Dr. Eggington co-founded the Center for Genomic Interpretation (CGI) in 2016, which became a nonprofit organization in 2017, with the mission to drive quality in clinical genetics. To accomplish its mission, CGI provides a variety of services to health insurers, laboratories, clinicians and patients. Dr. Eggington is an expert in the initial classification of novel clinical genetic variants, high throughput literature curation, as well as the accurate re-classification of Variants of Uncertain Significance (VUS) through optimized research methods. Dr. Eggington has directed variant classification and reclassification programs at Myriad Genetics, Courtagen, and 23andMe. Read her full bio.

Interview with Julie Eggington of Center for Genomic Interpretation

Q1a: Together with Robert Burton you founded the Center for Genomic Interpretation (CGI), a non-profit organization. Can you tell us more about CGI and the mission behind it?

A: CGI’s mission is to drive quality in clinical genetics and genomics. CGI works primarily with laboratories, health insurance payers, clinicians, and patients/consumers. CGI provides tailored services to educate and support these stakeholders so that more patients/consumers get clinically valid and accurate results.

Q1b: Why is CGI a non-profit organization instead of a for-profit organization? What is the idea behind it?

A: CGI is a 501(c)(3) deep tech humanitarian organization founded in 2017. As an independent and non-profit organization, CGI provides tailored services at reasonable prices to customers who are looking for unbiased technical support and education in the very niche area of commercial clinical genetics and genomics. Since CGI charges for services that are in line with its mission, CGI’s basic operations are self-sustained. To date, CGI has provided services to laboratories and health insurance payers, though CGI is expanding its services to support government policy makers, clinicians and patients/consumers.

CGI’s donor fundraising efforts focus on preparing for CGI’s much larger and longer term goal of making accurate clinical genetic variant classification and reclassification pre-competitive. CGI aims to provide just-in-time variant classification services at scale to commercial and academic laboratories at low cost, so that all labs are capable of providing the highest quality variant classifications and reclassifications to patients and consumers.

Q: What excites you about your work at CGI?

A: I am most excited about the positive patient impact we have in our work. By helping the genetics and genomics labs and health insurance payers implement improved quality initiatives, we get to help many thousands, if not millions, of patients.

Q: What organizations has CGI worked with in the context of genomic data interpretation?

A: We have non-disclosure agreements with all of the commercial labs that we help with genetic variant classification. Most of the labs we currently serve are medium to high volume laboratories wanting to supplement their current pipelines. Though we also support several startup companies.

We have also started helping health insurers on some very particular genomic data interpretation challenges related to true and false positive variant interpretations, where true positives may lead to a precision therapy. For example, RPE65 pathogenic variant interpretations may result in treatment with Luxturna, costing close to one million dollars per treatment.

Also, due to a recent press release made by Blue Shield of California (BSCA), we can now say that BSCA is partnering with CGI on CGI’s ELEVATEGenetics initiative, which is an initiative to provide more transparent and standardized laboratory quality metrics to stakeholders.

Q: Can you tell us more about a specific example?

A: Regarding variant classification, many laboratories have optimized their variant classification work flows to decrease false negative interpretation rates. This often results in the unintended consequence of higher false positive interpretation rates, which have contaminated ClinVar. ClinVar is the most widely used public variant classification database in the USA. False positive variant interpretations can sometimes contribute to erroneous medical procedures and therapies, so many laboratories double check the data behind the classification claims made in ClinVar before using the classifications. Sometimes these labs that are checking out ClinVar classifications will disagree with pathogenic or likely pathogenic consensus classifications. Before issuing a non-consensus report, these labs often ask CGI to independently assess the classifications on variants to see if CGI agrees or disagrees with the consensus classification. CGI’s stringent variant classification and reclassification protocols are well suited for this fact-checking work.

Q: Variant data interpretation has its challenges. How can we improve the interpretation of variant data in that are used in the clinic to diagnose a disease or make treatment patient treatment decisions?

A: CGI views its nonprofit business model as the operational solution to bring accurate variant classifications and reclassifications into the clinic. Accurate variant classification must be evidence based, and clinical scientists must guard against the heavy use of research data which is contaminated by ascertainment bias and publication bias. CGI has developed its own stringent evidenced based process that allows it to provide variant classification as a service to labs for any genes associated with monogenic disease. Also, excellent professional and academic consortia groups continue to publish updates to variant interpretation protocols.

Q: What are some of the biggest challenges the industry is currently facing when it comes to genomic data interpretation, and how will we overcome these challenges?

A: For all but the highest volume boutique commercial laboratories, the cost of accurate variant classification for many sequencing tests exceeds the reimbursement value of those tests. Some labs use venture capital funds to close this gap, and/or take low quality shortcuts to lower costs, or simply stop offering certain genetic tests. CGI is working to fix this in two ways:

  1. CGI is educating health insurers on the true costs of high quality genetic tests, and the benefits of using higher quality tests over lower quality tests. CGI’s ELEVATEGenetics initiative is part of this effort, providing needed transparency to laboratory quality metrics.
  2. CGI is fundraising in order to build out its larger scale and lower cost accurate variant classification service. In this way, CGI will act as a central nonprofit service, providing accurate variant classifications and reclassifications to all labs at a significantly reduced price through a just-in-time model. Due to the scale, and being able to serve many laboratories in a noncompetitive way, CGI will achieve an economy of scale unachievable by any single laboratory, thus driving costs of variant classification down for everybody.
Q: Who is mostly affected by these challenges?

A: Patients are most affected. In some hereditary diseases the false positive rate due to over-interpretation of sequence variants may currently exceed one in every two positive reports. These patients may end up being treated for diseases they do not have, while the diagnostic journey to find their true disease is abandoned.

In rarer cases, false positive variant interpretations may lead to erroneous fetal terminations. This was the case in the early 2000’s with the CFTR I148T variant which was included on the ACMG and ACOG panethnic panel of CFTR pathogenic variants. The variant was later demonstrated to be an interpretation false positive, and is now known to be a somewhat frequent and benign variant in the Indian population.

Q: Is there anything else you would like to share with the PMWC audience?

A: Much of precision medicine relies on accurate interpretation of genetics and genomics data. Unless we are able to improve the current quality of genetic variant interpretation in the industry, precision medicine will not advance at the rate we all hope it will. CGI is dedicated to fixing quality and accuracy problems in clinical genetics and genomics. CGI is always thrilled to receive donations in order to help patients get accurate results, and to help both established and start up commercial companies succeed with high quality offerings. So please support the Center for Genomic Interpretation in its mission to drive quality in clinical genetics.

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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Interview with Dominic Eisinger of Myriad RBM

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: Next generation immunotherapies include CAR-Ts, TCRs, cancer vaccines, ADCs, bi-specific antibodies, and checkpoint inhibitors.

Read More
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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