DNAnexus at ASHG: Accelerating Your Path from Genomic Data to Insight

We are looking forward to attending the annual American Society of Human Genetics (ASHG) meeting next week in Orlando.  

We’re excited to share updates on recent projects, including our new data analysis and management solution for NovaSeq™ instruments, our collaborative microbiome informatics platform, and the latest software tools available on DNAnexus from our partners at Edico Genome and PacBio.

If you’re headed to ASHG, stop by DNAnexus booth 811 to learn about the broad research and clinical applications of the DNAnexus Platform. Can’t make it to any of our events? Stop by booth 811 anytime during the conference, or email us to schedule a meeting with a member of our team.

Lunchtime Talk 

Optimize Your Path to Variant Production: Real World Examples

Friday, October 20th, 1:00pm-2:15pm
Hilton Orlando Hotel, Lake George Room, Lobby Level

Join our lunchtime discussion to learn about DNAnexus CloudSeq, a powerful solution for rapidly scaling cloud-enabled bioinformatics infrastructure for research and clinical sequencing applications. You will hear case studies from Baylor College of Medicine’s Human Genome Sequencing Center and Rady Children’s Hospital about navigating the complexities of integrating large multi-omic datasets, and developing pipelines to analyze and share data and insights across global R&D organizations.

Guest Speakers:

  • HGSC Baylor College of MedicineWill Salerno, PhD, Director of Genome Informatics, Human Genome Sequencing Center at Baylor College of Medicine
    • Talk: Translation of NIH Data in Discovery Commons
  • Narayanan Veeraraghavan, PhD, Director of IT at Rady Children’s Institute for Genomic Medicine
    • Talk: Creating a Critical Nexus: Making Rapid Whole-Genome (rWGS) Based Precision Medicine Accessible to NICUs and PICUs Across the Country

RSVP today; lunch will be provided.

Booth Activities

Debuting DNAnexus CloudSeq
Stop by to learn about our powerful data analysis and management solution for the NovaSeq™ series of sequencing systems.

  • Wednesday, October 18th, 1:00pm in DNAnexus Booth #811

Edico Genome’s DRAGEN on DNAnexus
See a demo of DRAGEN, Edico Genome’s ultra-rapid, accurate, and cost-efficient genomic data analysis pipeline on DNAnexus. Sign up here or in our booth to take advantage of limited-time promotional pricing on DNAnexus.

  • Wednesday, October 18th,10:40am in Edico Genome Booth #710 
  • Wednesday, October 18th, 2:30pm in DNAnexus Booth #811

PacBio SMRT Analysis Suite 5.0 Available Now on DNAnexus
Test drive PacBio’s SMRT Analysis software on DNAnexus. The suite of SMRT tools includes a comprehensive set of applications for genomic analysis, including de novo assembly, variant calling, transcriptome analysis, epigenomics, and more.

  • Thursday, October 19th, 1:00pm, DNAnexus Booth #811
  • Friday, October 20th, 11:00am, PacBio Booth #722

Join the Microbiome Research Community  
Stop by to learn how to get involved in a series of community challenges aimed at increasing the understanding of the human microbiome and its relation to disease

  • Thursday, October 19th, 2:30pm, DNAnexus Booth #811

Posters Featuring DNAnexus  

PgmNr 745: Access, visualize and analyse pediatric genomic data on St Jude Cloud.

  • Speaker: Scott Newman, St Jude Children’s Research Hospital
  • Time: Wednesday, October 18th, 2:00pm-3:00pm

View Details

PgmNr 2563: Improved molecular tracking of individual genomes for clinical whole-genome sequencing.

  • Speaker: Sergey Batalov, Senior Bioinformaticist, Rady Children’s Institute for Genomic Medicine
  • Time: Wednesday, October 18th, 2:00pm-3:00pm

View Details

PgmNr 1951: Exome-wide association study of kidney function in 55,041 participants of the DiscovEHR cohort.

  • Speaker: Claudia Schurmann, Statistical Geneticist, Regeneron Genetic Center, Regeneron Pharmaceuticals
  • Time: Wednesday, October 18th, 2:00pm-3:00pm

View Details

PgmNr 763: Whole genome sequencing signatures for early detection of cancer via liquid biopsy.

  • Speaker: Bahram Kermani, Founder & CEO, Crystal Genetics
  • Time: Wednesday, October 18th, 2:00pm-3:00pm

View Details

PgmNr 1281: Cloud-based quality measurement of whole-genome cohorts.

  • Speaker: Will Salerno, Human Genome Sequencing Center, Baylor College of Medicine
  • Time: Friday, October 20th, 11:30am-12:30pm

View Details

Upgrading to TLS 1.2

As a part of our continued efforts to maintain the highest security standards on the DNAnexus Platform, we will deprecate support of TLS 1.0 and TLS 1.1 on October 15th, 2017. We have been communicating this proposed change, and most of the customers and users have upgraded.

