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.

Interview with Gabriel Bien-Willner of Palmetto GBA

Q: What does your role entail as the director of the MolDX program at Palmetto GBA?

A: The job directing MolDX is multifaceted; first and foremost the MolDX program is responsible for assessing molecular diagnostic tests on the market and makes coverage and pricing determinations for such tests and technology. This is usually done through local coverage determination policies or technical assessments.

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Interview with Peter Marks of FDA

Q: The CBER’s Regenerative Medicine Advanced Therapy Designation program has been very successful, with about 100 requests for designation in the two years of its existence. Can you please tell us about the program and how it was put together?

A: The Regenerative Medicine Advanced Therapy (RMAT) Designation program came into being as part of the 21st Century Cures Act that was signed into law on December 13, 2016.

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Interview with Calum MacRae of Harvard Medical School

Q: What patient data do we need to better understand the underlying cause of disease and how to prevent it?

A: Medicine at present is highly underdetermined and data poor. To be precise, one must be comprehensive, so medicine (with our consent) will use not only what we currently conceive of as biomedical information, but also data from across our lives.

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Headlines from PMWC 2019 Silicon Valley

A big ‘Thank You’ to all of our presenters and attendees for celebrating 10 years of precision medicine progress with us! PMWC 2019 Silicon Valley was attended by 2000 participants from 35 countries, which included over 400 speakers in 5 parallel tracks!

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Interview with Ken Bloom of Ambry Genetics

Q: Tell us more about your organization/company. What patient population are you serving and which services are you specializing in?

A: Ambry Genetics is a recognized leader in high quality complex genetic testing. We seek to find the genomic cause or contributors to rare diseases, abnormal phenotypes and hereditary disorders.

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Interview with Lee Pierce of Sirius Computer Solutions

Q: What is the state of big data and analytics in healthcare, and how to best use the reams of data available?

A: More than ever, Healthcare organizations are achieving measurable value through use of their data and analytics assets. There is more raw material available than ever to create value. This raw material is the data flowing from internal systems and applications and also from devices and systems external to healthcare organizations.

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Interview with Anita Nelsen of PAREXEL

Q: There are various new, emerging technologies that bring us closer towards a cure for life-threatening disorders such as cancer, HIV, or Huntington’s disease. Prominent examples include the popular gene editing tool CRISPR or new and improved cell and gene therapies. By when can we expect these new technologies being part of routine clinical care?

A: Today’s emerging technologies are making the promise of individualized treatment a reality.

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Interview with Ilan Kirsch of Adaptive Biotechnologies

Q: The Nobel Prize in Medicine was awarded recently to James Allison and Tasuku Honjo for their work on unleashing the body’s immune system to attack cancer, a breakthrough that has led to an entirely new class of drugs and brought lasting remissions to many patients who had run out of options. The Nobel committee hailed their accomplishments as establishing “an entirely new principle for cancer therapy.” What is your first-hand experience the impact that those new drugs had on patients?

A: For decades cancer was viewed as solely a cell-autonomous condition.

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BMS buys Celgene | Lilly buys Loxo Oncology – Does this Signal a Return to Strong Deal-Making Activities in 2019?

Bristol-Myers Squibb’s blockbuster $74B deal to buy Celgene creates an oncology powerhouse amid industrywide excitement about the rapidly evolving science and explosive growth of the sector. The agreement could signal a return to deal-making for the pharmaceutical industry in the $133B global oncology therapeutics market.

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Interview with Gini Deshpande of NuMedii

Q: What need is NuMedii addressing?

A: NuMedii, has been pioneering the use of Big Data, artificial intelligence (AI) and systems biology since 2010 to accelerate the discovery of precision therapies to address high unmet medical needs. Artificial Intelligence approaches are a natural fit to harness Big Data as they provide a framework to ‘train’ computers to recognize patterns and sift through vast amounts of new and existing genomic

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Interview with Minnie Sarwal of UCSF

Q: Genomic medicine is entering more hospitals and bringing with it non-invasive technology that can be used to better target and treat diseases. What are some key milestones that contributed to this trend?

A: Completion of complete sequence data from the human genome project, and the advances in proteomic, microRNA and epigenetic assays added a layer of pathway biology to the understanding of human diseases.

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Interview with Shidong Jia of Predicine

Q: Once sequencing has been validated as a clinical solution via trusted workflows, and coinciding with the technological developments driving costs lower, we can expect accelerated human genome profiling for clinical Dx. How soon, do you think, will we see accelerated growth and what can we expect?

A: We will see accelerated human genome profiling for clinical Dx in 2019 and the coming years as more biomarker-based cancer drugs are gaining approval.

