ACMG: A Look at Applying Genomic Data to Clinical Reports

The annual American College of Medical Geneticists (ACMG) conference meets this week (March 21-25, 2017) in Phoenix, Arizona, providing an outstanding forum to learn how genetics and genomics are being integrated into medical and clinical practice. Eric Venner, from the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine, will present the following poster (Abstract Number 368): Generating Clinical Reports from Genomic Data on the Cloud-based Neptune Platform  on Friday March 24th 10:30AM-12:00PM

In order to meet the demand for timely and cost-efficient clinical reporting, HGSC developed Neptune, an automated analytical platform to sign out and deliver clinical reports. The process starts when a clinical site uploads a test requisition to the HIPAA compliant environment on DNAnexus. Next, de-identified samples are analyzed with HGSC’s variant calling pipeline, Mercury, which feeds into the reporting pipeline, Neptune. Variants of putative clinical relevance are identified for manual review and possible addition to a VIP database of clinically relevant variation. The VIP database currently holds 20,872 SNPs and 3,946 indels, as well as a curated set of copy number variants.

Neptune’s manual review interface was designed with a clinical geneticist in mind. Users can login, curate variants in their samples, update the VIP database accordingly and create clinical reports. Early applications include reporting for the NIH Electronic Medical Records and Genomics (eMERGE) Network III where more than 14,500 samples and a panel of 109 genes will be processed over the course of three years.

eMERGE is a national network that combines DNA biorepositories with electronic medical record (EMR) systems for large scale, high-throughput genetic research to support investigating how personalized treatments impact patient care. Research so far has led to significant discoveries across a wide range of diseases, including prostate cancer, leukemia, and diabetes.  DNAnexus and the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine worked to build the eMERGE Commons, a data repository where genomic data are merged with patient electronic medical records (EMR), as well as analysis results and bioinformatics tools to be accessed and applied by eMERGE researchers.

Countdown to Beantown: DNAnexus at Festival of Genomics

Next week we’ll be at Festival of Genomics in Boston, to join the three-day celebration of all things genomic! The Festival covers a broad range of topics; exploring new research, technology, and groundbreaking advancements in medicine. We’re excited to hear from the stellar lineup of speakers, such as renowned New York Times columnist, Carl Zimmer, providing journalistic perspective from the genome beat, and Diana Bianchi, from Tufts University School of Medicine, discussing prenatal testing in the genomics era. Like all good festivals, we mustn’t forget to take advantage of the full spectrum of attractions, including posters, workshops, exhibitors, technology forums, and more.

We’re particularly excited to showcase how the DNAnexus Platform has been powering precisionFDA. To date, more than 1,500 community members from 600 organizations are using the precisionFDA platform to help shape precision medicine. Members of the precisionFDA team will be at the DNAnexus booth to demo and answer questions about this community platform for NGS assay evaluation and regulatory science exploration.  

The announcement of the winners of precisionFDA’s second challenge, the Truth Challenge, will also be announced at the festival.  Genomic innovators were invited to participate by testing their informatics pipelines on two datasets: the well-characterized Genome in a Bottle’s NA12878 and a new reference sample HG002, of which the results were unknown. Truly a once in a blue moon challenge, the competition was fierce as thirty-five participants from around the world submitted entries. Join us for the announcement and help us congratulate the winners! 

Announcement of the Winners of the precisionFDA’s Truth Challenge
pFDAPresenter: Elizabeth Mansfield, PhD, Deputy Officer Director for Personalized Medicine, OIR/CDRH/FDA
When: Wednesday, June 29th at 9:00am – Main Stage

Additionally, during the Genomic Medicine track, our own Andrew Carroll will speak on the many factors involved when taking genomic data and medical applications global.

Taking Genomic Medicine Worldwide   

Andrew

Presenter: Andrew Carroll, PhD, VP Science, DNAnexus
When: Tuesday, June 28th at 12pm
Where: Genomic Medicine Track

 

 

 

Finally, we have a bevy of activities with DNAnexus and our partners. Check out our full list of booth activities below:


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We hope you join in our excitement as we gear up for the ultimate genomic gathering! Don’t forget to come say hello to the DNAnexus team and receive a demo of the DNAnexus Platform at Booth #240.

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.