If you are a user that still has programs or processes using TLS 1.0 or 1.1 when interfacing with the DNAnexus Platform you will need to take a few simple steps to upgrade. Please follow the instructions below to upgrade to TLS 1.2.

What is TLS?
TLS stands for “Transport Layer Security” and is a protocol that ensures connections made to a remote endpoint are the intended destination through encryption and endpoint identity verification. DNAnexus web and API connections use TLS as a key security component, thus it is important that the latest version of TLS is supported.

What do I need to do?
For macOS/OS X Users:
If you are using the DNAnexus Platform SDK (a.k.a. dx-toolkit) with the Python version provided with your operating system, you will need to install an alternative Python version with TLS 1.2 support. We suggest using the Homebrew package manager to install Python version 2.7.13:
Install Homebrew using the instructions at https://brew.sh/.

Once Homebrew is installed, run the following command in your terminal prompt:
brew install python

Once the Python version is installed follow the instructions at https://wiki.dnanexus.com/Downloads to download, unpack, and activate the latest dx-toolkit release.

For Internet Explorer Web Browser Users:
If you use Internet Explorer version 10 or earlier, you will need to upgrade your web browser to Internet Explorer 11 or later.

For All Other Users:
If you use a PC, or if your web browser is Internet Explorer 11 or later, Chrome, Firefox, or Safari, we do not expect that your access to DNAnexus will be impacted by this upgrade.

If you are impacted, please make the necessary modifications by October 15th, 2017 in order to maintain continued access to DNAnexus. Please do not hesitate to contact support@dnanexus.com with any questions or concerns.

DRAGEN Bio-IT Platform Accelerates Life-Changing Diagnosis

The following is a guest blog, written by our partners at Edico Genome.

When diagnosing acutely ill babies, it’s a race against time to ensure that physicians have access to accurate diagnoses to set the appropriate course of treatment. During the first few days of life, a few hours can save or seal the fate of patients emitted to the Neonatal Intensive Care Units (NICU) and Pediatric Intensive Care Units (PICU), making it essential to deliver diagnosis in an expedited manner while ensuring accuracy and keeping costs low for widespread adoption.

Seeking a dependable way to drastically cut down on diagnosis times, Dr. Stephen Kingsmore, M.D. D.Sc., President and CEO at Rady Children’s Institute for Genomic Medicine, in partnership with Edico Genome and Illumina, developed a scalable infrastructure to perform diagnosis from beginning to end in 26 hours.

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DRAGEN Rapid WGS Diagnosis

In order to receive such results, Dr. Kingsmore needed to address the largest bottleneck: secondary data analysis. Integrating Edico Genome’s DRAGEN Bio-IT Platform, which is now available on DNAnexus, Dr. Kingsmore was able to reduce analysis time from ~25 hours (using an optimized version of BWA-GATK) down to ~22 minutes.

This drastic acceleration was the result of DRAGEN’s field programmable gate array (FPGA) backed platform, based on a Xilinx FPGA, which provides hardware-accelerated implementation to all of the most widely used types of NGS workflows. In conjunction with Illumina’s optimized sequencing platform, Dr. Kingsmore was able to greatly expedite sample to answer turnaround time and earn the Guinness World Record for Fastest Genetic Diagnosis.

As a result of this initiative, 23 out of the first 48 Rady Children’s Hospital infants tested received diagnosis and 16 received substantial changes in NICU/PICU treatments. For one infant with liver disease, the expedited diagnosis resulted in the cancellation of a surgery that posed a 60 percent risk of mortality. For two other patients, one with heart failure and the other with liver failure, Dr. Kingsmore and his team were able to rule out disease which were a contra-indication to heart and liver transplants, respectively. Without this information, both infants may have been too high risk for transplant or may not have survived the procedure.

DRAGEN is now available in the cloud through the DNAnexus Platform, powered by Amazon Elastic Compute Cloud (Amazon EC2) F1 instance types. DNAnexus connects Edico Genome’s ultra-fast secondary analysis algorithms with Fabric Genomics’ interpretation software, and integrates seamlessly with Rady Children’s custom data interpretation portal. Through the DNAnexus Platform, users can monitor jobs, organize and share data, and compare patients’ data to a diagnostic resource within the network, making it an ideal solution for streamlining and expanding operations to other children’s hospitals across the country.

New and existing DNAnexus customers can now also take advantage of the highly accurate and ultra-rapid DRAGEN pipelines used by Dr. Kingsmore on the DNAnexus Platform. Sign up for our reduced-cost trial here.

To learn more about DRAGEN’s partnership with Dr. Kingsmore and his team, the full white paper can be found here.