Fine-tuning epigenetic methods to create new knowledge from old samples
“We have succeeded in extracting epigenetic information from scarce DNA from serum archived in the Janus Serum Biobank. This opens up new avenues for what serum banks can be used to achieve” says Trine B Rounge researcher at the Cancer Registry of Norway and Associate Professor at Centre for Bioinformatics.
The study, financed by Norwegian Cancer Society, was recently published in Clinical Epigenetics and can be found here.
In a collaborative national and international effort, the researchers conducted a study to test the feasibility of extracting more information from DNA from the Janus samples than was previously anticipated.
Innovative use from 50-year-old biobank
Nearly 50 years ago, when the Janus Serum Bank collection started, there was limited knowledge of epigenetics and no technology to uncover its behaviour. Epigenetics is the study of how the behaviour of genes can be regulated (switched on or off) without altering the DNA sequence itself. The epigenetic pattern can be altered by age and environmental factors, such as diet, chemical exposures or cancer.
The average DNA yield from the samples was very low, corresponding to about 10 percent of the recommended amount for a commonly used array technology. Using Whole Genome Bisulfite Sequencing with the NovaSeq 6000 required far smaller amounts of DNA, the researchers conducted a pilot study of 96 samples. With an optimized protocol and extensive bioinformatics, 94 out of the 96 serum samples obtained results that were satisfactory for Epigenome-Wide Association Studies (EWAS). This included methylation level of DNA from most of the 28 million methylation sites found in the human genome.
“Our study shows that Whole Genome Bisulfite Sequencing of very low amounts of DNA from serum samples, stored for up to 45 years, is now possible. These results show the potential for using large biobank cohorts of serum in future epigenetic studies” says Dr Marcin Wojewodzic, an expert in systems biology at the Cancer Registry of Norway.