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PubMed2003

Governing population genomics: law, bioethics, and biopolitics in three case studies.

Existing scholarship on population genomics has only superficially addressed issues of power and political process. Accordingly, questions of politics and governance pervade the analysis of three population genomics case studies that follow: the Human Genome Diversity Project, Iceland's Health Sector Database, and "Clinical Genomics" as defined by the Beth Israel-Ardais collaboration. An examination of these case studies reveals that the common law, U.S. regulatory law, and international law have not developed the political sophistication to make the traditional promises of biomedical ethics--respect for autonomy, justice, and beneficence--come to fruition. Further, comparisons of these projects illuminate three areas ripe for reframing--informed consent, expert ethical oversight, and commercial benefits. Four avenues of reform are suggested.

Advisory Committees↗
PubMed1999

Privacy issues in second stage genomics.

Research that identifies genes useful in the prevention and treatment of disease will require access to biologic samples and medical records protected by traditional notions of privacy and confidentiality. Resolving conflicts between privacy and genomic research will require articulating the ethical rules that should govern such practices and then implementing those rules in the national, regional, or local health systems in which the data of interest exists. As consensus develops about the ethical rules that should govern such research, attention will shift to the practical and political problems of installing and implementing those rules in the agencies and institutions where such research will occur.

Advisory Committees↗
PubMed2002

Proposal for an allele nomenclature system based on the evolutionary divergence of haplotypes.

The classical view of what constitutes an "allele" has been challenged by recent findings of a great deal of human genetic variability, i.e., we can expect, on average, one variant site every 100-250 bases of our haploid genome. The haplotype is defined as "the patterns of co-occurrence of variant sites on the same chromosome" (and therefore within each particular gene). Sufficient evidence exists for the divergence of haplotypes during evolution of Homo sapiens sapiens, and the total number of haplotypes per gene will reflect the amount of time any particular ethnic group has existed on the planet, e.g., greatest in Africans, fewer in East Asians, and still fewer in Caucasians. If the average gene spans 30 kb, we can expect approximately 170 polymorphic variant sites per gene in the world population. We do not see 2(170) haplotypes, however; we might find only 10 to 200 haplotypes (depending on the gene's size and degree of conservation of the gene product). This finite number allows for a reasonable haplotype nomenclature system for each gene, based on evolutionary divergence. For polymorphic variants (i.e., frequency > or = 0.01), I propose using Arabic numerals for the major clades (e.g., *1, *2, em leader *20, *21), capital letters for sublineages (e.g., *2A, *2B, *2C), and Arabic numerals for sub-sublineages (e.g., *22G12, *22G13); additional subcategories may be added, in an alternating number/letter/number/letter sequence, depending on the complexity of present-day haplotypes of a particular gene. Web sites with a web master and external advisory committee should be set up for each gene superfamily, family, or individual gene (depending on complexity), and an international haplotype nomenclature committee, perhaps comprised of several dozen of these web masters, should oversee haplotype nomenclature for the entire human genome. The higher heterozygosity and multiallelic nature makes haplotypes more informative than biallelic SNPs. Ultimately, our knowledge of haplotype patterns, rather than single variant sites, of perhaps several hundred genes will likely be helpful in finding associations between genotype and any multiplex phenotype (e.g., complex diseases including cancer, and/or toxicity of pharmaceutical agents or environmental pollutants).

Alleles↗
PubMedDate not supplied

The human genome and public policy: a nursing perspective.

The Human Genome Project has completed a rough draft of the sequence that comprises human DNA. For the first time, the scientific discoveries have been conducted in tandem with research exploring the social, legal, and ethical implications of the research. Several committees have studied the policy implications of the genetics information explosion. The Secretary's Advisory Committee on Genetic Testing's report was received by the Secretary of the U.S. Department of Health and Human Services in November 2000 and contains recommendations for the oversight of genetic testing. Public policy issues that affect nursing practice in the area of genetics must be explored by individual nurses and professional nursing organizations.

Genetic Engineering↗
PubMed2000

Population genetics and benefit sharing.

The majority of international or national guidelines, specific to human genetics concentrate on actual or potential clinical applications. In contrast, the Ethics Committee of the Human Genome Organisation (HUGO) attempts to provide guidance to the bench scientists engaged in fundamental research in genomics prior to any clinical applications. Often confused as constituting the Human Genome Project (HGP) itself, HUGO's (Human Genome Organization) ultimate goal is to assist in the worldwide collaboration underpinning the HGP. It is an international organisation with 1,229 members in approximately 60 countries. The Ethics Committee is one of HUGO's six international advisory committees. Composed of experts from a number of countries and disciplines, the HUGO Ethics Committee promotes discussion and understanding of social, legal, and ethical issues as they relate to the conduct of, and knowledge derived from, the Genome Initiative. Currently, it has 13 members from 11 difference countries. It has produced statements on the conduct of genetic research, on cloning, and, has most recently presented a 'Statement on Benefit-Sharing', April 11, 2000. The Intellectual Property Committee of HUGO has been active in the controversial area of patenting. The issue of benefit-sharing is one that has its source in the mandate of both committees. How to avoid both commodification of the person through payment for access to DNA and biopiracy with no return to benefits to the families or community? While patents are a legitimate form of recognition for innovation, there seems to be no therapeutic exception to some of its stringent rules and the 'morality' exclusion has lain dormant. The HUGO 'Statement on Benefit-Sharing' examines the issues of defining community, common heritage, distributive justice and solidarity before arriving at its conclusions in benefit-sharing. This communication reviews some of these issues.

Genetics, Population↗
PubMed2006

EGASP: the human ENCODE Genome Annotation Assessment Project.

BACKGROUND: We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. RESULTS: The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. CONCLUSION: This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence.

Alternative Splicing↗
PubMed1990

Controversies in research ethics affecting the future of human gene therapy.

A critical analysis is undertaken of the ethical debate on two general classes of research activities that bear on the future of human gene therapy: (i) the human fetus and (ii) the preimplantation human embryo after in vitro fertilization (IVF). The conclusion is that the hope of human gene therapy and of other clinical applications of the human genome initiative is in danger because of the obstacles to research in reproductive biology and human genetics in the federal sector.

Aborted Fetus↗