Some storiesMiguel Andrade – Ottawa Health Research Institute

23 FEBRUARY 2004

Academic - Industrial partnerships in Bioinformatics

Human Genome Project

June 2000

Francis Collins

Craig Venter

Stock value: June 1st 2000: 63.50June 30th 2000: 92.00February 19th 2004: 14.94

http://www.nhgri.nih.gov/

CELERA

• Celera Genomics was founded in 1998 to sequence and assemble the human genome. We completed a first draft sequence in just over two years, far sooner than most people expected and over a year ahead of our original goal.

• discovery, development and commercialization of diagnostics and drugs. • Pay per access to the sequence. No claim on benefits.

http://www.celera.com/

http://www.venterscience.org/

J. Craig Venter Science Foundation

Until Jan 2002

Human Genome Project

• Begun in 1990, the U.S. Human Genome Project is a 13-year effort coordinated by the Department of Energy and the National Institutes of Health. The project originally was planned to last 15 years, but effective resource and technological advances have accelerated the completion date to 2003.

• The Human Genome Project ends in 2003 with the completion of the human genetic sequence. A working draft of the entire human genome sequence was announced in June 2000, with analyses published in February 2001. An important feature of this project is the federal government's long-standing dedication to the transfer of technology to the private sector.

• Scientific vs Commercial Goals • “The HGP's commitment from the outset was to create a scientific standard (an entire

reference genome). Most private-sector human genome sequencing projects, however, focused on gathering just enough DNA to meet their customers' needs—probably in the 95% to 99% range for gene-rich, potentially lucrative regions. Such private data continue to be enriched greatly by accurate free public mapping (location) and sequence information. Celera's shotgun sequencing strategy, for example, created millions of tiny fragments that had to be ordered and oriented computationally using HGP research results. Most data at Celera, Incyte, and other genomics information-based companies are proprietary or available only for a fee.”

http://www.ornl.gov/sci/techresources/Human_Genome/

HAPMAP

• www.hapmap.org• a partnership of scientists and funding agencies from Canada, China, Japan, Nigeria, the United

Kingdom and the United States to develop a public resource that will help researchers find genes associated with human disease and response to pharmaceuticals

• Industry and academia• The goal of the International HapMap Project is to develop a haplotype map of the human genome,

the HapMap, which will describe the common patterns of human DNA sequence variation. The HapMap is expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors. The information produced by the Project will be made freely available.

The SNP consortium

The SNP Consortium (TSC) is a public/private collaboration that has to date discovered and characterized nearly 1.8 million SNPs

Single nucleotide polymorphisms (SNPs) are common DNA sequence variations among individuals.

October 2002 – 400,000 new SNPs released. Deposited in dbSNP (NCBI)

http://snp.cshl.org/

National Centre for Biotechnological Information

• Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease

http://www.ncbi.nlm.nih.gov/

SwissProt

• http://us.expasy.org/sprot/• Database of protein sequences with high quality annotation. Since 1986. Aimos Bairoch.• Public access. Download possible. Commercial users have to apply for a license.• Instability?• May 1996 funding crisis. • “About two years ago, the Swiss decided that, as SWISS-PROT was used by the

international community, it should not be funded solely by money reserved for national projects. Accordingly, an EU grant proposal was submitted asking for some 12 positions in Switzerland, the EBI, Ireland, Israel and France to maintain, develop and extend the existing service. This grant was favourably reviewed but ultimately rejected by Brussels. Furthermore, grants from Swiss funds which were contingent upon European funding were put into jeopardy. Hence the "End of SWISSPROT" announcement which was coupled with a request for demonstrations of support.

• The letters of support were immediately forthcoming and within a month some 1,500 scientists from 39 different countries responded. An interim solution has now been worked out which will keep SWISS-PROT afloat and in the public domain for another six months until a new funding proposal can be submitted. Good software and valuable databases really do cost money to maintain.

Genome Data Base

• The database started at Johns Hopkins University in 1990, and since 1998 The Hospital for Sick Children in Toronto, Canada, has maintained it.  Over the past year, these institutions have worked together to find a long-term home for the GDB.

• Shutdown during 2003.• 1 Nov 2003. Restored.

The Genome Database (GDB), a unique repository of confirmed information about human genes, has found a new home at RTI International, an independent, nonprofit research institute in North Carolina.

http://www.gdb.org/

ECOCYC

• Since 1999• Encyclopedia of Escherichia coli K12 Genes and Metabolism • EcoCyc is Copyright © 1996-2003 SRI International, Marine Biological Laboratory,

DoubleTwist Inc., The Institute for Genomic Research, University of California at San Diego, and UNAM. All rights reserved.

http://www.ecocyc.org/

TRANSFAC

• Database of transcription factors• Accessible for querying• Pay for purchase.• Non-commercial users• # Academic Research Group License (for an academic research group)• - 500 € each database (750 € in Japan)• “What are the advantages of the Professional databases compared to the Public

versions? • four updates per year (instead of one) • much larger data content • more attractive user interface • professional search engines • download versions (optional) • additional analysis software tools”

http://www.gene-regulation.com/

CONCLUSION

INDUSTRY

ACADEMIA

Focus ideas

Bring self-funding

Better interfaces

Constraints free flow of information

Less creativity

Productivity

Efficiency

Public benefit

Advancement of Science