Highlights from Festival of Genomics California 2016

PrecisionFDA, Explore Your Genome Giveaway, & Treadmills

Last week, we had the pleasure of attending Festival of Genomics California. We hope you were able to catch some of the truly inspiring talks from the plenary speakers, such as Karen Nelson from J. Craig Venter Institute, Manolis Kellis from MIT Computational Biology Group, and Carlos Bustamante from Stanford University School of Medicine.

Our big story at the conference was about precisionFDA – an open source platform to advance regulatory science about NGS-based analytic tools and datasets. DNAnexus is under contract with the FDA Office of Health Informatics to assist the FDA in preparation for a December 15th launch by developing the precisionFDA portal and assisting in the engagement of the genomics community. At the Festival, we organized a panel moderated by Omar Serang and George Asimenos who led a discussion involving Deanna Church, Personalis; Michael Eberle, Illumina; Kevin Jacobs, 23andMe; and Justin Zook, NIST.

We kicked off a closed panel discussion with a video overview of precisionFDA.

George showed screenshots of the precisionFDA platform, highlighting examples of how the community will be able to use the platform, including the variant call comparison tool that can compare results between a test dataset and a benchmark/reference dataset, and separate out true positives, false positives and false negatives.

From there, the panel delved into a lively discussion. Deanna pointed out that only roughly 1500 out of the 4000 genes that have some clinical relevance are represented in their entirety in the Genome in a Bottle/National Institute of Standards (NIST) and Technology NA12878 dataset. Therefore, the precisionFDA community needs to spend time expanding that sample, not just adding more samples to the community’s database. Michael stressed the importance of pedigrees in validating variants in a reference sample.

Kevin made a passionate speech for how the community needs to focus on conventions. How can we possibly enter an era of precision medicine if we are still unable to agree on where the human genome exons are located? Researchers use computers and algorithms to calculate the results with binary formats, however the reality is the computer is only doing what the human researcher tells it to do, and since humans are not very precise, how can we be confident in our results? Justin stressed the importance that NIST should not be the standards-making body for dictating these standards, they need to be developed and agreed upon by a community.

In addition to its variant call comparison functionality, the precisionFDA platform will allow participants to conduct in-silico experiments using software and publish their conclusions in the form of electronic notes that can be placed with their experiments and reference the data and analyses. Using this feature, participants have the opportunity to showcase to the community their views on certain “hot” topics such as “the utility of simulations”.

Be sure to visit precision.fda.gov and follow us on @precisionFDA to get the latest. The platform will be accepting applications for membership in the community beginning December 15th!

Explore Your Genome Giveaway!
In addition, we also want to thank Sure Genomics for joining us in our booth to demo their product and discuss how the DNAnexus Platform analyzes their customer’s whole genome sequencing data. During the festival Sure Genomics and DNAnexus announced two lucky winners that will have their genomes sequenced and analyzed by Sure Genomics.  Each winner will receive a complimentary Personal DNA Kit, personal DNA report mapping key markers, and one-year free storage.   

Day 1 Winner:  Alain C., Insilico
Day 2 Winner:  Jennifer P., Kapa Biosystems

Congratulations Alain & Jennifer!

Returning Winners of Race the Helix Treadmill Challenge
FoG CA Race the HelixBlazing fast. That’s the only way DNAnexus runs, whether in the cloud or on the treadmill. DNAnexus repeated its June victory in Boston to win the Race the Helix Treadmill Challenge in California.

We also want to thank all those that stopped by our booth. We look forward to seeing everyone again next year at Festival of Genomics Boston.

Festival of Genomics: Not Your Typical Genomics Conference

Whole Genome Sequencing Giveaway, FDA’s New Approach to
Science & Treadmill Challenge

FoG CA logoFront Line Genomics is bringing Festival of Genomics to California this week (Nov 3-5th). Their inaugural event, which was held in Boston in June, was a great success and we are looking forward to the festivities taking place in our own backyard. Festival of Genomics will include a stellar lineup of speakers, plus posters, workshops, exhibitors, and networking opportunities. DNAnexus returns as defending champion of the “Race the Helix” treadmill challenge, a fundraising event for the Greenwood Genetic Center.

If you’re headed to Festival of Genomics California, please visit the DNAnexus booth (#15) to learn about our latest research and development project with the FDA’s Office of Health Informatics to build precisionFDA, an open source platform to advance regulatory science around NGS-based analytic tools and datasets. Learn more.

