Next-Generation Data Analysis Software Helps Researchers to Understand the Link Between Genetics and Disease - Carl-Johan Ivarsson

Although modern gene expression studies are proving invaluable to the study of human biology, the amount of data that is produced by this kind of research is enormous. As a result, it is impossible to derive any real biological meaning from these findings unless sophisticated analysis methods are used to help interpret the data effectively.

To address this issue, a team of scientists at the Institute of Human Genetics of the Christian-Albrechts-University in Kiel, Germany, is currently using sophisticated data analysis software on a number of national and international projects in order to study the epigenetic alterations related to several cancers, including
malignant lymphoma, colorectal cancer, and hepatocellular carcinoma, as well as developmental disorders and other diseases.

The team of scientists at the Institute of Human Genetics of the Christian-Albrechts-University in Kiel, Germany, led by Dr Ole Ammerpohl, is currently studying the raw data obtained from array-based DNA methylation analysis, including Illumina’s HumanMethylation27k Bead Chip, which provides semi-quantitative data from more than 27,000 CpG loci. Along with his team of four scientists and three technicians, Dr Ammerpohl, is examining how alterations in the DNA methylation pattern contribute to a specific phenotype or disease like cancer, as well as the way in which tumor induction introduces epigenetic alterations, which support tumor growth and progression.

"Because of the amount of data being analysed, conducting microarray analysis has always been a hassle," said Dr Ammerpohl. "Larger studies, especially those which include multiple samples that need to be analysed on comprehensive array platforms, have traditionally been very time-consuming, and have also required a considerable amount of computer power. Plus, in most cases, it is mandatory to define the exact conditions before beginning the intended analysis, and just this process alone can take hours. Worse still, any recalculations – even if they are just minor adjustments to these initial conditions – would mean that the whole process would have to be restarted from the beginning."

Fortunately, new technological advances in this area are making it much easier for scientists to compare the vast quantity of data generated by epigenetic studies, to test different hypotheses, and to explore alternative scenarios within seconds. As a result, the latest generation of data analysis software is helping scientists to regain control of this analysis, and to realise the true potential of research in this area.