A Tale of Two Cities: Breaking Down Data Barriers to Deliver Precision Medicine

Delivering Precision Medicine

Advances in genome sequencing technologies and the growing availability of clinical and other health data present an opportunity to make targeted therapies a reality for patients – a true testament that the best of times are on the horizon for the field of precision medicine. 

Leading cancer center, City of Hope, is paving the way with ambitious goals to sequence every cancer patient that walks through their doors. This ultimately will accelerate the discovery of targeted therapies and deliver personalized and high quality care. At ASHG, we invited Linda Bosserman, MD, Assistant Clinical Professor at City of Hope, and Jonathan Keats, PhD, Director of Bioinformatics at the Translational Genomics Research Institute (TGen) and Scientific Director, Briskin Center for Multiple Myeloma at City of Hope, to discuss how they are leading the charge to deliver on this promise.

Dr. Bosserman and Dr. Keats alike believe that the way to achieve these ambitious goals is to un-silo  data stores and bring all data types into one view so the physician can be as informed as possible on the diagnostic details to facilitate discussions of the most effective treatment options in shared decision making with the patient.

Precision medicine in practice  

To achieve the goals set forth by City of Hope, the organization is leveraging DNAnexus’ Apollo Platform to integrate their clinical-rich enterprise data warehouse with genomics, multi-omics, and imaging data. With harmonized datasets, they will be able to seamlessly conduct genome-wide association studies and other analyses to look at the relationship between genotype, phenotype and clinical outcomes.

To diagnose and then present a patient with therapy options, clinicians need access to a myriad of data types. Dr. Bosserman spoke about the need for accurate and complete medical records to determine patient demographics, medications, immunizations, family history, and cancer data by episode, including stage, tumor features and mutations at diagnosis and progression. Only when physicians understand the full scope of the patient journey, can they weigh the costs and benefits of selected treatments and make suggestions for the best therapies or clinical trials to the patient. Breaking down data silos and making this detailed information available to the clinician, especially as we gain the capacity to add validated decision support information is crucial to deliver the most precise and personalized level of cancer care.

Precision medicine at the bedside – wherever that may be

City of Hope is an independent, cutting-edge cancer research and treatment center located near Los Angeles, CA and has expanded to provide their state-of-the-art targeted therapies to patients at 31 clinical network  locations throughout Southern California. City of Hope also works with employers across the country and international physicians and patients to provide access to its internationally renowned cancer expertise by written consultations, coordination of care with their primary clinicians, telemedicine or in-person visits to the campus.

Dr. Keats joined us from TGen, a City of Hope affiliate in Phoenix, Arizona, where they are building a genomics-enabled precision medicine model. TGen is breaking away from the traditional approach of evidence-based medicine using percentages to determine the best treatment option for generalized patients with a certain phenotype. Instead, they are working to determine the most precise treatment path based on what will work for that specific patient‘s tumor type using their comprehensive genomic analysis model and translating that to clinical care.

As a first step, Dr. Keats and his research team at TGen conduct tumor-normal whole exome and tumor RNA sequencing. Analysis is conducted with an internally configured and validated analysis pipeline with a mixture of open-source, commercial, and internal tools to identify single-nucleotide polymorphisms, copy number and structural variations, gene fusions and transcript variations. The team measures DNA and RNA changes for >20,000 genes and applies gene-drug matching to identify potential therapeutic options. Treatment is then recommended by a tumor board based on genomic characteristics of each patient’s tumor. 

Precision Medicine Workflow

Dr. Bosserman and Dr. Keats shared similar methodologies for how they are leveraging rich and varied data sources to gain insights, yet medical centers and clinical research labs continue to face hurdles to translate discoveries into clinical practice. To achieve actionable insights for delivery of precision clinical care, researchers must be equipped with the best possible technologies to determine correlations between real-world clinical and phenotype data and genomic and multi-omics data to better understand the molecular mechanisms of disease.

At DNAnexus, we are committed to solving this problem by bringing together people from different disciplines who are approaching this issue from various angles and supporting initiatives like these that seek to access and explore heterogeneous datasets, make meaningful discoveries faster, and deliver better and more targeted patient care. 

See how DNAnexus Apollo can accelerate your discovery with a molecular precision medicine hub for advanced data harmonization and exploration. 