Sure Genomics logoIn collaboration with Sure Genomics, we’ll be giving away one FREE full genome sequence each day! Stop by the DNAnexus booth (#15) between 1-2pm to learn more about Sure Genomics, their new personal genome sequencing service and interactive analytics platform, and be entered to win.  More details below.

DNAnexus and Sure Genomics will sequence and analyze the whole genomes of two lucky winners ($2500 value)!

Sure Genomics Hour (DNAnexus Booth #15)
• Wednesday, November 4th at 1:00pm – 2:00pm
• Thursday, November 5th at 1:00pm – 2:00pm

Learn how Sure Genomics, a solutions provider for personal DNA analytics for health, fitness, and medical reports, has adopted the DNAnexus Cloud Platform to support its full genome sequencing offering. Sure Genomics beta opens early December and starts taking reservations, genome sequencing starts at the beginning of Q1 2016.

Each winner will receive a complimentary Personal DNA Kit, personal DNA report mapping key markers, and one year free storage. STOP BY TO LEARN MORE & ENTER TO WIN!

Details on the giveaway rules:

  • Entry will be open during Sure Genomics Hour November 4-5th from 1-2pm at the DNAnexus booth (#15).
  • Simply drop of your business card in the bowl at the DNAnexus booth and receive a sneak peek of the Sure Genomics product.
  • No purchase necessary and you don’t have to be an existing DNAnexus customer.
  • Winners will be announced and contacted by Sure Genomics after the Festival.

DNAnexus at Festival of Genomics California

 Genomics in the Age of Ubiquitous, Cheap Sequencing
Presenter:  Andrew Carroll, PhD, Director of Science, DNAnexus
When:  Wednesday, November 4th at 3:00pm
Where:  Stage G

Panel Discussions
Panel Discussion: Preparing (for) 1,000,000 Whole Genomes
When: Wednesday, November 4th at 2:00pm
Where: Stage G

Will Salerno, Sr Staff Scientist, Next-Gen Sequencing Informatics Human Genome Sequencing Center, Baylor College of Medicine

Matthew Trunnell, CIO and VP of Center Information Technology and Services, Fred Hutchinson Cancer Research Center
Jeffrey Reid, Sr Director, Head of Genome Informatics, Regeneron Genetics Center
Ali Torkamani, Director of Genome Informatics, The Scripps Translational Science Institute
Andrew Carroll, Director of Science, DNAnexus
Deniz Kural, CEO, Seven Bridges Genomics

PrecisionFDA Panel Discussion:  Advancing Precision Medicine by Enabling a Collaborative Informatics Community
When: Thursday, November 5th at 3:45pm
Where: Tech Forum Stage

Omar Serang, Chief Cloud Officer, DNAnexus
George Asimenos, Director of Strategic Projects, DNAnexus

Deanna Church, Senior Director of Genomics and Content, Personalis
Michael Eberle, Associate Director, Scientific Research, Illumina
Kevin Jacobs, Director of Laboratory R&D, 23andMe
Justin Zook, Research Scientist, National Institute of Standards & Technology

Learn about the development of an open-source platform for community contribution to NGS-related regulatory science.

Talks Powered by DNAnexus:

Title: Genome Informatics & Cloud Computing – the Internet Isn’t Just for Cat Pictures Anymore!
Presenter: Jeffrey Reid, Sr Director, Head of Genome Informatics, Regeneron Genetics Center
When: Thursday, November 5th at 5:00pm
Where:  Stage G

Visit us in booth #15 at Festival of Genomics!

F-U-N (Yes, there will be a treadmill on the exhibition floor!)
The DNAnexus Team swept the Race the Helix treadmill challenge at the last Festival of Genomics conference in June; and we want a chance to R-E-P-E-A-T. Come cheer on team DNAnexus Thursday 11:30 am, November 4th as we defend our title. 100% of funds raised by this event will go directly to the Greenwood Genetic Center Trust.

Post-ASHG: The Future of Genomics & Informatics in the Next 5 Years

Reference Genome Improvement, cfDNA for Transplantation, & de novo
Reconstruction of Familial Relationships

As the dust settles from American Society of Human Genetics 2015, we’d like to reflect and bring you some highlights from our lunchtime talk: Genomics and Informatics for the Next Five Years. We had a packed house and a stellar lineup of customers showcasing their cutting edge research on the DNAnexus Platform.

