The Journey to Precision Medicine

A Recap of the 9th Annual Future of Genomic Medicine Conference

IMG_7411The Future of Genomic Medicine IX conference took place last week in the perpetually sunny La Jolla, California. The broad goal of this annual conference is to elevate the practice of genomic medicine by making it more precise, individualized, and effective. Key areas of focus for this year’s conference included cancer detection, rare disease genomics, and the exciting area of gene editing.

The meeting began each day with a biographical case study – a patient interviewed on the stage by Dr. Eric Topol, who organized and led the conference.  Friday’s story came from Dardanel Robinson, who shared the tragedy and sadness of growing up surrounded by sudden and unexpected death. She witnessed family members — great-aunts and uncles, cousins, and even her father – all succumb to an early and unexpected death.  She lived each day wondering what the future held for her and her six children. It wasn’t until the death of her 26 year-old son Daniel, that Robinson decided to seek answers. Via the Scripps Translational Science Institute Molecular Autopsy Study, she learned that  her son carried a genetic variant predisposing to sudden cardiac arrest. Robinson also found out she was a carrier as well.  There are still many unknowns, but at least now Robinson is armed with the knowledge of her family’s electrical rhythm defect and is taking preventative steps to reduce her family’s risk of sudden cardiac arrest. You can read more about Robinson’s story here.

Scripps packs a long list of speakers; inspiring individuals who are disrupting the genomics industry and changing the face of healthcare. Harvard geneticist George Church spoke about how reversing age in a number of different animals has been demonstrated in his lab and it’s only a matter of time that we translate this into larger animals and humans. Anne Wojcicki, CEO of 23andMe, discussed the company’s pivot into therapeutics. By leveraging the data of more than 1.2 million 23andMe customers, the company’s researchers are looking into their own drug discovery programs.  They hope to  engage customers and look at genomic and phenotypic data for effective and efficient drug discovery.

I was especially excited to hear from speakers how the DNAnexus platform is advancing their work.

Charles Chiu, associate professor of laboratory medicine at UCSF, talked about using genetic sequencing to identify potentially treatable infections in acutely ill patients. As part of the California Initiative to Advance Precision Medicine (CIAPM), the project aims to expand the reach of this genetic testing approach to identify infectious diseases throughout the UC hospital system. DNAnexus is proud to support Dr. Chiu’s efforts; an analytic pipeline that allows samples and sequences from different hospital locations to be processed securely and compliantly in the cloud.

David Ledbetter, Chief Scientific Officer at Geisinger Health System (GHS), provided an update on the inspiring work Geisinger and Regeneron have done in integrating genetic and electronic health records (EHR) data.   Dr. Ledbetter discussed the anticipated clinical volume associated with the first 250,000 patients whose exomes will have been sequenced by Regeneron Genetics Center on the DNAnexus Platform. The GHS is unique in that it has a relatively isolated patient population containing nearly 20 years retrospective longitudinal EHR data.  Out of 250,000 participants, Dr. Ledbetter expects to identify around 5,000 individuals that are carrying pathogenic variants. From these 5,000 participants, Geisinger expects to be able to identify 15,000 ‘at risk’ relatives. Among the implications, Dr. Ledbetter advised that there is a need to have enough genetic counselors in the GHS to advise 20,000 on the consequences and probability of developing or transmitting an inherited disorder. This is an ambitious goal, but not one to be discounted, Geisinger has been at the leading edge of healthcare practices for decades (e.g. Open Notes: the sharing of physician notes with patients).

During the first week of March, Geisinger and Regeneron published a paper in the New England Journal of Medicine where their geno/pheno integration approach revealed a genetic variant that appears to reduce levels of triglycerides and lower the risk of coronary artery disease. We are very proud of the fact that the success of this approach is enabled by DNAnexus, our secure and powerful genome informatics and data management platform that allows for the seamless data integration and distributed collaboration of multiple stakeholders.  Our Chief Medical Officer, David Shaywitz, shares his thoughts on this exciting research here.

One thing is abundantly clear: after two days of insightful and progressive talks, genomic medicine is reaching a point where the accumulated knowledge obtained by research is beginning to hit critical mass.  All the pieces – patient partnerships, EHRs, genomics, policy, Big Data – are coming together to drive precision medicine out of the research environment and into the clinic.

DNAnexus Heads to Orlando for AGBT 2016

AGBT_logo_350Each February, droves of scientists descend upon Florida for the annual Advances in Genome Biology and Technology (AGBT) conference. The conference is a mix of long days filled with presentations, and lively nights consisting of cocktail parties and networking. This February 10-13th , the conference takes place in Orlando, considered by some to be the “happiest place on earth,” where global researchers, leaders, and innovators will meet to share new discoveries and cutting edge breakthroughs.

If you’re headed to AGBT, please join us in Marbella 2 to discuss our latest projects, datasets, and tools. It’s been one heck of a rocket ship ride in 2015; already 2016 promises even more opportunities for fruitful collaborations.

Learn how DNAnexus is transforming the PacBio de novo assembly experience by providing industry-leading reference-quality genome assembly services. We’ve updated the most popular PacBio SMRT Analysis 3.0 tools and structural variant callers (e.g. Parliament) on the DNAnexus Platform.

