Posts Tagged genomics

Ethics and access to databases

This publication has attracted attention: Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays by Nils Homer and 9 co-authors, including David W Craig, PLoS Genet 2008( Aug 29);4(8): e1000167 [PubMed Record].

See, for example: NIH Limits Access to GWAS Databases Due to Privacy Concerns by Charles P Clayton, Alliance for Academic Internal Medicine, September 5, 2008. Excerpt:

The National Institutes of Health (NIH) announced new procedures for researchers to access previously public databases from genome-wide association studies (GWAS) in light of recently published research …

See also: NIH Tackles Privacy Concerns for GWAS, NIAID Funding News, September 17, 2008. Excerpts:

On August 25, 2008, NIH removed files of aggregate GWAS data from the public portion of its databases while keeping summary information public.

You will still be able to share and use these data. As an investigator, you must now apply for access and agree to protect confidentiality. This process matches the one NIH has required all along for individual-level data.

Read more about NIH’s new policy for accessing GWAS data at Modifications to Genome-Wide Association Studies (GWAS) Data Access.

Excerpts from NIH’s new policy:

The NIH developed a two-tiered access policy for GWAS data. The first level is the public posting (open access) of summary-level information and aggregate genotype data, including allele frequencies by case-control status, association tests odds ratios, and p values for each SNP in the scan. The second level is controlled access to individual-level data (genotypes and phenotypes). The controlled access data are available to investigators from scientific institutions who submit Data Access Request (DAR) packages that are reviewed and approved by the NIH Data Access Committees (DACs).

New statistical techniques for analyzing dense genomic information make it possible to infer the group assignment (i.e., case or control) of an individual DNA sample if one has access to high-density genomic data for that specific individual from another source and the allele frequencies for the case and control groups from publicly available aggregate datasets. …..

Two recent publications about research ethics in the genomics era:

Ethical and Practical Issues Associated with Aggregating Databases by David R Karp and 14 co-authors, PLoS Med 2008(Sep 23); 5(9): e190 [PubMed Record]. Excerpt:

Box 1. Recommendations

1. Determine whether initial consent and ethical approval will allow secondary research.
2. Ensure that there are appropriate data security mechanisms and review bodies to protect privacy interests in aggregated databases.
3. Informed consent should take into account the potential incorporation of data into aggregated databases.
4. Address special challenges of using data obtained from existing databases.
5. Pursue efforts directed at standardization of data.
6. Establish data sharing rules, including attribution of contributions.
7. Adopt “best practices” to avoid identifiability of the data.

And, Informed Consent in the Genomics Era by Deborah Mascalzoni, Andrew Hicks, Peter Pramstaller, Matthias Wjst, PLoS Med 2008(Sep 16); 5(9): e192 [PubMed Record]. Summary Points:

* Genetic cohort studies storing biological materials hold great promise for medical research, but also present new problems that are profoundly different from the classical clinical trial for which informed consent was developed.
* The classical risk/benefit analysis of physical harm doesn’t take into account new threats to the individual such as uninsurability, unemployability, genetic discrimination, or disruption of family relationships.
* Traditional informed consent may therefore no longer be appropriate when dealing with long-term studies using biological materials.
* Informed consent should be seen as an ongoing process between researcher and participant, and not just as a once-and-for-all decision.
* Research following the initial storage of samples needs to be likewise explained and may be announced using new communication methods.

The publications cited above are all in PLoS journals, and are OA.


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Open access genomes

Open access genomes! (but how is OA protected?), Dave Love, dave love’s blog, October 21, 2008. Excerpt:

We have come a long way in the last 15 years since Craig Venter and his company, Celera, refused to deposit their human genomic sequence in NCBI/GenBank and others who practice gene patenting deflated our collective tyres. I think that PGP understands the benefits of being OA, but I didn’t see anything on their website about a legal backbone to protect that access, such as a Creative Commons copyrights. I hope they will get some advice on this from librarians, lawyers, publishers, and others in the OA community!

For more about the PGP, see: More on the Personal Genome Project, Gavin Baker, Open Access News, October 20, 2008; Profile of the Personal Genome Project, Gavin Baker, Open Access News, August 06, 2008; The Personal Genome Project, George M Church, Mol Syst Biol 2005; 1: 2005.0030 [Epub 2005(Dec 13)].