Considering an IT Investment For Your Clinical Diagnostics Lab? Help is Here

Next-generation sequencing data analysis management systems are the backbone of clinical diagnostics labs, providing vital functionality for day-to-day workings and business delivery. As a result, decisions about the tools to invest in can have far-reaching implications. 

Would it be best to improve, augment or entirely replace your existing systems? 

Which is the most resource intensive? 

Cost effective? 

Secure?

These aren’t the only questions.

Other considerations include scalability and future expansion potential, flexibility, and impacts on operations and turnaround time. 

It can be overwhelming. Luckily, we’re here to help, with two new guides to help you assess your current and future needs, and how to achieve them. 

Build vs. Buy: Six Questions to Consider When Investigating Clinical Diagnostics Informatics Solutions

Feeling like a victim of your own success? As testing demand increases, so does complexity, and IT issues that were once hidden are probably starting to surface. Experiencing unplanned downtime, difficulty deploying new pipelines, and challenges in finding and accessing data? These could bottleneck future growth.

Sounds like you need a reliable system that is prepared to grow alongside you. Custom-built Cloud solutions provide scalability, security, and lots of other benefits, which we outline in this Whitepaper. We’ll walk you through the decision-making process, and point out the advantages and disadvantages of the different IT solutions.

10 Tips to Scale Your Diagnostics Business & Grow Your Test Portfolio Globally

Ready to take your business to the next level? Great! If that involves expanding your footprint, either locally or globally, things could get complicated, especially when it comes to data sharing, storage and access. Are you prepared to navigate all the data sovereignty requirements and IP protection across locations? Do you know how to control access to pipeline algorithms and sensitive health data, and to comply with regionally-specific regulations?

By bringing all production pipelines into a single, unified cloud environment, with version-controlled pipeline updates rolled out simultaneously across your locales, you can effectively manage growth. This Whitepaper lays it all out, and explain why letting experts do the heavy lifting can pay dividends.

Still not convinced? Perhaps this will help you decide:

Meet Us in Atlanta for AACR

We will be joining thousands of oncology researchers and clinicians this week at the American Association for Cancer Research Annual Meeting, March 29 – April 3 at the Georgia World Congress Center. Stop by our booth #3051 to learn how DNAnexus Apollo enables advanced exploration of cancer datasets for therapeutic target discovery. Our scientific experts will be onsite all week for demos and to answer all your bioinformatics questions.

Last year at AACR, in partnership with St. Jude Children’s Research Hospital and Microsoft, St. Jude Cloud was launched, the largest public repository of pediatric genomic cancer data. Offering a suite of unique analysis tools and visualizations, researchers can efficiently mine, analyze, and visualize next-generation sequencing data for pediatric cancer and other life threatening diseases to accelerate scientific discoveries.

This year, St. Jude Children’s Research Hospital is celebrating the one year anniversary of the St. Jude Cloud and since its inception, 10,000 WGS data have been analyzed in continuation of the search to find a cure for pediatric cancer and other life-threatening diseases. If you want to know more about the St. Jude Cloud, visit their booth #4136. We are excited to celebrate the one year anniversary with St. Jude Children’s Research Hospital and St. Jude Cloud team!

Make sure to stop by either DNAnexus booth or the St. Jude Cloud booth, to celebrate with us at AACR! Check out our conference activities below. Can’t make it to any of our events? Request a meeting.

Demo: Explore Millions of Clinico-Genomic Data Points in Seconds with DNAnexus Apollo

  • Monday, April 1st – 1:00pm-2:00pm
  • Tuesday, April 2nd – 10:30am-11:30am

Cancer genomics is advancing precision medicine, leading to better diagnoses and treatment strategies. The Cancer Genome Atlas (TCGA), extensively characterized over 20,000 primary cancer and matched normal samples, creating a deep resource of over 25 petabytes of genomic, epigenomic, transcriptomic, and proteomic data. This landmark program has already lead to improvements in researchers’ ability to diagnose, treat and prevent cancer, yet mining this type of data for novel findings remains a huge endeavor.

DNAnexus Apollo enables at-scale navigation and exploration on combined genotypic and phenotypic data, whether it is TCGA data, your own protected data, or a combination. What actionable information will you find in your cancer datasets?

Customer Poster

3671 / 29 – Visualize 10,000 Whole Genomes from Pediatric Cancer Patients on St. Jude Cloud 

  • April 2nd, 1 – 5pm
  • Presenter: Clay McLeod, St Jude Children’s Research Hospital