Diagnostic Kits/Commons based cases in Kits

Answer the questions:

1. Commons based cases (the cases that we know will appear in the right part of the quadrants)
   • Identify cases
   • Correlate them with their main outputs (Data. Narratives. Tools)
   • How and in what extent they are “experimenting” or “adopting” commons-based approach. Are they adopting OA policies, for instance? Are they adopting Social Responsible License approaches?
   • Identify these cases and treat them as entities that will also be placed in our mapping device (the quadrants)
   • Identify what actors are participating on this and what actors are just observers (Use the questionnaire to guide your research when appropriate - Carol will select specific relevant and helpful questions)

Specific Examples

• Cooperative clinical trial groups
  • Clinically validating a test is probably "the biggest barrier to progress" says Doug Ross, Chief Scientific Officer of Applied Genomics.
  • Genomic Health's Oncotype DX test was clinically validated with samples from the National Surgical Adjuvant Breast and Bowel Foundation (NSABP).
    • "Genomic Health's competitive advantage in the marketplace is derived in large part from the strength of the data from their published NSABP results," says Ross.
  • so sharing of tissue samples for clinical trials to validate a GDx could be an important force encouraging collaboration.
• More info at the National Cancer Institute's Clinical Trials Cooperative Group page.

• SNPedia
  • "SNPedia is a wiki investigating human genetics. We share information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA." There are currently 8732 snps (single-nucleotide polymorphisms) in SNPedia.

• Promethease
  • Promethease is a closed-source(?) freemium software tool developed by Mike Caruso that analyzes the raw data produced from DTC genetic tests (23andme, deCODEme, etc) using the SNPedia database.

• Trait-o-matic
  • open source tool that automates the identification, filtering, and annotation of genetic variants
  • the tool uses public datasets
  • Developed at Harvard Medical School
  • Discussed by: Completing the Personal Genomics Toolkit

• Biomarkers Consortium
  • members include many major pharmaceutical firms
  • participants are entitled to nonexclusive license to all intellectual property created from that project
  • Launched by:
    • The Foundation for the National Institutes of Health (FNIH)
    • The National Institutes of Health (NIH)
    • The Food and Drug Administration (FDA)
    • The Pharmaceutical Research and Manufacturers of America (PhRMA)
  • About the Biomarkers Consortium
  • General Intellectual Property and Data Sharing Principles (pdf)
    • Old Data: participants pre-existing Data and Intellectual Property remains with participants
    • New Data: New Data and Consortium Inventions
      • participants have a right to protect the inventions but must grant to all other participants (this includes inventions made under a Federal governmental grant or contract) subject to the Bayh-Dole Act
        • a non-exclusive, remuneration-free license
        • a non-exclusive research license
    • Licensing is not limited to members

• National Institutes of Health (NIH), Public Health Service, DHHS, NIH Principles and Guidelines for Sharing of Biomedical Resources -- Final (December 1999) Available at: http://www.ott.nih.gov/policy/research_tool.aspx

• Open Educational Resources for Cancer
  • The OERC Mission Statement (bullet points are quotes from the website)
    • To create an open resource repository of cancer educational materials covering diverse aspects of oncology.
    • To promote global sharing of cancer educational resources (WHO 2007 Cancer Report).
    • To utilize knowledge sharing to assist countries develop cancer control strategies.
    • To provide educational resources to enhance the capacities of physicians, nurses and care givers in developing countries to diagnose and treat cancer patients.
    • To provide free access to advances in basic and clinical cancer research information in user friendly format.
    • To contribute to the development of a research infrastructure and a research ethos for cancer care and prevention at a global level.

• Uniform Biological Material Transfer Agreement
  • used to facilitate the easy exchange of research tools

General Examples

• The Biological Innovation for Open Society (BIOS) license
  • This specifically aims to provide open access to patented DNA sequences.
  • Resources:
    • Wired Magazine Open-Source Biology Evolves
    • Geertrui Van Overwalle et al., 2005. Models for facilitating access to patents on genetic inventions. Available at: http://www.nature.com/nrg/journal/v7/n2/full/nrg1765.html [Accessed August 10, 2009].
    • BiOS site
  • Article describing the commons created by BiOS: Synthetic Biology: Caught between Property Rights, the Public Domain, and the Commons

• MIT Registry of Standard Biological Parts
  • "A collection of ~3200 genetic parts that can be mixed and matched to build synthetic biology devices and systems. Founded in 2003 at MIT, the Registry is part of the Synthetic Biology community's efforts to make biology easier to engineer."

