QIAGEN Silicon Valley

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QIAGEN Silicon Valley (formerly known as Ingenuity Systems, Inc) is a company based in Redwood City, California, USA, that provides software to help life science researchers explore, interpret, and analyze complex biological systems. QIAGEN Silicon Valley's first product, IPA, was introduced in 2003, and is used to help researchers analyze omics data and model biological systems. The software has been cited in thousands of scientific molecular biology publications and is one of several tools for systems biology researchers and bioinformaticians in drug discovery and institutional research. The company also offers analysis services and enterprise services.

In May 2013, Ingenuity Systems was purchased by QIAGEN. Its location was established as QIAGEN's Center of Excellence for Biological Analysis and Interpretation, developing software to help life science researchers explore, interpret, and analyze complex biological systems.


All QIAGEN Silicon Valley use the Ingenuity Knowledge Base, which contains biological and chemical interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. These modeled relationships include contextual details, link to the original article, and are manually reviewed for accuracy. Each relationship originates from reported experimental facts from primary literature sources, including peer-reviewed journal articles, review articles and textbooks. In addition to findings from the literature, the Ingenuity Knowledge Base contains findings and annotations from other sources, including EntrezGene, RefSeq, OMIM, GWAS database, Gene Ontology, Tissue Expression Body Atlas, NCI-60 Cell Line Expression Atlas, HumanCyc, protein-protein interactions (from BIND, DIP, MINT, MIPS, BIOGRID, INTACT, and Cognia), and microRNA-mRNA target interactions (from ARGONAUTE 2, TARBASE). The knowledge acquisition and extraction process is protected by multiple US Patents.[1]

Products and services[edit]


IPA is broadly adopted[according to whom?] in the life science community and has been cited in thousands of peer-reviewed journal articles.[2] IPA can be used with or without data. IPA helps researchers analyze data derived from expression and SNP microarrays, proteomics experiments, and small-scale experiments that generate gene lists, in order to gain insight into molecular and chemical interactions, cellular phenotypes, and disease processes within a system. IPA also lets researchers search for information on genes, proteins, chemicals, drugs, and reagents. Resulting information can be used to build biological models, design experiments, or get up to speed in an area of research.[3]

Ingenuity iReport[edit]

Ingenuity iReport is the fastest way to understand the biological meaning of expression data.[citation needed] It combines biological and statistical analysis for a rapid and accurate analysis of what genes are significantly differentially expressed in a dataset, and summarizes the affected biology. iReport includes novel interactive & visual tools that help researchers quickly identify the most interesting subset of genes for follow-up.

Ingenuity Variant Analysis[edit]

Ingenuity Variant Analysis combines analytical tools and integrated content to help researchers rapidly identify a short list of compelling variants from human resequencing data using selection criteria based both upon published biological evidence and their own knowledge of disease biology.


Ingenuity offers search and visualization tools that can be deployed on life science e-commerce websites to enable customers to use information about biological and chemical systems to better design their experiments and select their reagents. Ingenuity has two prominent partnerships. Sigma-Aldrich leverages Ingenuity technology in their Your Favorite Gene application, and BD Biosciences leverages Ingenuity technology in their BD Cell Pathways[4] application.

Analysis services[edit]

Ingenuity offers scientific services that accesses the capabilities of the software and knowledge base. Services include data analysis and interpretation, model building for target ID and validation, biomarker identification and prioritization, toxicity assessments, and help with result presentation.[5]


Ingenuity offers information solutions and enterprise solutions.[6]


Accel Partners, Three Arch Partners, Bay City Capital, Morgan Stanley Capital Partners, Oracle Venture Fund, Millennium Pharmaceuticals, Affymetrix Corporation