Tina Graves-Lindsay, Leader of the Reference Genomes Group at the McDonnell Genome Institute (MGI) at Washington University St. Louis, kicked off the session talking about the research involved in achieving the best human whole genome assembly. As a member of the Genome Reference Consortium, Tina’s team has been working to improve the current reference, GRCh38, and fixing a few genes that are not optimally represented for all individuals or ancestries.

The sequence plan starts with generating 60x coverage of PacBio long read data for a de novo assembly. From there, MGI incorporates BioNano or Dovetail data to create scaffolds that in some cases nearly cover entire chromosome arms. Since MGI is targeting difficult to assemble regions of the genome, they sequence bacterial artificial chromosomes (BACs) to fill the targeted regions and then incorporate all this data together to generate a very high quality whole genome assembly labeled the “Gold Genome”.


With these new technology improvements the MGI hopes to sequence more than 5 Gold Genomes as previously planned. With improvements in the BioNano pipelines, they hope to be able to automate some of the assembly breaks that need to be made to improve the final product. The DNAnexus Platform provides researchers with the computational power required and a turnkey solution for BioNano whole genome mapping and PacBio whole genome assembly. Labs of all sizes have fast and cost-effective access to the innovative technologies they need to reach their discoveries.

David Ross, Ph.D., Sr. Director of Bioinformatics at CareDx, presented his research on clinical-grade next generation sequencing (NGS) to monitor cell-free DNA (cfDNA) for transplantation. Post-transplant care is challenging. The main issue with organ transplantation is no longer organ rejection, but issues associated with over-immunosuppression; being able to balance immunosuppressive therapy with a titration tool is key.

Transplantation is the latest field to investigate the use of cfDNA for transplant surveillance. Research has shown that monitoring cfDNA for donor-specific homozygous single nucleotide polymorphisms (SNPs) can help identify transplant patients at risk of rejection. CareDx’s hypothesis is that cfDNA will be elevated at the time of rejection. CareDx’s cfDNA technology works by using NGS to measure donor-derived cfDNA (dd-cfDNA) as a percentage of total cfDNA. The dd-cfDNA can be detected at 0.25% level based on titration/calibration experiments; in contrast non-invasive prenatal testing cfDNA detection occurs between 5-20%.

CareDx is one of the few CLIA laboratories that has satisfied the rigorous review of the FDA when it received clearance for its laboratory developed AlloMap, a blood-based test used to monitor heart transplant recipients for rejection risk. CareDx worked closely with DNAnexus to complete the cloud-based computational analysis pipeline for the CareDx cfDNA test. The HIPAA compliant DNAnexus Platform, with full versioning and auditing, played a critical role in expediting CareDx’s cfDNA assay efforts, enabling them to deliver a novel surveillance management solution to the transplant setting.

Research-Grade vs. Clinical-Grade NGS
Difference in methods, processes, and validation


Lastly, Jeffrey Staples, Ph.D., Bioinformatics R&D Developer for Regeneron Genetics Center (RGC) discussed his latest research on de novo reconstruction of familial relationships in 42,880 exomes. The RGC has collaborated with Geisinger Healthcare System (GHS) to conduct large population-based studies integrating whole-exome sequencing (WES) with de-identified longitudinal health records. In this specific study, the RGC wanted to determine familial relationships in the GHS WES dataset, since this information can be used to build various studies and analyses requiring related or unrelated individuals. They used Identity By Decent (IBD), which measures a fraction of the genome shared between two people, as a measure of relatedness.
· IBD0 – proportion of the genome that is shared on 0 chromosomes
· IBD1 – proportion of the genome that is shared on 1 chromosomes
· IBD2 – proportion of the genome that is shared on 2 chromosomes

The results from distribution of IBD in >40,000 exomes showed 19,400 samples to have a first- or second-degree relatives in the dataset.


There is new thinking around handling relatedness in large-scale sequencing cohorts, performing de novo pedigree reconstruction to estimate the IBD between individuals and predict familial relationships. Initial findings show the Loss of Function (LOF) variant in CCR5, a protein on the surface of a white blood cell that is involved in the immune system, is transmitted through the family. The RGC is starting to leverage all family networks, including the 1,107-person second-degree family network.


This massive relatedness is a big emerging opportunity for large scale sequencing studies and these pioneering methodologies will be invaluable to other large scale initiatives, leveraging families for discovery in precision medicine for all phenotypes going forward.

If you missed our lunchtime talk you can learn more about BioNano’s physical genome mapping integration with DNAnexus here, or visit DNAnexus.com to explore how we make it easier to manage your genomic data.