Interview with Wendell Jones of Q² Solutions | EA Genomics

Dr. Jones is Principal Bioinformaticist and Scientific Advisor at Q² Solutions | EA Genomics. He conducts collaborative scientific research in multiple areas, most recently in immuno-oncology. His background includes analysis, development and validation of the bioinformatic systems that process complex genomic assays, including next generation sequencing assays, evaluating new and emerging genomic technologies, and developing bioinformatic implementation strategies. Read his full bio.

Interview with Wendell Jones of Q² Solutions | EA Genomics

Q: What need is Q² Solutions | EA Genomics addressing?

A: As a leading provider of genomic services in clinical trials and discovery, Q² Solutions | EA Genomics advances science by harnessing technological expertise to drive understanding of the human genome and disease biology to detect the effects of therapies. We offer tailored genomic services to support drug discovery, precision medicine, and companion diagnostics (CDx) development needs.

Q² Solutions | EA Genomics has end-to-end capabilities across a comprehensive suite of technology platforms. We have the genomics and bioinformatics expertise to successfully employ both existing and new technologies to support global clinical development programs. Our complete solutions allow for multi-partner relationships between the pharmaceutical sponsor, central laboratory and genomics laboratory to maximize the potential for successful outcomes.

Q: What are the products and/or services Q² Solutions | EA Genomics offers/develops to address this need? What makes Q² Solutions | EA Genomics unique?

A: Q² Solutions | EA Genomics offers a comprehensive suite of services and technologies to provide genomic and bioinformatic expertise and data to support pharmaceutical development. Our experienced commercial staff of over 170 employees are dedicated for accessioning, anatomic and molecular pathology, nucleic acid isolation and pre-analytical quality control, genomics analysis (RNA-Seq, Whole Genome Sequencing, Whole Exome Sequencing, Focused Gene Expression, Focused Panels), custom panel and diagnostic development, program management and bioinformatics data processing and delivery.

The company has key partnerships to facilitate the latest in technology offerings and flexibility and our bioinformatics scientists hold leadership positions in genomic data quality and analysis initiatives led by the FDA, NIST, NCI and other organizations. Q² Solutions | EA Genomics operates a state-of-the-art, CLIA-certified and CAP-accredited facilities covering more than 40,000 ft2 across our locations in Research Triangle Park, North Carolina and Beijing, China.

Q: What is your role at Q² Solutions | EA Genomics and what excites you about your work?

A: I am Principal Bioinformaticist and Scientific Advisor at EA Genomics. I consult with clients regarding their needs for various assays but especially RNA. More recently, I have been able to work with clients to link their outcome information (such as response-to-therapy) with genomic data, including immune factors, that may greatly influence patient response to therapy in their oncology trials. This is important not only for immunotherapies but any oncology therapy as the immune system is often present for many cancers whether directly targeted or not. There is general excitement in oncology regarding the application of immunology to not only treat cancer patients but possibly provide a durable response to dramatically change their long-term survival and I share in that excitement.

Q: When thinking about Q² Solutions | EA Genomics and the domain Q² Solutions | EA Genomics is working in, what are some of the recent breakthroughs that are propelling the field forward and how will they impact healthcare?

A: There are several areas of genomic testing where there have been recent or continual advances in either understanding the importance of the biological area or our ability to provide informative tests:

  1. Perhaps the biggest innovation in the last 10 years is in more deeply understanding the interaction between the adaptive immune system and cancer cells and developing drugs that allow the patient’s own immune system to drive the eradication of those cells.   This is important as our immune system can provide a long-term benefit to the patient long after the patient has ceased therapy, yielding a durable response.    Q² Solutions | EA Genomics have supported this effort in general and specific ways by (for example) providing genomic testing that describes immune activity levels in the tumor microenvironment as well as characterizing the immune repertoire of the patient.
  2. Continual improvements in isolating and testing nucleic acids extracted from formalin-fixated samples (FFPE samples) have allowed for more comprehensive testing of cancer patients, allowing doctors to better discern proper treatments and pharma companies to uncover mechanisms for variations in response-to-therapy.   This will improve the nature of clinical trials and should increase the rate in which new drugs are approved or widen the labeling of existing drugs.  Q² Solutions | EA Genomics offers dual isolation of DNA and RNA from FFPE along with a wide array of methods of testing either from FFPE samples.
  3. Genomic testing of circulating material has allowed for big advancements in monitoring minimal residual disease (MRD) through highly sensitive assays such as ddPCR and deep focused sequencing.  It has also enabled much earlier and less invasive detection of diseases such as cancer without requiring the knowledge of the tissue-of-origin.   The implications are numerous for previously treated cancer patients monitoring remission and also for new patients who may have a known predisposition for certain cancers that are difficult to detect.
  4. There are many recent breakthroughs related to understanding the impact of the microbiome on a person’s health.   The microbiome has been implicated in many gut-related diseases including Crohn’s and IBS as well as having interactions with the host’s adaptive immune system.  As a result, Q² Solutions | EA Genomics offers regulatory-grade testing of 16S to uncover and quantify bacterial species in patient samples.
Q: What are the short-term challenges that Q² Solutions | EA Genomics and its peers are facing?

A: A. All companies working in genomics are challenged by the data storage and processing requirements for assays, especially those created by deeper whole genome sequencing (WGS). WGS of individual tumors for many cancers can create up to a half a terabyte of data per patient. When one is required to sequence hundreds or thousands of patients this way, the sequence-related data adds up quickly to a level where it can tax many storage systems.

B. Measuring and understanding structural variation in cancers and their impact on tumor evolution, tumor heterogeneity and treatment is also a challenge. Of all the types of variations that are present in tumors, measuring the structural variations and their impact are the most difficult to precisely pin down. To be certain of the nature of specific structural variants, it often helps to have technology that reads long DNA sequences. We are getting better as a community of recognizing these changes which are frequent in cancer cells but which can be missed if only looking for single nucleotide mutations, and we still have room for improvement.