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.

Removing the NGS Analytics Data Bottleneck with Field-Programmable Gate Arrays (FPGA’s)

Edico Genome’s FPGA-backed DRAGEN Bio-IT Platform Now Available on DNAnexus

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

With rapid adoption across a variety of practices, next-generation sequencing (NGS) is on track to become one of the largest producers of big data by 2025. While the integration of NGS poses exceptional breakthroughs in its applied practices, one major problem threatens its expansion: a lack of computing power to analyze the rapidly growing body of data.

Current projections calculate genomic data to continue doubling every seven months, a stark acceleration in comparison to Moore’s Law, which states CPU capabilities will double every two years. The void left in-between creates a bottleneck for genomics labs.

Designed to uncork this big data bottleneck, Edico Genome’s DRAGEN™ (Dynamic Read Analysis for Genomics) Platform leverages FPGA (Field-Programmable Gate Array) technology to provide customers with hardware-accelerated implementation of genome pipeline algorithms. Leveraging FPGAs, DRAGEN allows customers to analyze NGS data at unprecedented speeds with extremely high accuracy and unwavering dependability.

Uncorking the big data bottleneck with DRAGEN

In contrast to conventional CPU-based systems, which must execute lines of software code to perform an algorithmic function, FPGAs implement algorithms as logic circuits, providing an output almost instantaneously. By replicating these logic circuits thousands of times over, DRAGEN is able to achieve industry-leading speeds by allowing for massive parallelism, unlike CPUs, which are limited to running only one task per core. FPGAs are also fully reconfigurable, enabling customers to switch between functions and pipelines within seconds.

As a result, DRAGEN delivers high accuracy while functioning with industry-leading speed, efficiency, and parallelism. DRAGEN can process an entire human genome at 30x coverage in about 90 minutes, as compared to over 30 hours using a traditional CPU-based system, saving customers time and money. DRAGEN’s Genome Pipeline is now available on DNAnexus at a reduced trial rate until October 31, 2017. To sign up for exclusive promotional pricing, visit: https://www.dnanexus.com/edico-trial .