New sequencing technology raises questions about existing data

Sequencing technology has advanced so far in the last few years that questions are now being asked about the value of existing research data and the techniques for acquiring it.

Dr Mark Robinson and Professor Susan Clark from Sydney’s Garvan Institute of Medical Research have published a paper in the journal Genome Research showing that the more detailed structural changes in the genome revealed by today's sequencing technologies is challenging our interpretation of the epigenome far more than previously thought.

While for most us our DNA is all in perfect order when we are born; two copies of each gene from our parents. However, as we age, especially in cancers where diseases like cancer appear, this genetic material undergoes complex changes such as genetic mutations, deletions, insertions and rearrangements. Occasionally these can affect large sections of the genome.

“Our cancer genome is actually in great disarray,” said project leader and co-author of the study Professor Clark.

“In the past, we have been able to examine chromosomes under electron microscopes and see this disorganisation. With new genome sequencing technologies, you can see what’s taking place at a much higher resolution.”

As a result scientists are noticing that errors in data are much more common than previously thought, concluding that this has likely led to incorrect interpretations of the epigenetic layers of the genome.

“We’re generating a huge amount of data about the genome sequence, as well as the next epigenetic layers that occur above the genetic sequence – the biochemical changes that take place affecting expression of genes,” said professor Clark.

Key among these biochemical changes are the quantity of methylation, whereby methyl groups attach to DNA, altering how much of a gene is expressed, and the numbers of histone marks, which relates to the proteins that form the beads-on-a-string in DNA strands.

The paper by Robinson and Professor Clark posed the question of whether these genetic alterations demand a different interpretation of DNA methylation or histone marks.

“Lo and behold we found that, yes indeed, many of the changes that appear to be observed as epigenetic changes are just a readout of the underlying genetic sequence alterations,” Clark observed.

“I suppose you could say sometimes the data is a mirror image of the underlying genetic sequence. If there’s more DNA, then it looks like there’s more methylation, and vice versa.”

“If a DNA sequence has been deleted, we would have interpreted that in the past as unmethylated.”

“Integrating the data provided by new technologies is proving to be an enormous challenge and the scientists need to understand what the pitfalls are.

“Our paper is breaking new ground in providing both genetic and epigenetic researchers with a more accurate way of interpreting and reinterpreting the minefield of complex next generation sequencing data.”