Future Developments of Medical Informatics from the Viewpoint of Networked Clinical Research

Objectives: To be prepared for future developments, such as enabling support of rapid innovation transfer and personalized medicine concepts, interoperability of basic research, clinical research and medical care is essential. It is the objective of our paper to give an overview of developments, indicate problem areas and to specify future requirements.

Methods: In this paper recent and ongoing large-scaled activities related to interoper-ability and integration of networked clinical research are described and evaluated. The following main topics are covered: necessity for general IT-conception, open source/open community approach, acceptance of eSource in clinical research, interoperability of the electronic health record and electronic data capture and harmonization and bridging of standards for technical and semantic inter-operability.

Results: National infrastructures and programmes have been set up to provide general IT-conceptions to guide planning and development of software tools (e.g. TMF, ca BIG, NIHR). The concept of open research described by transparency achieved through open access, open data, open communication and open source software is becoming more and more important in clinical research infrastructure development (e.g. ca BIG, ePCRN). Meanwhile visions and rules for using eSource in clinical research are available, with the potential to improve interoperability between the electronic health record and electronic data capture (e.g. CDISC e SDI, eClinical Forum/PhRMA EDC/eSource Taskforce). Several groups have formulated user requirements, use cases and technical frameworks to advance these issues (e.g. NHIN Slipstream-project, EHR/CR-project, IHE). In order to achieve technical and semantic interoperability, existing standards (e.g. CDISC) have to be harmonized and bridged. Major consortia have been formed to provide semantical inter-operability (e.g. HL7 RCRIM under joint leadership of HL7, CDISC and FDA, or BRIDG covering CDISC, HL7, FDA, NCI) and to provide core sets of data collection fields (CDASH).

Conclusions: The essential tasks for medical informatics within the next ten years will now be the development and implementation of encompassing IT conceptions, strong support of the open community and open source approach, the acceptance of eSource in clinical research, the uncompromising continuity of standardization and bridging of technical standards and the widespread use of electronic health record systems.

Health Data for Public Health: Towards New Ways of Combining Data Sources to Support Research Efforts in Europe

Objectives: To present the European landscape regarding the re-use of health administrative data for research. Methods: We present some collaborative projects and solutions that have been developed by Nordic countries, Italy, Spain, France, Germany, and the UK, to facilitate access to their health data for research purposes. Results: Research in public health is transitioning from siloed systems to more accessible and re-usable data resources. Following the example of the Nordic countries, several European countries aim at facilitating the re-use of their health administrative databases for research purposes. However, the ecosystem is still a complex patchwork, with different rules, policies, and processes for data provision. Conclusion: The challenges are such that with the abundance of health administrative data, only a European, overarching public health research infrastructure, is able to efficiently facilitate access to this data and accelerate research based on these highly valuable resources.

Ethical concerns caused by integrative patient empowerment solutions for personalized medicine

Personalized medicine that promises targeted treatments with high therapeutic effectiveness requires an unmatched degree of participation of the patient. To enable this high degree of patient empowerment, the project p-medicine developed a Patient Empowerment Tool that is part of a clinical research infrastructure consisting of data management, data warehouse, biobank access, imaging, simulation and decision support tools. Patient autonomy is enhanced by giving patients access to their data and by providing means for informed choices and consent. Because the highly integrative nature of the Patient Empowerment Tool raised ethical concerns, an ethical requirements analysis was carried out, resulting in the assignment of five ethical clusters. The one concerned with the Patient Empowerment Tool was used to identify several concerns, like the access to unfavorable information or negative diagnosis, incomprehensible risk/benefit display, and other factors that may overstress certain patients. From the ethical point of view, the user interface should contain different profiles and control mechanisms to protect the patient and to provide an adaptable and intelligent display of information, sufficient guidance and help for users from vulnerable populations as well as for patients with life threatening diseases.

Future developments of medical informatics from the viewpoint of networked clinical research. Interoperability and integration

OBJECTIVES

To be prepared for future developments, such as enabling support of rapid innovation transfer and personalized medicine concepts, interoperability of basic research, clinical research and medical care is essential. It is the objective of our paper to give an overview of developments, indicate problem areas and to specify future requirements.

METHODS

In this paper recent and ongoing large-scaled activities related to interoperability and integration of networked clinical research are described and evaluated. The following main topics are covered: necessity for general IT-conception, open source/open community approach, acceptance of eSource in clinical research, interoperability of the electronic health record and electronic data capture and harmonization and bridging of standards for technical and semantic interoperability.