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Interview with Iya Khalil of GNS Healthcare

Q: Artificial intelligence (AI) techniques have sent vast waves across healthcare, even fueling an active discussion of whether AI doctors will eventually replace human physicians in the future. Do you believe that human physicians will be replaced by machines in the foreseeable future? What are your thoughts?

A: I think that there’s a lot of speculation and uncertainty around AI, but I don’t foresee a time when we won’t need physicians.

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Interview with Ilya Michael Rachman of Immix Biopharma Inc.

Q: The Nobel Price in Medicine was awarded recently to James Allison and Tasuku for their work on unleashing the body’s immune system to attack cancer, a breakthrough that has led to an entirely new class of drugs and brought lasting remissions to many patients who had run out of options. The Nobel committee hailed their accomplishments as establishing “an entirely new principle for cancer therapy.” Besides CAR T-cell therapy what do you think next generation immunotherapies will look like to successfully combat cancer?

A: The next generation of immunotherapies will build on the insights discovered by immunologists like James Allison and Tasuku Honjo and extend them to modify the body’s response to tumors.

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Join me to Kick off PMWC Silicon Valley in the Santa Clara Convention Center, Focusing on Every Element of Precision Medicine

My team worked in collaboration with Bill Dalton, Kim Blackwell, Atul Butte / India Hook Barnard, Nancy Davidson and Sharon Terry to create a program that touches every component of precision medicine while bringing together all of its key stakeholders. Leading participating institutions including Stanford Health Care, UCSF, Duke Health, Duke University, John Hopkins University, University of Michigan and more will share their learnings and experiences and their successes and challenges, as they make precision medicine the new standard of care for all.

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Johns Hopkins
University Of Michigan

The Precision Medicine World Conference (PMWC), in its 17th installment, will take place in the Santa Clara Convention Center (Silicon Valley) on January 21-24, 2020. The program will traverse innovative technologies, thriving initiatives, and clinical case studies that enable the translation of precision medicine into direct improvements in health care. Conference attendees will have an opportunity to learn first-hand about the latest developments and advancements in precision medicine and cutting-edge new strategies and solutions that are changing how patients are treated.

See 2019 Agenda highlights:

  • Five tracks will showcase sessions on the latest advancements in precision medicine which include, but are not limited to:
    • AI & Data Science Showcase
    • Clinical & Research Tools Showcase
    • Clinical Dx Showcase
    • Creating Clinical Value with Liquid Biopsy ctDNA, etc.
    • Digital Health/Health and Wellness
    • Digital Phenotyping
    • Diversity in Precision Medicine
    • Drug Development (PPPs)
    • Early Days of Life Sequencing
    • Emerging Technologies in PM
    • Emerging Therapeutic Showcase
    • FDA Efforts to Accelerate PM
    • Gene Editing
    • Genomic Profiling Showcase
    • Immunotherapy Sessions & Showcase
    • Implementation into Health Care Delivery
    • Large Scale Bio-data Resources to Support Drug Development (PPPs)
    • Microbial Profiling Showcase
    • Microbiome
    • Neoantigens
    • Next-Gen. Workforce of PM
    • Non-Clinical Services Showcase
    • Pharmacogenomics
    • Point-of Care Dx Platform
    • Precision Public Health
    • Rare Disease Diagnosis
    • Resilience
    • Robust Clinical Decision Support Tools
    • Wellness and Aging Showcase

See 2019 Agenda highlights:

    • Five tracks will showcase sessions on the latest advancements in precision medicine which include, but are not limited to:
      • AI & Data Science Showcase
      • Clinical & Research Tools Showcase
      • Clinical Dx Showcase
      • Creating Clinical Value with Liquid Biopsy ctDNA, etc.
      • Digital Health/Health and Wellness
      • Digital Phenotyping
      • Diversity in Precision Medicine
      • Drug Development (PPPs)
      • Early Days of Life Sequencing
      • Emerging Technologies in PM
      • Emerging Therapeutic Showcase
      • FDA Efforts to Accelerate PM
      • Gene Editing / CRISPR
      • Genomic Profiling Showcase
      • Immunotherapy Sessions & Showcase
      • Implementation into Health Care Delivery
      • Large Scale Bio-data Resources to Support Drug Development (PPPs)
      • Microbial Profiling Showcase
      • Microbiome
      • Neoantigens
      • Next-Gen. Workforce of PM
      • Non-Clinical Services Showcase
      • Pharmacogenomics
      • Point-of Care Dx Platform
      • Precision Public Health
      • Rare Disease Diagnosis
      • Resilience
      • Robust Clinical Decision Support Tools
      • Wellness and Aging Showcase
  • Luminary and Pioneer Awards, honoring individuals who contributed, and continue to contribute, to the field of Precision Medicine
  • 2000+ multidisciplinary attendees, from across the entire spectrum of healthcare, representing different types of companies, technologies, and medical centers with leadership roles in precision medicine
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