We compiled this list of San Diego genomics companies as part of our research for our upcoming 10th Anniversary of the Human Genome event August 18th and it is featured in this Xconomy article. Genomics is a large area, and we restricted our list to the companies who were either founded as a result of the sequencing of the human genome or those that have made significant contributions. Please feel free to list any we’ve missed in the comments below. We utilized a variety of online resources for the list, including web archives, access the links through the Delicious sdgenome tag. Also check out our San Diego Biotechnology Company Directory.

Company Details Founded or important dates Fate
Sequenom Founded before the sequencing of the human genome by Hubert K?ster, but likely benefited from the promise of the human genome sequencing with the third most successful biotech IPO in 2000. Pioneered use of mass spectrometry to sequence DNA and to monitor variations (e.g. SNPs) or modifications (e.g. methylation). Perhaps most ‘famous’ scientist is Charles Cantor, CSO. Sequenom appeared to ‘ride out’ the genomics bubble burst by expanding into diagnostic tests, but has recently been investigated for data mishandling Founded 1994, IPO 2000 (Nasdaq; SQNM) 250 employees (LinkedIn)
Life Technologies (Invitrogen) Invitrogen had acquisitions and involvement with genomics and informatics in the early part of the decade with acquisition of Resgen (clone collection) and Informax (informatics). More recently, their merger with Applied Biosystems and investment in Synthetic Genomics indicates more of an interest in genomics for human health. Research tools facilitating genomics (e.g., Gateway cloning) in early 00’s, 2008 Merged with Applied Biosystems 9,000 employees (LinkedIn)
Agilent (Stratagene) Stratagene has a long history of creating research tools for molecular biology/genomics. Acquisition by Agilent in 2007 merged these tools with microarray capabilities. Research tools facilitating molecular biology and genomics, 2007 acquisition by Agilent. 19,000 employees (LinkedIn)
Illumina David Walt, Ph.D., CW Group (Larry Bock), John Stuelpnagel, D.V.M., Anthony Czarnik, Ph.D., and Mark Chee. Company has pioneered methods for sequencing, helping to drive the costs down significantly, with a significant presence in diagnostics and offering the ‘$50,000 personal genome.’ Founded 1998, IPO 2000, 2006 Solexa acquisition, 2009 Personal genome sequencing available 1600 employees (LinkedIn)
SGX Pharmaceuticals Started as Structural Genomix (aka Stromix) in 1999 by Wayne Hendrickson, Barry Honig, Linda Grais and Tim Harris. Part of the high throughput structural genomics initiatives, aiming to solve the three-dimensional structures of all of the proteins encoded by the human genome. Stephen Burley raised eyebrows in 2001 by leaving Rockefeller University to taking a lead role at the company, which eventually morphed into focusing on oncology and kinases, with an IPO in 2006 (Nasdaq: SGXP). Acquired by Eli Lilly in 2008. Founded 1998, IPO 2006. Acquired by Eli Lilly in 2008 for $64M
Genomics Institute of the Novartis Foundation (GNF) San Diego’s ‘flagship’ genomics and translational research institution, with 560 employees with active drug discovery programs in cancer biology, cardiovascular/metabolism, immunology, respiratory disease, neuroscience and infectious disease. Operates under the umbrella of the Novartis Institute for Biomedical Research (NIBR) and is affiliated with the Novartis Institute for Developing World Medical Research (NIDWMR). Peter Schultz is thought to have had a major influence in the institution locating here and in its focus for ten years, and he left GNF earlier this year. Founded in 1999 560 employees (company website)
Geneformatics, Inc. Founded by Jeffrey Skolnick, Jacquelyn Fetrow, Andrzej Kolinski, and Adam Godzik. Aimed to use structural prediction algorithms to find functions for new proteins discovered by the human genome. Founded 1999 Merged with Structural Bioinformatics in 2003 to form Cengent, which eventually dissolved.
Syrrx Founded in 2000 by Peter Schultz, Raymond Stevens, and Nathaniel David. Strong ties to GNF and Scripps. Known for developing robotic systems which were important for industrializing HTS and X-ray crystallography. Founded 1999 Acquired by Takeda in 2005.
ActivX Founded by Robert Hillman, Benjamin Cravatt (TSRI), Jeffrey Smith (Burnham) using technology developed by Cravatt’s lab to identify and analyze protein function using high throughput chemistry. Founded 2000 Acquired by Kyorin 2004.
Ambit Founded in 2001 by by Kevin J. Kinsella, David J. Austin, Ph.D., and David J. Lockhart based on ‘ProteomeScan’ technology from Austin’s lab at Yale. Developed ‘KinomeSCAN’ technology, a competition-based screen for kinase inhibitor specificity. Therapeutic focus on kinases/oncology with two compounds in clinic. Founded 2001 96 employees (LinkedIn)
Kalypsys Spun out of GNF in 2001 by Peter Schultz, Jeremy Caldwell, Kevin Lustig, and several others. Aimed to combine automation with pathway analysis to study a broad spectrum of diseases. Founded 2001 Still in operation–rumored to have been running with skeleton crew recently, but LinkedIn profile states 55 employees. May be surviving through partnering of compounds and/or sales of robotic systems.
Phenomix Founded to use ‘forward genetics’ which identifies physiological models of disease first, then identifies relevant genes. According to website, has two compounds for diabetes in phase 3 clinical trials. Founded 2002 49 employees (LinkedIn company profile)
Synthetic Genomics Genomic-driven commercial solutions focused initially on biofuels, but with aspirations for improving human health. Founded 2005 90 employees (LinkedIn)
Verdezyne Founded in 2005 as Coda Genomics, provided expression optimized synthetic genes to researchers. Renamed Verdezyne in recent years with focus on renewable fuels. Founded 2005 25 employees (LinkedIn)
Pathway Genomics Direct to consumer genomics test retailer. Founded 2010 50 employees (LinkedIn)

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