior Research Associate in Genome Analysis, University College of London

"[Ingenuity Variant Analysis] provides easy access to excellent gene variant interpretation, especially for those without a bioinformatics background. It has also greatly reduced the time from variant call to seeing “final” results."

David Crockett, Director, Bioinformatics, ARUP Laboratories.

Picture of David Crockett, Director, Bioinformatics, ARUP Laboratories

"Identifying the causal variants supported by high confidence literature is the key thing in which our institute is interested. Ingenuity makes it so simple and easy. [Our] thanks to Ingenuity. "

Pankaj Kumar, Research Associate, Cornell University.

Picture of Pankaj Kumar, Senior Research Associate in Genome Analysis, University College of London

"[Ingenuity Variant Analysis] streamlines the analysis for our whole exome studies on the etiology of diseases."

Honggang Ye, Post Doctoral Researcher, The University of Chicago

Picture of Honggang Ye, Senior Research Associate in Genome Analysis, University College of London

Ingenuity offers online training with our product technicians and web seminars presented by notable third parties, sign up below!

Ingenuity Variant Analysis Overview [3:47 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.

documents iconOnline Training

Getting Started with QIAGEN’s Ingenuity® Variant Analysis

Variant Analysis combines analytical and statistical tools with manually curated 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. We offer different training media to help you get started and to help familiarize you with the application. Our free online live events cover the basic and intermediate functionalities of the application. For all our other pre-recorded and written materials please consult our Customer Portal.

Part 1: Getting Started with QIAGEN’s Ingenuity Variant Analysis (30 min)

This session is recommended for all new Variant Analysis users.

This introduction to Variant Analysis shows you which files you need and how to upload data and run an analysis. You will also learn about the biological context and the basic functionalities of the Genetic Analysis filters which are unique to Variant Analysis and provide powerful ways to quickly identify disease-causing variants.

Part 1 re-recorded version (Jan 2014) can be access at: Variant Analysis: Getting Started and Sample Upload

Part 2: Analysis Interpretation and Advanced Functionalities (30 min)

This session is recommended for users that have a good understanding of the acceptable file formats, uploading and running a basic analysis or have attended Part 1.

In this session, you will be introduced to the pedigree and clinical annotations as well as the use of custom annotations – both chromosomal and transcript level annotations. You will also learn how to change and edit the settings of your Genetic Analysis filter to incorporate the pedigree information along with a review of the filter cascade for an analysis that reflects your particular research needs.

Part 2 pre-recorded version (Jan 2014) can be access at: Variant Analysis: Analysis and Filter Cascade Basic

Register for Part 1 & 2 using the links below. The Part 2 will start at the half hour mark if you would like to attend Part 2 only.

*please contact us for more details about pricing or sign up for a free preview

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