Debadeep (Deb) Bhattacharyya, PhD, is the senior global director of marketing at Covaris. He holds a MSc in chemistry from the Indian Institute of Technology and a PhD in chemistry from Emory University. At Covaris, Deb capitalizes his expertise and experience in critical focus areas such as protein analysis, genomics, epigenetics, and next-generation sequencing. He has authored more than 50 peer-reviewed journal articles and led the launch of multiple cutting-edge technologies including LC-MS based solutions.
Q: How is Covaris changing the landscape of sample preparation for cancer research?
A: Understanding cancer has a lot to do with studying cancer genomes. DNA sequencing can be used to characterize the full set of mutations associated with tumor development and progression. This sequencing requires a very long piece of DNA extracted from a tumor to be cut into shorter fragments in a very robust and reliable manner for downstream analysis (including amplification). Covaris’ Adaptive Focused Acoustics™ (AFA) technology uses acoustic in an isothermal, non-contact environment to maintain the integrity of DNA during the shearing process.
Q: How does AFA improve analyte extraction from formalin fixed and paraffin embedded samples?
A: Working with formalin fixed and paraffin embedded (FFPE) samples can be a whole different ball game. First, the tissue needs to be extracted from the wax. Then, the analyte is extracted from the tissue and purified for analysis. The frequency at which AFA operates has a fairly short targeted wavelength so that it can directly target the sample and not heat up the whole vial. The user can adjust the power applied to the sample as well as the duration for which it is applied. With such benefits, AFA can emulsify paraffin in a matter of seconds, ensuring the tissue is separated, and can then disrupt the tissue in a very robust and reliable manner for confident extraction of DNA, RNA, and protein into the buffer.
Q: How can Covaris technology help increase throughput when working with challenging FFPE samples?
A: Our technology combines multiple steps into a single workflow that is easy to implement. This reduces the risk of sample loss, saves time, and provides a greater total nucleic acid yield. The instrument also integrates with automated liquid handling systems to increase throughput to hundreds or thousands of samples per day. Reliable, high-throughput analyte extraction is important for every cancer research laboratory. Robust sample preparation contributes to more accurate analyses, which can help clinical researchers make better decisions about developing and/or optimizing therapeutic regimens.
Q: Can AFA technology be used for other applications?
A: Yes. Every AFA user has the ability to adjust the power level and number of cycles applied to the sample (among other parameters that can be controlled as well), depending on the thickness and complexities of the matrices involved. Each matrix will have a unique set of complications—think of hard skin tissue compared to softer liver tissue, for example. While AFA has been used for next-generation sequencing in cancer research for several years, there has been a tremendous uptake for proteomics applications in the last five or six years. This technology also fosters epigenetic research, which involves analytes such as chromosomes and RNA-protein complexes.
Q: How do you think the approach to cancer research will change in the future?
A: I think cancer research is becoming increasingly comprehensive. It is being examined not only from a genomics perspective, but from a systems biology perspective involving transcriptomics, genomics, proteomics, and metabolomics. This is achieved with wide a range of end detection technologies including PCR or genomic sequencing, ELISA or mass spectrometry for protein analysis, and mass spectrometry for metabolite analysis. These technologies require high-quality samples for analysis. Our platform can serve as a single conduit for efficient sample preparation resulting in extraction of necessary analytes not only in high yield, but also with remarkable purity. AFA is designed to produce high-quality samples enabling its users with the highest confidence in the data that is generated.