Webinar Series: Enabling PacBio Long-Read Bioinformatics in the Cloud

We are excited to be hosting, in collaboration with our partner PacBio, an inaugural webinar series focused on best practices for analyzing SMRT® Sequencing data.

De novo genome assembly and structural variant calling are complex tasks, which can require massive computational resources to weave long-reads into a final, polished assembly or run a variety of SV detection methods across multiple data types. Reference genome assembly is done far less frequently than whole genome sequencing, just as the case with SV detection vs. SNP detection.  DNAnexus and PacBio are collaborating to make tools and resources easily accessible and enabling researchers to take long-read bioinformatics to new heights. Learn about today’s best practices for PacBio sequencing data.

Session 1: Rapid Reference-Quality Genome Assembly
May 4, 2016
8:00am PST, 11:00am EST, 5:00pm CET

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Brett Hannigan, PhD, Director, Scientific Partnerships at DNAnexus, will present how running FALCON on the DNAnexus Platform can provide a fast, accurate, and cost-efficient solution for de novo genome assembly. In this webinar, we’ll examine the challenges around assembling the tobacco genome (comprised of 4.5 billion base pairs), which is tetraploid in nature and highly repetitive.

Session 2: Simplifying Structural Variant Discovery
June 16, 2016
8:00am PST, 11:00am EST, 5:00pm CET

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AndrewAndrew Carroll, PhD, Vice President, Science at DNAnexus will present how current solutions that use PacBio data can greatly improve the accuracy of SV-calling by using fast and easy to run cloud-optimized apps (PBHoney, Parliament, & Sniffles). We will also explore the current work we are doing with Genome in a Bottle (GIAB) to develop high confidence truth sets for structural variants. Finally, Andrew will discuss how sequencing coverage correlates with the ability to accurately call structural variants, to inform decisions about the ideal depth to sequence.

Who should attend?
Researchers currently working with or those who desire to work with PacBio RSII and/or Sequel data.

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.

Precision Medicine from Birth

Tute 2How many lives could be saved or significantly improved if precision medicine began at birth? Tute Genomics is aspiring to answer this question. Yesterday, Tute announced that they are working with Newborn Screening Ontario (NSO), part of the Children’s Hospital of Eastern Ontario (CHEO), to establish new next-generation sequencing (NGS) testing capabilities in Ontario, Canada. Tute, a leading genome annotation and interpretation platform, provides clinical sequencing informatics and interpretation to deliver meaningful reports of a patient’s full genomic profile to researchers and clinicians. Tute is providing its clinical customers, like Newborn Screening Ontario, with an end-to-end solution – taking raw sequence data through genome interpretation in a single step – DNAnexus is proud to be a part of that solution.

NSO 2NSO operates one of the largest and most modern newborn screening programs in the world.  In the past decade, NSO has tested more than one million newborns for serious but treatable rare diseases, making it the highest volume molecular lab in Canada. Working in conjunction with Tute, organizations like NSO can easily perform best practice data analysis in a single environment, avoiding the hassle of transferring large datasets between analysis and interpretation platforms, or deploying costly local solutions.

Tute is passionate about making genomics more accessible to healthcare providers and scientific researchers in order to advance precision medicine. Through integration with the DNAnexus Platform, Tute offers its customers upstream primary and secondary analyses and downstream interpretations in a seamless fashion. The NSO’s new genetic testing project is a perfect end-to-end example, connecting sequencing instruments, LIMS (UNIConnect), downstream clinical reporting software and report delivery.   Ultimately, these Tute employed services will help make medical intervention and care decisions faster and more effective for newborns suffering from genetic illness.

Email us directly to learn how DNAnexus can help data interpretation tool providers operate in a secure, compliant, and scalable platform on which they can deploy and expand their product portfolios.