Sparse redundancy analysis of high-dimensional genetic and genomic data.

MOTIVATION: Recent technological developments have enabled the possibility of genetic and genomic integrated data analysis approaches, where multiple omics datasets from various biological levels are combined and used to describe (disease) phenotypic variations. The main goal is to explain and ultimately predict phenotypic variations by understanding their genetic basis and the interaction of the associated genetic factors. Therefore, understanding the underlying genetic mechanisms of phenotypic variations is an ever increasing research interest in biomedical sciences. In many situations, we have a set of variables that can be considered to be the outcome variables and a set that can be considered to be explanatory variables. Redundancy analysis (RDA) is an analytic method to deal with this type of directionality. Unfortunately, current implementations of RDA cannot deal optimally with the high dimensionality of omics data (p≫n). The existing theoretical framework, based on Ridge penalization, is suboptimal, since it includes all variables in the analysis. As a solution, we propose to use Elastic Net penalization in an iterative RDA framework to obtain a sparse solution. RESULTS: We proposed sparse redundancy analysis (sRDA) for high dimensional omics data analysis. We conducted simulation studies with our software implementation of sRDA to assess the reliability of sRDA. Both the analysis of simulated data, and the analysis of 485 512 methylation markers and 18,424 gene-expression values measured in a set of 55 patients with Marfan syndrome show that sRDA is able to deal with the usual high dimensionality of omics data. AVAILABILITY AND IMPLEMENTATION: http://uva.csala.me/rda. CONTACT: a.csala@amc.uva.nl. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The interactive presentation of 3D information obtained from reconstructed datasets and 3D placement of single histological sections with the 3D portable document format.

Interpretation of the results of anatomical and embryological studies relies heavily on proper visualization of complex morphogenetic processes and patterns of gene expression in a three-dimensional (3D) context. However, reconstruction of complete 3D datasets is time consuming and often researchers study only a few sections. To help in understanding the resulting 2D data we developed a program (TRACTS) that places such arbitrary histological sections into a high-resolution 3D model of the developing heart. The program places sections correctly, robustly and as precisely as the best of the fits achieved by five morphology experts. Dissemination of 3D data is severely hampered by the 2D medium of print publication. Many insights gained from studying the 3D object are very hard to convey using 2D images and are consequently lost or cannot be verified independently. It is possible to embed 3D objects into a pdf document, which is a format widely used for the distribution of scientific papers. Using the freeware program Adobe Reader to interact with these 3D objects is reasonably straightforward; creating such objects is not. We have developed a protocol that describes, step by step, how 3D objects can be embedded into a pdf document. Both the use of TRACTS and the inclusion of 3D objects in pdf documents can help in the interpretation of 2D and 3D data, and will thus optimize communication on morphological issues in developmental biology.

More than a decade of developmental gene expression atlases: where are we now?

To unravel regulatory networks of genes functioning during embryonic development, information on in situ gene expression is required. Enormous amounts of such data are available in literature, where each paper reports on a limited number of genes and developmental stages. The best way to make these data accessible is via spatio-temporal gene expression atlases. Eleven atlases, describing developing vertebrates and covering at least 100 genes, were reviewed. This review focuses on: (i) the used anatomical framework, (ii) the handling of input data and (iii) the retrieval of information. Our aim is to provide insights into both the possibilities of the atlases, as well as to describe what more than a decade of developmental gene expression atlases can teach us about the requirements of the design of the 'ideal atlas'. This review shows that most ingredients needed to develop the ideal atlas are already applied to some extent in at least one of the discussed atlases. A review of these atlases shows that the ideal atlas should be based on a spatial framework, i.e. a series of 3D reference models, which is anatomically annotated using an ontology with sufficient resolution, both for relations as well as for anatomical terms.

Tertiary teledermatology: a systematic review.

Telemedicine is becoming widely used in healthcare. Dermatology, because of its visual character, is especially suitable for telemedicine applications. Most common is teledermatology between general practitioners and dermatologists (secondary teledermatology). Another form of the teledermatology process is communication among dermatologists (tertiary teledermatology). The objective of this systematic review is to give an overview of studies on tertiary teledermatology with emphasis on the categories of use. A systematic literature search on tertiary teledermatology studies used all databases of the Cochrane Library, MEDLINE (1966-November 2007) and EMBASE (1980-November 2007). Categories of use were identified for all included articles and the modalities of tertiary teledermatology were extracted, together with technology, the setting the outcome measures, and their results. The search resulted in 1,377 publications, of which 11 were included. Four categories of use were found: getting an expert opinion from a specialized, often academic dermatologist (6/11); resident training (2/11); continuing medical education (4/11); and second opinion from a nonspecialized dermatologist (2/11). Three modalities were found: a teledermatology consultation application (7/11), a Web site (2/11), and an e-mail list (1/11). The majority (7/11) used store-and-forward, and 3/11 used store-and-forward and real-time. Outcome measures mentioned were learning effect (6), costs (5), diagnostic accuracy (1), validity (2) and reliability (2), patient and physician satisfaction (1), and efficiency improvement (3). Tertiary teledermatology's main category of use is getting an expert opinion from a specialized, often academic dermatologist. Tertiary teledermatology research is still in early development. Future research should focus on identifying the scale of tertiary teledermatology and on what modality of teledermatology is most suited for what purpose in communication among dermatologists.

A pilot study on tertiary teledermatology: feasibility and acceptance of telecommunication among dermatologists.

Tertiary teledermatology (TTD), where a general dermatologist consults a specialized dermatologist on difficult cases, is a relatively new telemedicine service. We evaluated TTD in a Dutch university hospital, where 13 general dermatologists used TTD to consult 11 specialized dermatologists and two residents at the university medical centre. We measured the avoided referrals to the university centre, the usability of the system and the user acceptance of it. During a three-month study, general dermatologists consulted via TTD 28 times. In 17 of the consultations (61%), the general dermatologists would have referred their patients to the university centre if teledermatology had not been available. Referral was not necessary after teledermatology for 12 of these 17 consultations (71%). The mean usability score (0-100) of all the users was 80. All dermatologists were satisfied with TTD (mean satisfaction of 7.6 on a 10-point scale) and acceptance was high. The baseline measurements showed that half of tertiary referrals were suitable for TTD. These results suggest that TTD reduces unnecessary physical referrals and that users are satisfied with it. A large-scale evaluation is now required.