DNAnexus Events at AGBT
Software Demo
DNAnexus, The Global Network for Genomics
From structural variant analysis to ENCODE pipelines & more, just ask Singer how DNAnexus might help your genomics research project.
Singer Ma, Scientist, DNAnexus
Thursday, February 11th, 5:00pm – 7:00pm
Coquina North & South

Party Under the Stars
Friday, February 12th, 9:30pm
Fairways Lawn
Join us for libations and lively discussions under the stars.
Co-hosted with Pacific Biosciences, BioNano Genomics, New England BioLabs, Sage Science, and DNAnexus.

DNAnexus Supported Science
We’re proud to support the truly innovative research of our customers who push the envelope in advancing genomic science and medicine. Be sure to check out these posters at AGBT!

Poster #609:  Challenges in Large-Scale Human Whole Genome Sequencing with HiSeq X Ten: Towards Clinical Applications 
Yi Han, Baylor College of Medicine

Poster #704:  Rapid Capture Methods for Comprehensive Carrier Screening
Donna Muzny, Baylor College of Medicine

Poster #705:  Transplanted Organ Surveillance by Genomic Analysis of Donor-derived cfDNA 
Marica Grskovic, CareDx, Inc.

Poster #1210:  Rapid and scalable typing of structural variants with assembly-based indexing 
Will Salerno, Baylor College of Medicine

Poster #1906:  Analytical Validation of a Clinical Grade NGS dd-cfDNA Assay: Lessons from cloud computation Infrastructures and methods-based proficiency using NIST–GIAB Resources 
Yue Sarah Wang, CareDX Inc.

For more details on this year’s meeting, and to see the complete agenda check it out here.

See you in Orlando!

DNAnexus Presents at JP Morgan Healthcare Conference

JP Morgan Healthcare 2016Today kicks off the 34rd annual JP Morgan Healthcare Conference, which continues to be healthcare’s greatest deal-making and high-powered networking event of the year. Each year industry leaders unveil new products, as attendees scope out emerging trends in healthcare’s rapidly-evolving sectors such as digital health and diagnostics. Last year the introduction of the the HiSeq X Ten from Illumina made great waves as it would continue to drive down sequencing costs and democratize genomics. We look forward to this year’s announcements in genomics which will undoubtedly be focused on what can be achieved with large scale sequencing.

However, biotech wasn’t always big business; leading up to 1980 it was Big Pharma that attributed to the majority of drug discovery. If you’re curious on how biotech evolved from risky investment to booming business, Luke Timmerman and Meg Tirrell do an outstanding job chronicling biotech’s coming of age in The Signal podcast.

DNAnexus is honored to be presenting this year. Richard Daly, CEO, will deliver a presentation on Tuesday, January 12th at 2pm PST in the Elizabethan D room at the Westin St. Francis. In his talk, titled The Network is the Solution in Genomics, Richard will discuss the convergence of genomics and cloud computing and how DNAnexus has acquired market leadership in this sector by building out a global network via its integrated genome informatics and data management platform.

2015 was a breakout year for DNAnexus, expanding our global network of key customers and partners by 6-fold, many of which we have announced publicly. We help biopharmaceutical companies (Regeneron), leading genome centers (Baylor College of Medicine, Stanford University), pioneering diagnostic test providers (Natera, CareDx, Intermountain), sequencing service providers (The Garvan Institute, WuXi NextCODE), research consortia (ENCODE, CHARGE, 3000 Rice Genomes Project) and the US Government (precisionFDA) accelerate their genomics programs globally. Our focus on secondary analysis and building out a partner/collaboration network drives substantial growth. Laboratory information management systems (LIMS) and sequencing instruments easily integrate with DNAnexus, as well as downstream tertiary analysis and reporting solutions.

DNAnexus workflow

Genomics has been called the original big data, and it’s only going to get bigger. Organizations participating in global large-scale sequencing projects studying thousands or even millions of genomes are becoming the norm. In an article, Big Data: Astronomical or Genomical?, in PLOS Biology projects that by 2025 the genomics industry will outpace three other major big data generators: astronomy, YouTube, and Twitter, in projected annual storage and computing needs by a factor of 2-20x. Our own projections suggest more than 400,000 TB of genomic data in 2016, and only 0.01% of the world’s population has been sequenced.

As big data aggregates online, new standards will need to emerge for discovering and querying datasets, for authenticating requests, encrypting sensitive information, and controlling access. DNAnexus, along with the Global Alliance for Genomics and Health and others are already working together to develop approaches that facilitate interoperability.

At DNAnexus, we believe the cloud is the only technology that is capable of keeping pace with big data. It eliminates time and the capital expenditure of creating and upgrading local infrastructure for data analysis. The elasticity of the cloud allows for near limitless scalability and immediate availability to resources. And with the cloud’s online nature, researchers are able to share data and tools and collaborate instantaneously with others around the world. Our industry is long overdue to replace hard drives and FedEx as the means for collaboration, and patients and researchers worldwide will benefit from a simpler means to collaborate. DNAnexus, and its global genomics network, is addressing the challenges of genomics big data.