RESULTS

National infrastructures and programmes have been set up to provide general IT-conceptions to guide planning and development of software tools (e.g. TMF, caBIG, NIHR). The concept of open research described by transparency achieved through open access, open data, open communication and open source software is becoming more and more important in clinical research infrastructure development (e.g. caBIG, ePCRN). Meanwhile visions and rules for using eSource in clinical research are available, with the potential to improve interoperability between the electronic health record and electronic data capture (e.g. CDISC eSDI, eClinical Forum/PhRMA EDC/eSource Taskforce). Several groups have formulated user requirements, use cases and technical frameworks to advance these issues (e.g. NHIN Slipstream-project, EHR/CR-project, IHE). In order to achieve technical and semantic interoperability, existing standards (e.g. CDISC) have to be harmonized and bridged. Major consortia have been formed to provide semantical interoperability (e.g. HL7 RCRIM under joint leadership of HL7, CDISC and FDA, or BRIDG covering CDISC, HL7, FDA, NCI) and to provide core sets of data collection fields (CDASH).

CONCLUSIONS

The essential tasks for medical informatics within the next ten years will now be the development and implementation of encompassing IT conceptions, strong support of the open community and open source approach, the acceptance of eSource in clinical research, the uncompromising continuity of standardization and bridging of technical standards and the widespread use of electronic health record systems.

Extended cooperation in clinical studies through exchange of CDISC metadata between different study software solutions

OBJECTIVES

Our objectives were to analyze the possibility of an exchange of an entire clinical study between two different and independent study software solutions. The question addressed was whether a software-independent transfer of study metadata can be performed without programming efforts and with software routinely used for clinical research.

METHODS

Study metadata was transferred with ODM standard (CDISC). Study software systems employed were MACRO (InferMed) and XTrial (XClinical). For the Proof of Concept, a test study was created with MACRO and exported as ODM. For modification and validation of the ODM export file XML-Spy (Altova) and ODM-Checker (XML4Pharma) were used.

RESULTS

Through exchange of a complete clinical study between two different study software solutions, a Proof of Concept of the technical feasibility of a system-independent metadata exchange was conducted successfully. The interchange of study metadata between two different systems at different centers was performed with minimal expenditure. A small number of mistakes had to be corrected in order to generate a syntactically correct ODM file and a "vendor extension" had to be inserted. After these modifications, XTrial exhibited the study, including all data fields, correctly. However, the optical appearance of both CRFs (case report forms) was different.

CONCLUSIONS

ODM can be used as an exchange format for clinical studies between different study software. Thus, new forms of cooperation through exchange of metadata seem possible, for example the joint creation of electronic study protocols or CRFs at different research centers. Although the ODM standard represents a clinical study completely, it contains no information about the representation of data fields in CRFs.

Identification of mRNAs regulated by interferon-gamma in cultured rat astrocytes by PCR differential display

We have used RNA differential display to identify specific mRNA species that are regulated by interferon-gamma (IFN gamma) treatment of enriched astrocyte cultures. Following a 24-hour treatment with IFN, mRNA was subjected to differential display using 15 different random primers. 105 upregulated and 5 downregulated cDNAs were selected for further sequencing and identification. Northern blot analysis confirmed the upregulation of 13 genes identical or highly similar to: intercrine adrenomedullin, H-rev 107, CAP-like protein, ATP synthase epsilon-subunit, complement C3, S-100 beta, Ca2+ ATPase, mg11, IFN-upregulated 56-kD protein mRNA, laminin receptor-like protein, protein tyrosine phosphatase, and zic. These data suggest that exposure to IFN gamma results in a complex change in the pattern of astrocyte gene expression.

Fibronectin-induced cell spreading and down-regulation of 12-lipoxygenase expression in megakaryocytic DAMI cells

During maturation of small immature megakaryocytes to mature platelet producing megakaryocytes the arachidonic acid metabolizing enzyme 12-lipoxygenase is expressed. Here we show that cells of the megakaryocytic cell line DAMI flatten and spread on fibronectin substrate in a way which may be similar to the spreading observed with bone marrow-derived megakaryocytes. The effect on DAMI cell morphology may be attributed to the RGD motif (Arg-Gly-Asp) of fibronectin. Incubation of DAMI cells with fibronectin down-regulated 12-lipoxygenase expression about 85-90%. We discuss the hypothesis that 12-HETE in megakaryocytes may act as a sensor for megakaryocyte attachment to matrix components.

