(1) the sodium bisulfite modification of DNA samples
(2) the detection of the resulting single-base polymorphisms on complex microarrays and
(3) bioinformatics platforms for subsequent data analysis, with a special focus on combining the epigenetic information with transcript profiles and clinical information.
For the analyses performed within the SMP, clinical material with corresponding clinicopathological information is available.
Infrastructure will be provided that will be used in collaborations within the NGFN network and beyond for a global analysis of epigenetic variations. By comparison between the platform’s different systems, standards will be defined that will allow comparability of data across systems and across various areas of analysis. The platform combines groups with complementary but nevertheless sufficiently overlapping expertise, competence and capability. Parallel to application, technical developments will be performed in order to improve quality and reliability.
The work plan for the microarrays platforms can be divided into three parts: standardisation, evaluation, production. Initially, the four array systems will be compared. Also, the preparative steps will be harmonised. Objective of this work portion is a standardisation of protocols, handling steps, analysis tools, algorithms and processes that allow the comparison of the data irrespective of their origin. During the evaluation phase, the SMP will establish across the platform the entire process of high-throughput screening, transfer of the gained knowledge into appropriate chip formats and their subsequent use in actual analyses. In terms of biology, there will be a focus on chronic lymphocytic leukemia, melanoma, pancreatic and prostate cancer, since well-defined material for these tissues is available within the SMP. After these two phases, the platform will then offer a portfolio of systems, from which the combination can be select that will be best suited to achieve the respective objectives.
The subproject „DNA methylation profiling of human chromosome 21“ runs in parallel to the array platforms. It complements the development of high throughput technologies by providing basic information about the biological distribution of DNA-methylation patterns. The aim of this subproject is to generate a first comprehensive DNA methylation map along all genes on a human chromosome using bisulphite sequencing technologies. These data will help to understand the genetic and epigenetic basis for DNA-methylation variation in the human genome, to asses sequence specificity of DNA-methylation patterns in normal tissues. The project is a pilot study in the context of wordwide efforts to establish comprehensive epigenomic maps along the human genome. In addition the project aims to investigate the DNA methylation variation between normal (Disomic) and disease (Trisomy 21) situations. All tools and data generated will be made publically available.
Website: Analysis of the DNA methylation profiling of human chromosome 21