Deliverables
RESULT DESCRIPTION:
The website of the project, www.ECARUCA.net, consists of two sections: public pages that are freely available to each Internet user and restricted pages containing patient information that are only accessible for account holders. At the public pages general information is available including the objectives of the project, its rules and regulations, as well as downloadable information and informed consent forms in different European languages.
In addition to the public pages, the following restricted options on the ECARUCA website are available to professional account holders:
- Submit cytogenetic and molecular information;
- Submit clinical information;
- Search by chromosomal aberration;
- Search by clinical feature(s);
- List of all cases submitted by the centre of the account holder;
- List of all participating centres;
- Detailed Case of the Month information.
A unique feature of the website is the restricted page for parents of children whose data have been submitted to the ECARUCA database. A case-specific parent account is created for all newly submitted cases and sent to the referring clinician. With this account parents have access to the information of their own child in the database and can directly send follow-up information to the Clinical Database Managers.
DISSEMINATION:
The account holders and other interested visitors of the website are regularly updated by a Newsletter. The project is also promoted by a booth at the annual meeting of the European Society of Human Genetics, via the network of National Coordinators (see result 34581) and there are regular contacts with several patient support groups as well as with Eurochromnet, Eurordis and Orphanet. Articles extensively describing the ECARUCA project will be published in the Newsletter of the European Cytogeneticists Association and in the European Journal of Medical Genetics in the beginning of 2006.
INNOVATIVE FEATURES:
The website is a platform for all people interested in clinical cytogenetics. It brings together clinicians and researchers (see also result 34585 on research platforms) and provides information on rare chromosome disorders that can not be found elsewhere on the world wide web. Especially through the collection of clinical information on rare chromosome disorders an improvement of both research and patient care is achieved.
CURRENT STATUS AND USE OF THE RESULTS:
At the moment the website is visited more than 300 times per week and over 500 professionals in the field of clinical (cyto)genetics have an account. Through the website over 200 new cases have been submitted to the database in 2005 (see result 34580) and several research contacts have been established.
EXPECTED BENEFITS:
The website provides easy and free access to the database for doctors and scientists and is a good basis for collaboration in genotype-phenotype studies. ECARUCA can be considered to be a system that meets the needs of scientists, physicians and patients and their family members involved with rare chromosomal aberrations in an interactive way. It has the potential to become the international platform for clinical cytogenetics.
RESULT DESCRIPTION:
ECARUCA will create a platform for exchanging clinical information on rare (sub)microscopic chromosomal aberrations which can be used for research related purposes as well.
DISSEMINATION:
The accountholders will be able to visit the specific websites of the research platforms. The accountholders will also be frequently informed on new changes within those research platforms. Moreover, those with a specific research interest will be encouraged to moderate a research website related to the topic of their interest.
INNOVATIVE FEATURES:
Bringing together researchers in the field of cytogenetics through a web based application is new and will both initiate and facilitate new European collaborative research activities.
CURRENT STATUS AND THE USE OF RESULTS:
In the near future, it will be possible for all ECARUCA account holders to announce their special research/clinical interest related to a specific chromosome region. The latter will be done by creating web pages, linked to the ECARUCA website, for the announcement of special research interests and calls for collaboration. The lay-out of webpages are, currently, being developed for several groups of aberrations including telomeric and interstitial submicroscopic aberrations.
EXPECTED BENEFITS:
New collaborations on specific chromosome regions between various European groups. This will lead to a better insight of the origin, frequency and clinical significance of specific (rare) chromosomal abnormalities. This will lead to a better care of the patients with these specific chromosome aberrations and information to the families and professionals involved.
The ECARUCA database software system has been developed using a relatively conventional client-server framework with tiered design. In all, there are four tiers within the system: a data tier, a general (middleware) software tier and two distinct client interfaces. Java technologies (www.javasoft.com) have been utilised for all tiers of the framework.
Data tier and middleware tier:
The database engine comprises a relational database management system (RDBMS), with a suite of software libraries providing a bespoke application programming interface (API) that facilitate modular development between the database and business object within the middle tier. A mid-range enterprise scale DBMS has been utilised, which easily copes with the current volume of data and will certainly support future expansion of the data set.
The database application programming interface has been designed and developed using (mature) Java database connectivity libraries (JDBC). More recent component libraries, known as JDO (Java Database Objects), were available and were considered for this system component, but ultimately they were deemed too immature for the
ECARUCA project at the time of development. JDO may have simplified some of the (high-level) software design, however, in terms of database connectivity and the database query (software) modules, ECARUCA did not present itself as anything other than a conventional RDBMS system.
With regard to the underlying database structure (i.e., relational design) ECARUCA data model is approximately 95 per cent normalised (with respect to relational database model theory). There were several iterations with respect to the design of the underlying model, and these reflected the complexity of the biological processes and relationships that were being represented within a strictly relational (tabular) model. In this respect, some ECARUCA-specific design features have been included in the final data model, but with no significant impact on the efficiency of database queries, and all database search algorithms fall well within the standard capabilities of SQL (Structured Query Language).
One specialist query algorithm has been designed and developed for chromosome band matching. However, in practise, this (middleware) software component implements an adapter design pattern to underlying SQL routines.
