Sentieon on DNAnexus: License-Free Access Through April 7th

Test drive Sentieon’s pipelines on DNAnexus and see how you can achieve faster and more cost-efficient results with equivalent or improved accuracy and consistency

Editor’s Note: This blog post is written by Brendan Gallagher, Business Development Director at Sentieon.

We are excited to officially announce our collaboration with DNAnexus and the availability of our tools on the scalable cloud-based DNAnexus Platform. At Sentieon, we are enabling  precision data for precision medicine by improving upon industry-leading bioinformatics tools. Our suite of secondary analysis tools produce equivalent or improved results while running much faster and more cost-efficient than GATK, MuTect and MuTect2 bioinformatics tools.

For a 2 month period, DNAnexus users will have license-free access to test, validate, and use:

  • DNAseq (BWA + GATK 3.5) – From FASTQ / BAM to VCF
  • TNseq (BWA + MuTect or MuTect2) – From FASTQ to VCF
  • Rapid DNAseq (BWA + GATK 3.5) – From FASTQ to VCF in 1 hour

Register today to take advantage of this time-limited and license-free opportunity to access Sentieon pipelines on DNAnexus! General commercial availability begins April 8th.

Sentieon tools produce equivalent results to GATK/MuTect/MuTect2 suite of tools by using mathematical methods identical to the Broad Institute’s Best Practice Workflow pipeline. Sentieon has improved the efficiency of the computation algorithms and engineered robust software implementations to speed up the pipeline while providing equivalent or improved accuracy and 100% consistency.

Delivering Better  Results

On the same compute infrastructure, Sentieon software is an order of magnitude faster in terms of core-hours, while producing 100% consistent results with no run-to-run difference. Sentieon software does not down-sample in high-coverage regions, enabling rigorous analysis for deep-coverage sequence data. By removing the down-sampling and other run-to-run error sources, Sentieon tools also improve the accuracy and quality of the results.

SPEED

Sentieon DNAseq processes a 30x NA12878 Genome from fastq to gVCF in ~6 hours and 15 minutes on a single 32 virtual core instance on the DNAnexus platform.  Sentieon and DNAnexus are also offering a rapid-turnaround distributed version of the app that can complete a 30x genome in approximately 1 hour while adding minimal additional compute cost.  

In our 2015 white paper comparing DNAseq to then-current GATK version 3.3, we showed that Sentieon DNAseq has a runtime improvement of 20-50x while producing identical results. Download the white paper.

The figure below shows the performance of our current version matching BWA-GATK3.5 on the DNAnexus Platform from FASTQ to VCF:

CONSISTENCY

Sentieon is 100% consistent and has no run-to-run variation You will get the same result every time you run an individual sample.

Sentieon Concordance to GATK – Identical within GATK’s run to run difference

The above figure shows the concordance analysis in our white paper. Over 99.8% of the variant calls produced by GATK 3.3 and Sentieon DNAseq were identical. After removing the differences from GATK downsampling, the variant calls were over 99.99% concordant. Learn more.

The same concordance performance is maintained in our current DNAseq version as compared to GATK3.5.

COST

With Sentieon, you can process a 30x genome from FASTQ to VCF for the previous price of an exome.  DNAseq costs 5x less for whole exome sequencing (WES) and 7x less for whole genome sequencing (WGS) than GATK3 run on the DNAnexus Platform.  For cost comparison purposes, please contact sales@dnanexus.com.

But don’t take my word for it.

Sentieon has been a top performer in many independent studies, and  last year, we were recognized for accuracy and consistency in the precisionFDA community challenges: precisionFDA Consistency Challenge and precisionFDA Truth Challenge.

Furthermore, Sentieon software enables large cohort joint calls with tens of thousands of whole genomes without intermediate file merging, enabling much easier and much more efficient population-scale studies.

So go ahead, register here to try it out, and let us know what you think. 

Email me anytime at brendan.gallagher@sentieon.com or talk to the DNAnexus team. 

This is the start of a nice partnership as DNAnexus and Sentieon will continue to collaborate on the acceleration and improvement of genomic analysis by providing our customers with the most accurate and cost-conscious tools. We look forward to expanding the tools available on DNAnexus in the future.

Salute! Nexus Negronis On Us at AGBT!

The DNAnexus team is gearing up for the biggest genomics party of the year: AGBT. This annual meeting brings together leaders in the field of genomics to network and share the latest advances in cutting edge sequencing technologies, analytical approaches for genomic studies, and groundbreaking new discoveries.

If you’re headed to Hollywood (Florida), we invite you to visit DNAnexus, any time, in our Hospitality Suite (#218) where you can rub elbows with your colleagues and ask our team about the far-reaching applications and powerful network effect of our secure and collaborative platform. And don’t worry about whetting your whistle, we have you covered.  We’ll be serving our signature Negroni cocktails.

If you find you want to spend even more time with the DNAnexus team, you have many opportunities, including these other great events:

Bites & Insights: Collaborative Genomics at Scale
Tuesday, February 14th, 5:15pm

Join us Tuesday night to share bites and insights with Rady Children’s Hospital and Baylor College of Medicine, two research rock stars performing collaborative genomics at scale. Refreshments will be provided.

  • Scaling the World’s Fastest  Clinical Whole Genome Pipeline for Pediatric Clinical Care
    Narayanan Veeraraghavan, Ph.D., Rady Children’s Hospital
  • eMERGE: Clinical & NIH Data Commons
    Eric Venner, Ph.D., Baylor College of Medicine

Passport Party
Tuesday, February 14th, 9:30pm -11:30pm

Make your way to the DNAnexus suite to get your passport stamped and sample our signature AGBT cocktail: the Nexus Negroni!