A lung type prostaglandin F synthase is expressed in bovine liver: cDNA sequence and expression in E. coli

Using the cDNA of bovine lung prostaglandin F synthase (EC 1.1.1.2) as a probe, we isolated a clone from a bovine liver cDNA library which differed in only eleven nucleotides from the probe. The corresponding protein contained three amino acid substitutions, including a leucine residue which is conserved throughout all aldo-keto reductases. We inserted the liver cDNA into expression vector pUC19 and expressed the recombinant liver enzyme in E.coli. The purified liver enzyme reduced prostaglandin H2 as well as prostaglandin D2 and various carbonyl compounds. The high relative activity against prostaglandin H2 in combination with a high Km value for prostaglandin D2 identified this liver enzyme as a lung type prostaglandin F synthase. However, the binding constant for NADPH of the liver enzyme was 3.5 fold higher than that of lung prostaglandin F synthase.

Linker mutagenesis in the lacZ gene of Escherichia coli yields variants of active beta-galactosidase

Synthetic octameric oligonucleotides that code for a unique restriction site were cloned into a randomly linearized plasmid that carries the lacZ gene. The insertions were mapped by digestion with appropriate restriction endonucleases. 12 mutants were identified which carry an insertion within the lacZ gene and still express active beta-galactosidase. Small deletions or duplications of the wild-type sequence occurred at these positions which restore the correct reading frame. The insertions occurred in the first and the last third of the internal duplication of the lacZ gene and within the domain homologous to dihydrofolate reductase.

The border residues of the dihydrofolate reductase domain in Escherichia coli beta-galactosidase correspond to the positions of introns 1 and 5 of dihydrofolate reductase of chicken

In beta-galactosidase of Escherichia coli residues 820-934 are similar to residues in dihydrofolate reductase of E. coli. Dihydrofolate reductase of E. coli and chicken are also similar and have identical tertiary structures. I used the similarity of the three-dimensional structure of prokaryotic and eukaryotic dihydrofolate reductases to align the chicken dihydrofolate reductase and the similar residues of beta-galactosidase. The positions of introns 1 and 5 of the chicken dihydrofolate reductase gene correspond exactly to the start and the end of the dihydrofolate reductase-like domain in the beta-galactosidase polypeptide chain. This equivalence of intron positions in a eukaryotic gene and domain structure in a prokaryotic protein was interpreted as evidence for a common origin of both genes.

50 residues coded by exon 2 of chicken lysozyme carry residual catalytic activity

The generally accepted hypothesis that exons code for fundamental polypeptide structures was tested with a fusion protein consisting of almost the entire polypeptide coded by exon 2 of chicken lysozyme fused to the N-terminus of beta-galactosidase of E.coli. Exon 2 encodes residues 28-81 of lysozyme. It thus contains Glu 35 and Asp 52, which are essential for hydrolysis of glycosidic bonds. The exon 2-beta-galactosidase fusion protein hydrolysed the substrate 4-methylumbelliferyl-N,N',N''-triacetyl-chitotrioside with a reaction rate about 1/40,000 of that of native lysozyme. The low hydrolysis rate of exon 2-peptide is partially caused by its low affinity to its substrate.

Fused lacZ genes code for di-, tri- and tetra-beta-galactosidase in Escherichia coli

Plasmids were constructed which carry two, three or four active lacZ genes of Escherichia coli fused head-to-tail in phase. The products of these oligomeric lacZ genes are shown to be polypeptides with expected subunit mol. wts. of 230 kd (di-beta-galactosidase), 350 kd (tri-beta-galactosidase) and 460 kd (tetra-beta-galactosidase). Di-beta-galactosidase has the same enzymatic activity as the wild-type enzyme. It subunits are practically not degraded proteolytically in vivo. It aggregates predominantly to a dimer which has the same sedimentation constant as the wild-type tetrameric enzyme. Furthermore, it is more heat stable than the wild-type enzyme. Tri- and tetra-beta-galactosidase have strongly reduced enzymatic activities and are largely degraded. Our experiments lead us to propose that covalent joining of two subunits through proper gene duplication may possibly be an intermediate in the evolution of self aggregation of homo-oligomeric proteins.