2003 - Ingenuity first offers Ingenuity Knowledge Base[7]
2004 - Stanford University licenses IPA[8]
2004 - Independent analysis finds significant ROI for pharmaceutical companies using IPA[9]
2005 - US Food and Drug Administration adopts IPA to review pharmacogenomics submissions[10]
2006 - Ingenuity enters into partnerships with Asuragen, Spotfire, Agilent, Genedata, and Inforsense[11]
2007 - Ingenuity introduces toxicology and biomarker capabilities within IPA 5.0[12]
2007 - IPA 5.0 wins Best in Show - Best New Product at Bio-IT World[13]
2007 - Ingenuity and FDA enter three year collaboration to enhance regulatory review process[14]
2008 - IPA's newest feature, Path Designer, wins Best New Product at Molecular Medicine[15]
2009 - Sigma Aldrich launches Your Favorite Gene - Powered by Ingenuity[16]
2009 - BD Biosciences launches BD Cell Pathways, powered by Ingenuity[17]
2011 - Ingenuity announces early access to Ingenuity iReport[18]
2012 - Ingenuity announces commercial availability of Ingenuity iReport and Ingenuity Variant Analysis[19][20]
2013 - Ingenuity announces collaborations with both Laboratory Corporation and Quest Diagnostics to develop a solution for scoring genetic variation for next generation sequencing data (NGS) and is purchased by QIAGEN in May of the same year

See also[edit]


  1. ^ "United States Patent: 7943742". US Patent Office. Retrieved April 7, 2012. 
  2. ^ "Bibliography" (PDF). Ingenuity Systems. Retrieved April 7, 2012. 
  3. ^ "Ingenuity IPA Software - Pathway Analysis, miRNA, NGS, RNA-Seq, Microarrays, Gene Expression, Biomarkers". Ingenuity Systems. Retrieved April 7, 2012. 
  4. ^ BD Cell Pathways
  5. ^ "Ingenuity Analysis Services". Ingenuity Systems. Retrieved April 7, 2012. 
  6. ^ "Products & Services". Ingenuity Systems. Retrieved April 7, 2012. 
  7. ^ "Ingenuity Systems Announces Immediate Availability Of The Ingenuity Pathways Knowledge Base" (Press release). Ingenuity Systems. May 27, 2003. Retrieved April 7, 2012. 
  8. ^ "Stanford University Licenses IPA, Collaborates on Systems Biology Solutions" (Press release). Ingenuity Systems. November 3, 2003. Retrieved April 7, 2012. 
  9. ^ "The Return on Investment for Ingenuity Pathways Analysis within the Pharmaceutical Value Chain", Zimmerman, Reeve, and Golden, Life Science Insights, an IDC company, July 2004
  10. ^ "The U.S. Food and Drug Administration to use IPA in review of Pharmacogenomics Submissions" (Press release). Ingenuity Systems. June 21, 2005. Retrieved April 7, 2012. 
  11. ^ "Press release archive". Ingenuity Systems. Retrieved April 7, 2012. 
  12. ^ "Ingenuity Systems releases IPA™ 5.0 software, offering new biomarker and molecular toxicology capabilities" (PDF) (Press release). Ingenuity Systems. April 17, 2007. Retrieved April 7, 2012. 
  13. ^ "Best of Show: Life Science Software & Informatics". Bio-IT World. June 13, 2007. Retrieved April 7, 2012. 
  14. ^ "Ingenuity Systems and FDA Enter 3-Year, $6 Million Collaboration to Enhance Regulatory Review Process" (Press release). Ingenuity Systems. November 27, 2007. Retrieved April 7, 2012. 
  15. ^ "Best of Show Award Winners Named at the Fifteenth International Molecular Medicine Tri-Conference" (Press release). Cambridge Healthtech Institute. April 3, 2008. Retrieved April 7, 2012. 
  16. ^ "Sigma-Aldrich Launches Your Favorite Gene Powered by Ingenuity, Sigma-Aldrich Co" (Press release). Sigma-Aldrich Co., Inc. January 27, 2009. Retrieved April 7, 2012. 
  17. ^ "Ingenuity's Technology Powers BD Cell Pathways Tool on New BD Biosciences Website" (Press release). Ingenuity Systems. August 10, 2009. Retrieved April 7, 2012. 
  18. ^ "Ingenuity Systems Unveils Early Access to Revolutionary New iReport" (Press release). Ingenuity Systems. September 29, 2011. Retrieved April 7, 2012. 
  19. ^ "New Products: Randox Laboratories' Beta-Lactams Array; Ingenuity Systems' iReport". BioArray News (GenomeWeb). January 24, 2012. Retrieved April 7, 2012. 
  20. ^ "Ingenuity Preps New NGS Variant Analysis Tool, Signs Translational Oncology Group as Beta Tester". BioInform (GenomeWeb). January 13, 2012. Retrieved April 7, 2012. 

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