Sentieon Coffee Breaks: A Better Alternative to GATK
Tuesday, February 14th, 10:30am-11:00am and
Wednesday, February 15th, 10:20am -10:55am

Learn how Sentieon’s variant discovery pipelines improve upon BWA, GATK, MuTect, and MuTect2 to deliver results 20-50x faster, while reducing costs by 5-7x. Try it license-free for a limited time on DNAnexus.

Can’t make it to one of our events? Email us (info@dnanexus.com) to schedule a 1:1 meeting ahead of time.

We look forward to seeing you in the Sunshine State!

Collaborative Genomics: Highlights From 2016

This has been a remarkable year for DNAnexus and the genomics industry at large. As 2016 comes to a close, we celebrate the year’s accomplishments, and everyone who contributed to its successes.

The past 12 months were jam-packed with innovative research, strategic partnerships, platform enhancements, productive meetups, and plenty of conferences. Here are some of our favorite highlights from 2016!

  • In that vein, we are humbled to have contributed to a wide range of efforts with the goal of working together to advance precision medicine. We kicked off the year by powering a collaborative breast cancer study by the National Comprehensive Cancer Network. Researchers from 14 different institutions worked together to identify potential therapies for a patient with metastatic triple-negative breast cancer — an unprecedented level of collaboration as a result of leveraging the DNAnexus Platform.
  • We also celebrated the one-year anniversary of President Obama’s Precision Medicine Initiative (PMI) with the first PMI Summit. This set in motion much of our year to come, particularly our work delivering the precisionFDA platform, an important component of the President’s PMI. PrecisionFDA, a Bio-IT World Best Practices award-winning program, was designed to leverage community participation to advance regulatory science for next-generation sequencing assay evaluation. 

Highlights of precisionFDA’s initiatives this year included three challenges with the goal of engaging and sharing data to improve DNA test results. Community members had the opportunity to test pipelines, discuss best practices, and add software to the precisionFDA platform. These challenges were wildly successful, and garnered a great amount of community involvement.

  • We would be remiss not to mention the powerful insights coming out of the Geisinger and Regeneron collaboration, powered by DNAnexus. De-identified EMR data from Geisinger’s MyCode Community Health Initiative is integrated with whole exome sequencing data from these same patients. The power of this joint approach was apparent in a paper published in the New England Journal of Medicine, revealing a genetic variant that appears to result in reduced levels of triglycerides and a lower risk of coronary artery disease. As the partnership continually adds more patients with associated EHR data and sequenced exomes, the power of these studies will only increase. Learn more about the program in this Mendelspod podcast.
  • To further move the needle on cancer research, Singapore-based POLARIS (Personalized OMIC Lattice for Advancing Research and Improving Stratification) began using DNAnexus to enable a series of genomic tests for cancer. These include gastrointestinal and solid tumor cancer tests, which are part of a systematic effort to develop a framework for omics-based tests within Singapore.
  • M2Gen also adopted the DNAnexus Platform to support data data analysis and collaboration for the Oncology Research Information Exchange Network (ORIEN) Avatar Research Program. This innovative program joins academic cancer centers and pharmaceutical companies in their efforts to study and treat cancer through the development of more precise treatments for patients.
  • In addition to powering POLARIS and ORIEN, DNAnexus reanalyzed The Cancer Genome Atlas (TCGA) dataset. TCGA is a joint effort between the National Cancer Institute and National Human Genome Research Institute, and includes data from 10,487 patients across 33 cancer types. This reanalysis project was a massive undertaking, whereby during a four-week period, approximately 1.8 million core-hours of computational time were used to process 400 TB of data — a testament to the scalability of the DNAnexus Platform.
  • A number of partnerships were announced to further build out DNAnexus as a seamless end-to-end solution for genome analysis. The integration of the DNAnexus Platform with Sapio Science’s Exemplar Next Generation Sequencing Laboratory Information Management System (LIMS) enables laboratory management and informatics solutions in the cloud. We also partnered with SolveBio to provide access to their curated data analysis services, offering a rapid and secure progression from data analysis through interpretation. Finally, Genomics plc entered into a collaborative effort with DNAnexus to break down the barriers for population-scale sequencing analysis.
  • Together with PacBio, we worked to simplify structural variant discovery and decrease barriers to de novo assembly. As PacBio’s cloud bioinformatics partner, we are able to support researchers working with long-read sequencing data. Through this effort, the SMRT Analysis Suite v3.1.1 has been optimized for the cloud environment and is available on the DNAnexus Platform. Other long-read analysis tools, such as PBHoney, PBJelly, and the Parliament are also optimized for use on the platform.

A particularly exciting development in the realm of long-read sequencing was the release of the first public Sequel dataset of NA12878, demonstrating you don’t need expensive high-fold coverage to discover novel structural variants. The Sequel System is faster, half the cost, and provides higher throughput, delivering around 7 times the amount of data as the PacBio RS II. These added benefits will hopefully make long-read sequencing available to a broader audience.

  • Finally, from a corporate perspective, DNAnexus also had some serious wins. Our team  nearly doubled in 2016 to keep up with the ever-increasing activity from our customers, and to keep pace with the burgeoning genomics industry. We couldn’t be more fired up about the growth of our team!

Special thanks to all our customers, partners, and collaborators for contributing to another amazing year filled with exciting milestones. We’re delighted by the developments within the genomics industry, and look forward to 2017 with excitement and inspiration.

What is your favorite memory from 2016? Let us know on Twitter. #Genomics16