Discussing the State of Biomedical Data & Looking Towards the Future at PMWC

DNAnexus once again attended the Precision Medicine World Conference (PMWC) in January in Santa Clara, California, to learn about new innovative technologies, thriving initiatives, and clinical case studies that enable the translation of precision medicine into direct improvements in health care.

George Asimenos, Chief Technology Officer, hosted a panel discussing the challenges in applying AI on biomedical data and the future of using AI in regulated contexts. Brady Davis, VP Strategy and Marketing, also moderated a discussion on the future of DNA sequencing interpretation, touching on how visualizations are driving the understanding of human genomes & diseases.

You can view the recorded panel discussions below:

Challenges In Applying AI On Biomedical Data

Challenges in AI Panel

Moderator: George Asimenos, PhD, CTO, DNAnexus

Panelists:

  • University of Washington, Paul G. Allen School of Computer Science & Engineering – Su-In Lee, PhD, Associate Professor
  • UCSF, Helen Diller Family Comprehensive Cancer Center – Laura J. van’t Veer, PhD, Leader, Breast Oncology Program, and Director
  • Regeneron Genetics Center – Jeffrey Reid, PhD, Head of Genome Informatics

Abstract:

AI methods promise to revolutionize the way we approach medicine, by building and training models that make accurate predictions. But the application of AI in actual biomedical contexts comes with distinct challenges. This session features speakers in the forefront of real-life AI applications, who will discuss challenges such as how to reach an interpretable/explainable AI model and how to apply AI in a regulated context.

Data Curation, Integration and Visualization

Data Curation Panel

Moderator: Brady Davis, VP Strategy and Marketing, DNAnexus

Panelists:

  • Stanford University, Department of Genetics – J. Michael Cherry, PhD, Professor
  • AncestryDNA – Eurie Hong, PhD, Senior Director of Genomics
  • UC Santa Cruz Genomics Institute – Benedict Paten, PhD, Assistant Professor

Abstract:

Understanding the relationship between the millions of functional DNA elements and their protein regulators, and how they work in conjunction to manifest diverse phenotypes, is a key to advancing our understanding of the human genome and diseases. As the cost of DNA sequencing continue to drop, the interpretation of the ever increasing amount of data generated represents a considerable challenge.

See our Talk at HiMSS 2019 – Integrating Clinico-Genomic Data for Precision Health

We’ve landed in Orlando and are ready to enjoy our time at the annual HiMSS Global Conference! In addition to 45,000 other healthcare professionals attending, we are taking the full opportunity of the sun to discuss and discover new ways to utilize information and technology to accelerate healthcare insights. Learn more about the HiMSS Conference.

Join us at the Amazon Web Services Booth #5058 where we will be presenting how population-scale data collection initiatives are pioneering new frontiers in precision medicine, while simultaneously bringing about new challenges on integration of diverse datasets and extraction of high-impact insights. Researchers must overcome the complexities of datasets including multi-omic and clinical data securely and at scale.

We will discuss the recently launched DNAnexus Apollo™, a scalable cloud platform, with flexible data models and intuitive analysis & visualization tools that eliminates the complexities many researchers face, enabling integration of big data, driving to actionable insights and rapid discovery. Additional topics covered:

  • Success in powering precision medicine
  • Trends shaping the future of healthcare
  • Showcase multi-omic & clinical data science exploration, analysis, & discovery
  • How cloud-based data analysis and secure collaboration drive scientific discovery
Integrating clinico-genomic data for precision health

Aniket Deshpande, Science Lead

Tuesday, February 12 at 4:30pm

AWS Booth #5058

                   Aniket Deshpande

Leveraging the trusted best-in-class DNAnexus security and privacy framework, including HIPAA, CLIA, GxP, and FedRAMP compliance DNAnexus Apollo™ was designed to seamlessly integrate and analyze diverse datasets, including multi-omic & clinical data, driving actionable insights in real time. DNAnexus Apollo™ is currently powering large-scale geno/pheno projects, including the RGC UK Biobank Consortium Data Delivery — one of the largest population-scale projects containing exome sequencing results and clinical data from 500,000 individuals.

Find us at the talk or schedule a meeting with a member of our team.

PAG 2019: Pioneering Frontiers in Genome Assembly

DNAnexus is headed to San Diego! We’re excited to join over 3,000 leading genomic scientists in plant and animal research for the 27th International Plant & Animal Genome Conference, taking place January 12-16. The conference exhibition and symposium brings the community together to discuss recent advancements, ongoing projects, and future studies in the field. Learn more and register for the conference here.

Come by Booth #227 to learn about our exciting genome assembly projects, including the Vertebrate Genomes Project and the new maize population assembly involving 26 cultivars, and how DNAnexus can partner with you for fast, accurate, and cost-efficient reference-quality assembly. Join us for our activities listed below or schedule a meeting with a member of our team.

DNAnexus Talks

Jason ChinDeveloping Deep Learning Models and Reusable Machine Learning Workflows for Genomics in the Cloud: From Single Cell Images to Variant Effects
Saturday, January 12, 8:50am – 9:05am
Location: California Room

Jason Chin, PhD, Senior Director of Deep Learning at DNAnexus, discusses how new advances in machine and deep learning are being leveraged to perform large-scale alignments, variant calling and more efficiently process plant and animal genomes. Jason will focus specifically on how utilizing Docker, Conda and JupyterLab simplifies interactive and reproducible research workflows.

Chai FungtamassanPragmatic Solutions for Scaling your Analysis: Machine Learning, Imaging, Containers, Clouds and APIs
Monday, January 14, 4:00pm – 5:30pm
Location: Towne Room

Join Arkarachai Fungtammasan, Ph.D. (Chai), DNAnexus Scientist at this workshop centered around popular toolkits for machine learning. The session includes a guided tutorial on PyTorch and includes free-form discussion and Q&A.

Sam WestreichExploring a Landscape of Genetic Variation in Virtual Reality
Wednesday, January 16, 12:00pm – 12:15pm
Location: California Room

Sam Westreich, PhD, DNAnexus Microbiome Scientist, will showcase BigTop, a fully immersive data exploration experience that uses virtual reality to examine genomic data. Sam will demonstrate how scientists can use the open source to view multiple supported datasets.

Customer Talks

Iowa StateAssembly and Comparative Genomic Analysis of the Maize NAM Founders
Speaker: Matthew B. Hufford from Iowa State University
Sunday, January 13, 8:40am – 9:00am
Location: Golden West Room

Whole Genome Assembly and Annotation of the Maize NAM Founders
University of GeorgiaTuesday, January 15 at 2:30pm – 2:42pm
Location: California Room

Kelly Dawe, PhD, & Jianing Liu from Dawe Lab at the University of Georgia will discuss how their study sequencing and assembling the complex and genetically diverse maize genome. The team utilizes PacBio, BioNano and Illumina sequencing to assembly the B73 maize inbred genome and along with 25 other maize inbreds. The talk is part of the Gramene workshop examining community approaches for improving structural annotations of genes and transposable elements.

VGPVertebrate Genome Project (VGP) / Genome 10K (G10K) Planning Meeting
Wednesday, January 16 at 9:30am – 3:30pm
Location: Sunrise Room

Join the planning session dedicated to coordinating efforts for upcoming VGP & G10K projects. The workshop is open to all PAG attendees, so come learn how to join the effort to generate reference-quality genome assemblies of all 66,000 extant vertebrate species.