Sequencing technologies have created a dizzying number of opportunities for epigenetic researchers to explore questions that couldn’t be tackled before. Despite the immense power that sequencing delivers, though, the whole process still isn’t quite as simple as pushing a big red button, and watching the groundbreaking discoveries roll in. Even as sequencing becomes faster, easier, and less expensive those experienced in the field have realized that the work doesn’t end once the run is finished.
We recently caught up with Dr. Keith Booher, who clued us into some of the things that the Epigenetics Sequencing Group at Zymo Research has learned from their extensive experience running NGS studies for both clients and internal R&D teams, and how it’s shaped the services that they offer.
Bioinformatics – Insights, Not Just Data
One of the first things that the Zymo crew recognized from early their NGS work, was that researchers really need more than just a hard-drive filled with terabytes of data from their sequencing service; they need help processing that information, too.
Data analysis and bioinformatics is crucial to making sense out of the complex data that sequencing generates, but while epigenetics researchers have a keen understanding of biological mechanisms, they may not always have the time or specialized resources to translate large data sets.
“Our services clients wanted insights, not just data. So, we began to offer up our bioinformatics expertise to create a way for researchers to bypass the data crunching, and focus their efforts on scientific discovery.” said Booher.
These days that couldn’t be easier – just send in samples, and the Zymo Bioinformatics Team will provide a customizable, comprehensive, genome-wide analyses report complete with publication-ready graphs and figures.
DNA Methylation Analysis Isn’t One-size-fits-all
Sure, it would be wonderful to sequence an entire genome for every tissue, in every organism, under every condition. But, is that really the most efficient approach?
Zymo employs a variety of DNA methylation sequencing methodologies for their services, and has found that when used in combination, they can be a streamlined and cost-effective way to zero-in on exactly the data you need.
“In the early stages of a DNA methylation investigation, our clients often opt to look at global methylation trends under certain conditions first using one of the many genome-wide approaches available (including Zymo’s Methyl-MiniSeq™, Methyl-MidiSeq™, and Methyl-MaxiSeq™ services). Then, once a particular site or region of interest is identified, opt for a targeted approach that can analyze smaller loci across several samples or conditions with much greater depth, like with our Targeted Bisulfite Sequencing methodology”, recommends Booher.
The experts at Zymo Research have figured out that selecting the right technique, or combination of techniques, enables scientists to get the most bang for their sequencing buck.
Integrate Those Epigenetic Mechanisms
If the advanced sequencing revolution has proven anything, it’s that genomic regulation is way more complex than originally predicted. While early epigenetic studies generally focused on one type of epigenetic mechanism, recent investigations have highlighted the need to look at epigenetic regulation from multiple angles, and today’s high-powered sequencing methods have made this possible.
“We noticed the need for researchers to take a comprehensive look at the epigenomic states within a sample. To accomplish that, we now customize services packages to look at more much than just DNA methylation…but can also include: Chromatin Analysis via ChIP-seq, Genome-wide Hydroxymethylation (5hmC) analysis, RNA-seq, Mass-spec analysis, and much more to generate a highly integrated genomic view of the customer’s samples”, explains Booher.
The flexibility to take an integrated snapshot of the epigenome from multiple angles at once makes the Zymo Research suite of services an attractive option for researchers in need of comprehensive data, but without the resources to conduct multiple analyses simultaneously.
To take advantage of the hard won knowledge and expertise of the Zymo crew, check out their Epigenetics Services page, to see available options.