Genomics. Are you ready for the revolution?

Controlling new knowledge: Genomic science, governance and the politics of bioinformatics

The rise of bioinformatics is a direct response to the political difficulties faced by genomics in its quest to be a new biomedical innovation, and the value of bioinformatics lies in its role as the bridge between the promise of genomics and its realization in the form of health benefits. Western scientific elites are able to use their close relationship with the state to control and facilitate the emergence of new domains compatible with the existing distribution of epistemic power - all within the embrace of public trust. The incorporation of bioinformatics as the saviour of genomics had to be integrated with the operation of two key aspects of governance in this field: the definition and ownership of the new knowledge. This was achieved mainly by the development of common standards and by the promotion of the values of communality, open access and the public ownership of data to legitimize and maintain the governance power of publicly funded genomic science. Opposition from industry advocating the private ownership of knowledge has been largely neutered through the institutions supporting the science-state concordat. However, in order for translation into health benefits to occur and public trust to be assured, genomic and clinical data have to be integrated and knowledge ownership agreed upon across the separate and distinct governance territories of scientist, clinical medicine and society. Tensions abound as science seeks ways of maintaining its control of knowledge production through the negotiation of new forms of governance with the institutions and values of clinicians and patients.

Bioinformatics and the Politics of Innovation in the Life Sciences: Science and the State in the United Kingdom, China, and India

The governments of China, India, and the United Kingdom are unanimous in their belief that bioinformatics should supply the link between basic life sciences research and its translation into health benefits for the population and the economy. Yet at the same time, as ambitious states vying for position in the future global bioeconomy they differ considerably in the strategies adopted in pursuit of this goal. At the heart of these differences lies the interaction between epistemic change within the scientific community itself and the apparatus of the state. Drawing on desk-based research and thirty-two interviews with scientists and policy makers in the three countries, this article analyzes the politics that shape this interaction. From this analysis emerges an understanding of the variable capacities of different kinds of states and political systems to work with science in harnessing the potential of new epistemic territories in global life sciences innovation.

Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa

Background

Cytochrome P450 3A5 (CYP3A5) is an enzyme involved in the metabolism of many therapeutic drugs. CYP3A5 expression levels vary between individuals and populations, and this contributes to adverse clinical outcomes. Variable expression is largely attributed to four alleles, CYP3A5*1 (expresser allele); CYP3A5*3 (rs776746), CYP3A5*6 (rs10264272) and CYP3A5*7 (rs41303343) (low/non-expresser alleles). Little is known about CYP3A5 variability in Africa, a region with considerable genetic diversity. Here we used a multi-disciplinary approach to characterize CYP3A5 variation in geographically and ethnically diverse populations from in and around Africa, and infer the evolutionary processes that have shaped patterns of diversity in this gene. We genotyped 2538 individuals from 36 diverse populations in and around Africa for common low/non-expresser CYP3A5 alleles, and re-sequenced the CYP3A5 gene in five Ethiopian ethnic groups. We estimated the ages of low/non-expresser CYP3A5 alleles using a linked microsatellite and assuming a step-wise mutation model of evolution. Finally, we examined a hypothesis that CYP3A5 is important in salt retention adaptation by performing correlations with ecological data relating to aridity for the present day, 10,000 and 50,000 years ago.

Results

We estimate that ~43% of individuals within our African dataset express CYP3A5, which is lower than previous independent estimates for the region. We found significant intra-African variability in CYP3A5 expression phenotypes. Within Africa the highest frequencies of high-activity alleles were observed in equatorial and Niger-Congo speaking populations. Ethiopian allele frequencies were intermediate between those of other sub-Saharan African and non-African groups. Re-sequencing of CYP3A5 identified few additional variants likely to affect CYP3A5 expression. We estimate the ages of CYP3A5*3 as ~76,400 years and CYP3A5*6 as ~218,400 years. Finally we report that global CYP3A5 expression levels correlated significantly with aridity measures for 10,000 [Spearmann’s Rho= −0.465, p=0.004] and 50,000 years ago [Spearmann’s Rho= −0.379, p=0.02].

Conclusions

Significant intra-African diversity at the CYP3A5 gene is likely to contribute to multiple pharmacogenetic profiles across the continent. Significant correlations between CYP3A5 expression phenotypes and aridity data are consistent with a hypothesis that the enzyme is important in salt-retention adaptation.

