NEW YORK (GenomeWeb News) – Genotype-phenotype resources offer great promise for use by researches and physicians alike, but measures should be taken to help ensure the uptake, accessibility, and utility of these resources, according to a new white paper from a European Union-funded think tank.
The new report from INBIOMEDvision was drafted to survey the genotype-phenotype resources field and to assess opportunities and obstacles that Europe in particular confronts in this area.
One obstacle is that it is still mostly impossible to establish clear correlations between the increasing amounts of genotypic information from clinical studies, such as genome-wide association studies, and phenotype information at the population level, the panel found.
Still, linking genotype and phenotype is valuable for many biomedical applications, such as early-stage drug discovery, toxicology studies, and clinical trials. To enhance the potential for these applications, the INBIOMEDvision group proposed recommendations for academic and industrial researchers, funding agencies, and journal publishers.
First, the white paper acknowledges that genotype-phenotype resources involve both bioinformatics and medical informatics, and that care should be taken in bridging the gap between these areas. Also, the central goal for biomedical researchers is to publish their work, while clinical goals are focused on practical validity and utility.
The panel also noted that not every new valid biomedical research publication will have valid clinical applications, and that systems biology studies rely on large amounts of 'omics data that is not fully validated or of high quality.
A number of genotype-phenotype resources are already in use, the group found, but primarily for research purposes, and these resources will be incorporated into clinical practice slowly, the authors noted. Researchers' methods, models, and tools may need to earn the trust of physicians over time, they advised.
The white paper recommends that members of the biomedical, clinical, and commercial drug discovery communities be encouraged to collaborate using genotype-phenotype resources, and funding should be encouraged for such joint efforts.
The report also advises that the EU provide more infrastructure for establishing standards and developing text mining tools and ontologies for biomedical and clinical support.
A major barrier to the use of genotype-phenotype resources in research and in the clinic is the difficulty of locating, evaluating, and selecting these resources. The authors advise that new tools can be developed to help researchers and clinicians navigate in this area. These tools could possibly be based on the National Institutes of Health's Phenotype-Genotype Integrator, the Database for Genotypes and Phenotypes, the Virus Pathogen Database and Analysis Resource, and other resources that are planned by NIH.
The authors also note that improvements in sequencing technology are not always accompanied by equally rapid improvements in data analysis techniques, and advise that that lag should be taken into account when planning how to exploit the "coming availability of near ubiquitous genome sequencing."