• The proposed BioBricks Foundation (BBF) license for BioBrick-standard biological "parts"
  • More information here: http://openwetware.org/wiki/The_BioBricks_Foundation:Legal
  • Drew Endy from the BBF has been increasingly focused on developing the license, organizing legal workshops and spending more time talking about it in lectures, but I couldn't find much online describing progress the BBF has made recently (they have been spending significant time working on it for at least the last 12 months).
  • We could touch base with the BBF to find out of there are any publications in preparation or an expert who could provide more information in an interview by subscribing to and emailing legal@biobricks.org. If that doesn't work, contacting someone from the recent BBF + Berkeley Law Samuelson Clinic would probably be effective.
  • Example set of parts: http://partsregistry.org
  • Janet Hope covers the BBF & CAMBIA in her book, Biobazaar, on pages 316-317: here's a scan (and here's a google book search)
  • http://bbf.openwetware.org/
  • MIT Registry of Standard Biological Parts

• DNA Patent Database
  • http://dnapatents.georgetown.edu/
  • Updated weekly, the DPD contains over 51,000 DNA-based patents issued from 1971 to the present and over 73,000 patent applications published from 2001 to the present.

• The science commons in health research: structure, function, and value
  • http://www.springerlink.com/content/782310p623282449/
  • "early algorithms for interpreting DNA sequence—such as the BLAST and Smith-Waterman algorithms—were developed by individuals committed to open science."

• National Center for Biotechnology Information: GeneTests
  • http://www.ncbi.nlm.nih.gov/sites/GeneTests/?db=GeneTests
  • "A publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons."
  • The site offers:
    • peer-reviewed disease descriptions
    • An international directory of genetic testing laboratories
    • An international directory of genetics and prenatal diagnosis clinics
    • A compilation of educational materials

GDx Standardization and Calibration Efforts

• Genetic Testing Reference Materials Coordination Program (GeT-RM) (associated with the CDC)
  • the project provides reference materials for molecular genetic testing
  • three categories:
    • Genetic Inherited Disease & Pharmacogenetics
      • "information about cell lines, DNA, and other samples that can be used as reference materials for various inherited diseases (including cystic fibrosis, fragile X, Huntington disease, and Ashkenazi Jewish-related diseases), pharmacogenetic loci, and biochemical genetics." (GeT-RM)
    • Molecular Oncology
      • "information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various types of cancers, including leukemia/lymphoma and solid tumors." (GeT-RM)
    • Infectious Disease
      • "information about commercially available cell lines, DNA, and other kinds of materials that could be used as reference materials for various infectious disease pathogens including viruses, bacteria, and protozoa." (GeT-RM)
  • Sources of Reference Materials
  • Regulatory guidelines and standards associated with the sources of reference materials

Reference Standards

Groups of physicians, GDx labs, and experts collaborate to develop testing standards and materials to ensure GDx quality.

• See the 2001 Nature Genetics article: Quality control in molecular genetic testing

  • "DNA-based testing for genetic diseases has developed from nothing into a principal part of laboratory medicine over the past 15 years. In the rush to bring these powerful new technologies into medical use, issues of quality have not always been given sufficient attention. Efforts are now being made to assess the quality of the output of genetic testing laboratories, and the results show that there is room for improvement."

• Development of Genomic DNA Reference Materials for Genetic Testing of Disorders Common in People of Ashkenazi Jewish Descent
  • 25 disease alleles far a variety of genetic disorders common to people of AJ descent were prepared and made available by Coriell Cell Repositories, coordinated by CDC GeT-RM.

• Development and Characterization of Reference Materials for MTHFR, SERPINA1, RET, BRCA1, and BRCA2 Genetic Testing
  • DNA for clinically relevant mutations from the listed genes are available via Coriell Cell Repositories. Work coordinated by CDC GeT-RM

• Development of Genomic Reference Materials for Cystic Fibrosis Genetic Testing
  • test materials available from Coriell; program coordinated by GeT-RM

• Consensus Characterization of 16 FMR1 Reference Materials: A Consortium Study
  • Coordinated by CDC (abstract doesn't specify GeT-RM); materials deposited in Coriell

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