Whole-genome patenting

Gene patenting is now a familiar commercial practice, but there is little awareness that several patents claim ownership of the complete genome sequence of a prokaryote or virus. When these patents are analysed and compared to those for other biological entities, it becomes clear that genome patents seek to exploit the genome as an information base and are part of a broader shift towards intangible intellectual property in genomics.

Evaluation of physiologically based models of pregnancy and lactation for their application in children's health risk assessments

In today's scientific and regulatory climates, an increased emphasis is placed on the potential health impacts for children exposed either in utero or by nursing to drugs of abuse, pharmaceuticals, and industrial or consumer chemicals. As a result, there is a renewed interest in the development and application of biologically based computational models that can be used to predict the dosimetry (or ultimately response) in a developing embryo, fetus, or newborn. However, fundamental differences between animal and human development can create many unique challenges. For example, unlike models designed for adults,biologically based models of pre-and postnatal development must deal with rapidly changing growth dynamics (maternal embryonic, fetal, and neonatal), changes in the state of differentiation of developing tissues, uniquely expressed or uniquely functioning signal transduction or enzymatic pathways, and unusual routes of exposure (e.g., maternal-mediated placental transfer and lactation). In cases where these challenges are overcome or addressed, biological modeling will likely prove useful in assessments geared toward children's health, given the contributions that this approach has already made in cancer and non-cancer human health risk assessments. Therefore, the purpose of this review is to critically evaluate the current state of the art in physiologically based pharmacokinetic (PBPK) and pharmacodynamic (PD) modeling of the developing embryo, fetus, or neonate and to recommend potential steps that could be taken to improve their use in children's health risk assessments. The intent was not to recommend improvements to individual models per se, but to identify areas of research that could move the entire field forward. This analysis includes a brief summary of current risk assessment practices for developmental toxicity, with an overview of developmental biology as it relates to species-specific dosimetry. This summary should provide a general context for understanding the tension that exists in modeling between describing biological proceses in exquisite detail vs. the simplifications that are necessary due to lack of data (or through a sensitivity analysis, determined to be of little impact) to develop individual PBPK or PD models. For each of the previously published models covered in this review, a description of the underlying assumptions and model structures as well as the data and methods used in model development and validation are highlighted. Although several of the models attempted to describe target tissues in the developing embryo, fetus, or neonate of laboratory animals, extrapolations to humans were largely limited to maternal blood or milk concentrations. Future areas of research therefore are recommended to extend the already significant progress that has been made in this field and perhaps address many of the technical policy, and ethical issues surrounding various approaches for decreasing the uncertainty in extrapolating from animal models to human pregnancies or neonatal exposures.

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Primer on medical genomics part II: Background principles and methods in molecular genetics

The nucleus of every human cell contains the full complement of the human genome, which consists of approximately 30,000 to 70,000 named and unnamed genes and many intergenic DNA sequences. The double-helical DNA molecule in a human cell, associated with special proteins, is highly compacted into 22 pairs of autosomal chromosomes and an additional pair of sex chromosomes. The entire cellular DNA consists of approximately 3 billion base pairs, of which only 1% is thought to encode a functional protein or a polypeptide. Genetic information is expressed and regulated through a complex system of DNA transcription, RNA processing, RNA translation, and posttranslational and cotranslational modification of proteins. Advances in molecular biology techniques have allowed accurate and rapid characterization of DNA sequences as well as identification and quantification of cellular RNA and protein. Global analytic methods and human genetic mapping are expected to accelerate the process of identification and localization of disease genes. In this second part of an educational series in medical genomics, selected principles and methods in molecular biology are recapped, with the intent to prepare the reader for forthcoming articles with a more direct focus on aspects of the subject matter.

Neuroscience databases: tools for exploring brain structure-function relationships

Faster than ever, neuroscience is generating vast amounts of data that await cross-referencing, comparison, integration and interpretation in the endeavour to unravel the mechanisms of the brain. The complex, diverse and distributed nature of these data requires the development of advanced neuroinformatics methodologies for databases and associated tools that are now beginning to emerge. This paper presents an overview of current issues in the representation, integration and analysis of neuroscience data from molecular to brain systems levels, including issues of implementation, standardization, management, quality control, copyright, confidentiality and acceptance. Particular emphasis is given to integrative neuroinformatics approaches for exploring structure-function relationships in the brain.