At Bio-IT World: Technological Innovation Advancing Genomic Science and Medicine

2Bio-IT World Conference & Expo comes early this year (April 4-7th), where more than 3,000 researchers, life science, pharmaceutical, clinical, and IT professionals descend upon Boston.  If you’re headed to Bio-IT World, please stop by the DNAnexus booth (#317) to explore and discuss our latest projects, new datasets, and tools.

This year, Big Data is a featured theme at the event. Our friend and collaborator, Dr. Taha Kass-Hout (Chief Health Informatics Officer and Director of the FDA’s Office of Health Informatics) kicks off the Big Data: Sharing vs. Privacy vs. Security in Healthcare session (Track 3, Thursday at 2:00pm) with an overview of precisionFDA, the new community platform for NGS assay evaluation and regulatory science exploration. Additional fascinating talks follow: John E. Mattison (Co-Chair, eHealth Workgroup, Global Alliance for Genomics and Health) will present emerging initiatives from the GA4GH and Robert Grossman (Director, Center for Data Intensive Science) will discuss large-scale data commons for genomic and clinical data.  The final session includes those experts along with John M. Conley (Robinson Bradshaw & Hinson), Andrew K. Porter (Merck & Co.), and Mollie Shields-Uehling (SAFE-BioPharma Assoc.) for a panel discussion looking at data sharing innovations and the regulatory environment.

Best_Practices_Logo_2016_finalist-blue (1)Precision medicine continues to be a strong theme for 2016, bolstered by President Obama’s recent Precision Medicine Initiative (PMI) Summit. At DNAnexus, we like to think of genetic data as the original Big Data, and we are passionate about Big Data’s role in advancing medical discovery and treatments. We are proud to announce that precisionFDA is a Bio-IT World Best Practice Award finalist.  The Best Practice Award highlights outstanding examples of how technological innovation can be powerful forces of change in the life sciences.  The precisionFDA platform was developed under contract for the FDA by DNAnexus, and currently provides over 1,000 users from nearly 500 organizations in the genomics community a sandbox for NGS assay evaluation and regulatory science exploration.  Be sure to be there when the winners are announced live on Wednesday, April 6th at 9:30am.

Dr. Taha Kass-Hout, Chief Health Informatics Officer and Director of FDA’s Office of Health Informatics, will be making a cameo appearance at the DNAnexus booth to answer questions and showcase the precisionFDA platform.  Learn how precisionFDA is leveraging community participation to advance regulatory science in the area of next-generation sequencing – DNAnexus is proud to have collaborated with the FDA to develop the community platform.  

PrecisionFDA Demo & Dr Taha Meet & Greet at the DNAnexus Booth (#317)

  • Wednesday, April 6th at 10:00am-11:00am
  • Wednesday, April 6th at 5:30pm-6:30pm

DNAnexus Booth (#317) Activities
Unite your workflows. DNAnexus offers end-to-end tailored solutions. We’ll be demoing a few upstream and downstream partner options at our booth:  Sapio
Sciences LIMS, Pacific Biosciences tools, and WuXi NextCODE Cloud platform.    

Wednesday, April 6th
3:25pm Sapio’s Exemplar NGS LIMS Demo
See how the integration of the DNAnexus platform with Sapio Sciences’ LIMS solution is enabling seamless integration with bioinformatics operations, enabling secure scalability and flexible workflows.

Thursday, April 7th
10:00am WuXi NextCODE Cloud Demo
Learn how the WuXi NextCODE Cloud — powered by DNAnexus — is accelerating the use of genomics to benefit patients worldwide. China cloud solution now available.

1:20pm PacBio de novo Assembly & SV Analysis Tools Demo
Demo the latest PacBio tools on the DNAnexus platform. See how complex bioinformatics is made simple.

Must-See Presentations
We’re proud to support our customers who push the envelope in advancing genomic science and medicine.  Be sure not to miss these talks!

Track 3 Software Applications & Services:  Regeneron Genetics Center’s  Use of the DNAnexus Annex in the Amazon Cloud for Large-Scale NGS Downstream Compute
Presenter:  Christopher Sprangel, Director, IT, Human Genetics, Genome Informatics, Regeneron Genetics Center and Nathan Wallace, Founder & CEO, Turbot
When:  Wednesday, April 6 at 2:25pm

Track 3 Software Applications & Services:  Featured Presentation: precisionFDA
Presenter:  Taha A. Kass-Hout, MD, MS, Chief Health Informatics Officer & Director, Office of Health Informatics, FDA
When:  Thursday, April 7 at 2:00pm

Track 3 Software Applications & Services: Panel Discussion:  How will data sharing innovations fare in the regulatory environment?
Moderator:  John M. Conley, JD, PhD, Robinson Bradshaw & Hinson
Panelists:  Robert Grossman, PhD, University of Chicago, Taha A. Kass-Hout, MD, MS, FDA, John E Mattison, MD, Kaiser Permanente, Andrew K. Porter, Merck & Co., and Mollie Shield-Uehling, SAFE-BioPharma Association
When:  Thursday, April 7 at 3:30pm

To learn more about DNAnexus and see a demo of the DNAnexus Platform, visit booth #317 in the exhibit hall at the Bio-IT World Conference & Expo.

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!