The client tiers:
Two client interfaces to the database have been designed and developed: a dedicated client program with (super-user) administrator privileges for overseeing all the data input, updating validation etc, and a web-based (medical expert) User program for case pre-registration and data upload (registration).
The administrator client tier has been designed and developed as a Java JFC Swing (Java Foundation Classes) application. That is to say, it is essentially designed for standalone mode rather than for remote administration over a network. Thus, at present the administrator client program resides on the ECARUCA
server.
However, basic networking support modules have been developed in order that this application may run remotely (although this facility is not a requirement).
The (medical expert) User client program, which is a web-based client, has been designed using the Java struts framework, and this is integrated with JSP (Java Server Pages) components. Whilst these technologies facilitate the development of web-based client interfaces, they are, essentially, server-side technologies. Ultimately, they come under the control of the server, leaving the client-side as a relatively thin-client model. JSP is a web scripting technology that is specifically employed to allow a web author to further develop and enhance the web interface (www.ECARUCA.net) with respect to those software modules that provide case pre-registration and (cytogenetic) data upload.
This part of the project concerned molecular cytogenetic studies with the aim to better define breakpoints of structural chromosome aberrations in cases to be referred to the ECARUCA database, especially from laboratories with limited facilities for e.g. FISH diagnostics and microsatellite marker analysis.
The investigations so far included 153 cases, partly with inclusion of parental samples. The cases came from the following countries: Armenia, Austria, Bulgaria, Georgia, Germany, Italy, Lebanon, Lithuania, Romania, Russia, Serbia, Slovenia, Spain, Switzerland, Syria, Turkey, Ukraine. In most of these cases, an initial attempt was already made to define the breakpoints and chromosomes involved in the rearrangement, but in a few cases the aberration was only vaguely described.
In all cases the examination yielded results in the sense that the breakpoints could be confidently defined. In the majority of the cases, the initial determination had to be revised, in some cases even the chromosome(s) involved was/were incorrectly described. For example, a ring(Y) turned out to be a ring(21), a monosomy 21 was an unbalanced 18;21 translocation with partial monosomy 21 and 18q, and a deletion within the long arm of chromosome 1 had breakpoints which did not even overlap with the initially assumed breakpoints.
The general rule was that we reported the results to the referring laboratory or physician in order to allow him or her to refer the case directly to the database, but in some cases, we did the referral ourselves. Especially interesting cases were subject to particular case reports for publication in specialized journals, see below.
There would be an ongoing need for further such examinations. However, the budget of the project has been fully consumed, and the budget of our institute allows only in exceptional (scientifically interesting) cases to go on with such examinations.
RESULT DESCRIPTION:
In order to facilitate communication and collaboration between countries, physicians and scientists, a European Network of National Coordinators has been set up.
A National Coordinator has been assigned in each participating European country.
DISSEMINATION:
The National Coordinator represents ECARUCA during national meetings and informs colleagues on new developments within the project. Furthermore, the National Coordinator can assist and stimulate colleagues to submit new cases to the ECARUCA database. An up-to-date list of all National Coordinators including contact information is available on the ECARUCA website.
INNOVATIVE FEATURES:
The National Coordinators have formed a novel European Network that will facilitate the exchange of information regarding ECARUCA related issues and the input of both cytogenetic and clinical data into the Database.
CURRENT STATUS AND USE OF RESULTS:
The European Network of National Coordinators has been established. Each National Coordinator is either currently or will be promoting ECARUCA in his/her country through meetings and national publications.
EXPECTED BENEFITS:
Further spreading of the awareness and knowledge on the possibilities of the Register for both clinical and cytogenetic purposes. This will lead to better care of the individuals with a rare chromosomal abnormality and better information to their families and involved physicians and other medical care takers.
RESULT DESCRIPTION:
A Microdeletion Research Network consisting of 7 European scientific groups, derived from Antwerp, Nijmegen, Oxford, Pavia, Stockholm, Troina and Zurich, all working on chromosomal microdeletions has been established.
DISSEMINATION:
This European Network will work, in close collaboration, on the identification of new microdeletion/duplication syndromes and the gene(s) involved in those syndromes. The new findings of the Network will be made available to the (cyto)genetic professionals through the ECARUCA website and its Register, and through publications in the medical and scientific literature.
INNOVATIVE FEATURES:
All scientific groups work with the novel techniques such as microarray based comparative genomic hybridisation (array CGH) and Multiplex Ligation-dependent Probe Amplification (MLPA)in order to identify, sofar unknown, chromosomal microdeletions and -duplications. Sharing these novel data and information within the European Network will facilitate insight in the frequency, clinical significance and mechanism of those novel chromosomal microaberrations.
RESULTS:
The Network has come together twice. At these meetings the Methods for a collaborative study on the frequency of specific novel microdeletions and -duplications have been set up. Subsequently, each group has started a part of the project in its own Centre. In 2006 the various data will be combined and, as a whole, interpreted.
EXPECTED BENEFITS:
The results generated by the Microdeletion Network will lead to a better understanding of the clinical relevance of submicroscopic alterations in mental retardation and congenital abnormalities. The findings of this Network will be made available to the ECARUCA members when applicable so that this information can subsequently be used for improving patient care.
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