Modified on October 21, 2008:

See also: From genetic privacy to open consent, Jeantine E Lunshof, Ruth Chadwick, Daniel B Vorhaus and George M Church, Nat Rev Genet 2008(May); 9(5): 406-11. Excerpts from the full text (not OA):

Box 3 | Key features of the Personal Genome Project’s open-consent policy

Open consent as part of the Personal Genome Project implies that research participants accept that:

* Their data could be included in an open-access public database.
* No guarantees are given regarding anonymity, privacy and confidentiality.
* Participation involves a certain risk of harm to themselves and their relatives.
* Participation does not benefit the participants in any tangible way.
* Compliance with monitoring of their well-being through quarterly questionnaires is required.
* Withdrawal from the study is possible at any time.
* Complete removal of data that have been available in the public domain may not be possible.

The moral goal of open consent is to obtain valid consent by effectuating veracity as a precondition for valid consent and effectuating voluntariness through strict eligibility criteria, as a precondition for substantial informed consent.

[End of Box 3]

Open consent. Open consent means that volunteers consent to unrestricted re-disclosure of data originating from a confidential relationship, namely their health records, and to unrestricted disclosure of information that emerges from any future research on their genotype–phenotype data set, the information content of which cannot be predicted. No promises of anonymity, privacy or confidentiality are made. The leading moral principle is veracity — telling the truth — which should precede autonomy. Although, in clinical medicine, veracity is the legal norm in many jurisdictions, physicians may try to justify the withholding of information by invoking the ‘therapeutic privilege’. In research, there is no such privilege, and when seeking informed consent from research subjects, distorted or incomplete information could undermine trust in researchers and in science.

Comment: Those contemplating OA to genetic data need to pay careful attention to the concept of “open consent“, and its emphasis on “telling the truth” and on “voluntariness”. It’s also noted in the full text that “in the PGP potential volunteers are strongly advised to discuss their participation with relatives“.

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Articles in Nature Reviews Genetics (Oct 2008)

A series of articles in Nature Reviews Genetics are Gratis OA (after free registration): Table of Contents, Nature Reviews Genetics, 2008(Oct); 9(10).


Human genomic variation initiatives in emerging economies and developing countries, Béatrice Séguin, Billie-Jo Hardy, Peter A. Singer & Abdallah S. Daar, Nature Reviews Genetics 2008(Oct); 9(10 supp): S3-S4.


Genomics, public health and developing countries: the case of the Mexican National Institute of Genomic Medicine (INMEGEN), Béatrice Séguin, Billie-Jo Hardy, Peter A. Singer & Abdallah S. Daar, Nature Reviews Genetics 2008(Oct); 9(10 supp): S5-S9.

From diversity to delivery: the case of the Indian Genome Variation initiative, Billie-Jo Hardy, Béatrice Séguin, Peter A. Singer, Mitali Mukerji, Samir K. Brahmachari & Abdallah S. Daar, Nature Reviews Genetics 2008(Oct); 9(10 supp): S9-S14.

Universal health care, genomic medicine and Thailand: investing in today and tomorrow, Béatrice Séguin, Billie-Jo Hardy, Peter A. Singer & Abdallah S. Daar, Nature Reviews Genetics 2008(Oct); 9(10 supp): S14-S19.

South Africa: from species cradle to genomic applications, Billie-Jo Hardy, Béatrice Séguin, Raj Ramesar, Peter A. Singer & Abdallah S. Daar, Nature Reviews Genetics 2008(Oct); 9(10 supp): S19-S23.

The next steps for genomic medicine: challenges and opportunities for the developing world, Billie-Jo Hardy, Béatrice Séguin, Federico Goodsaid, Gerardo Jimenez-Sanchez, Peter A. Singer & Abdallah S. Daar, Nature Reviews Genetics 2008(Oct); 9(10 supp): S23-S27.

Added September 21, 2008: See also: Human Genomic Variation Studies in Developing Countries, McLaughlin-Rotman Centre for Global Health, Sep 18, 2008.

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