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.

DNAnexus at ASHG: Elevating Translational Informatics

ASHG Logo

We are gearing up for the annual American Society of Human Genetics (ASHG) meeting next week in San Diego, and are especially excited to debut our new ApolloTM platform for multi-omic and clinical data science exploration, analysis, and discovery. ApolloTM provides translational researchers with a scalable cloud environment, flexible data models, intuitive analysis and visualization tools to simplify research workflows for R&D teams globally and dramatically improve the efficiency of research organizations.

Visit DNAnexus in booth 622 to learn more about how to leverage our newApolloTM to inform decision making, save time, and maximize value at each step of the drug discovery process. Stop by our booth anytime during the conference, or email us to schedule a meeting with a member of our science team.

Lunchtime Talk:

Leveraging Translational Informatics for the Advancement of Drug Discovery & Improved Clinical Outcomes

Thursday, October 18th, 12:30pm – 1:45pm
San Diego Convention Center, Upper Level, Room 30E

Join us to learn how biopharma customer MedImmune and academic medical center, Baylor College of Medicine’s Human Genome Sequencing Center are leveraging massive volumes of biomedical data to gain better insights into biological, environmental, and behavioral factors that influence health.

Speakers:

  • Medimmune LogoDavid Fenstermacher, PhD, Vice President R&D & Bioinformatics, MedImmune
  • Will Salerno, PhD, Director Genome Informatics atBaylor College of Medicine Human Genome Sequencing CenterHGSC Logo
  • Brady Davis, VP Strategy, DNAnexus  

Lunch will be provided; RSVP to reserve your spot!

Activities in DNAnexus Booth 622:

Visualization Hour – Come Explore GWAS data in 3-D, using virtual reality!

Human brains are wired for spatial reasoning, making virtual reality a potentially powerful way for scientists to achieve an intuitive understanding of data. To test VR on genomic data, we combined two iconic visualizations in genomics, the Manhattan plot and the circos plot, into a fully immersive data exploration experience called BigTop. Come explore the GWAS circus with us and learn about other exciting visualization projects at DNAnexus!

  • Wednesday, 10/17, 12-1pm
  • Thursday, 10/18, 12-1pm
  • Friday, 10/19, 12-1pm

Translational Informatics Hour – Elevating Translational Informatics

Come demo the new DNAnexus ApolloTM and hear how biopharma customer MedImmune is using it to inform decision making, save time, and maximize value at each step of the drug discovery process.

  • Wednesday, 10/17, 2-3pm
  • Thursday, 10/18, 2-3pm
  • Friday, 10/19, 2-3pm

Meet the xVantage Group

Come meet members of xVantage Group, a dedicated team with deep technical and scientific expertise, ready to create innovative and tailored solutions for customers and partners. From data ingestion to pipeline and software development, learn more about the broad range of services and customers xVantage is supporting.

  • Wednesday, 10/17, 10-11am
  • Thursday, 10/18, 10-11am

Customer Talks:

Wednesday, October 17th
Time Title Speaker Location
5:30 PM Sequencing of whole genome, exome and transcriptome for pediatric precision oncology: Somatic variants and actionable findings from 253 patients enrolled in the Genomes for Kids study Scott Newman, St Jude Children’s Research Hospital Session #25 – Integrated Variant Analysis in Cancer Genomics; Ballroom 20BC
6:15 PM Structural variation across human populations and families in more than 37,000 whole-genomes Will Salerno, Human Genome Sequencing Center, Baylor College of Medicine Session #33 – Characterization of Structural Variation in Population Controls and Disease; Ballroom 20A

Posters Featuring DNAnexus:

Wednesday, October 17th
2:00pm-3:00pm
Poster Number Title Affiliation
PgmNr 1761 Variant identification from whole genome sequencing at the UPMC Genome Center UPMC Genome Center
3:00pm-4:00pm
Poster Number Title Affiliation
PgmNr 1998 Hi-C-based characterization of the landscape of physically interacting regions and interaction mechanisms across six human cell lines using HiPPIE2. University of Pennsylvania, DNAnexus
PgmNr 1554 A high-quality benchmark dataset of SV calls from multiple technologies Illumina, Baylor College of medicine
PgmNr 3186 Identification of novel structural variations affecting common and complex disease risks with >16,000 whole genome sequences from ARIC and HCHS/SOL. Human Genetics Center, University of Texas Health Science Center, Baylor College of Medicine HGSC, Albert Einstein College of Medicine, DNAnexus, Fred Hutchinson Cancer Research Center, University of Washington, Johns Hopskins University

 

Thursday, October 18th, 3:00pm-4:00pm
Poster Number Title Affiliation
PgmNr 1222 Novel mutations of SCN9A gene in patient with congenital insensitivity to pain identified by whole genome sequencing. Intermountain Healthcare
PgmNr 1648 How well can you detect structural variants: Towards a standard framework to benchmark human structural variation. NIST, NHGRI, Genome in  a Bottle Consortium Baylor College of Medicine HGSC, PacBio, Spiral Genetics, NCBI, BioNano Genomics, 10x Genomics, Max Planck Institute, USC, Boston University Medical School, DNAnexus, Joint Initiative for Metrology in Biology

 

Friday, October 19th, 2:00pm-3:00pm
Poster Number Title Affiliation
PgmNr 1439 Are we close to constructing a fully diploid view of the human genome? DNAnexus
PgmNr 1505 How well can we create phased, diploid, human genomes? An assessment of FALCON-Unzip phasing using a human trio. DNAnexus
PgmNr 2732 A population genetics approach to discover genome-wide saturation of structural variants from 22,600 human genomes Center for Integrative Bioinformatics Vienna, University of Vienna, Baylor College of Medicine HGSC

Integrating Multiple Data Sources to Power Discovery and Analysis

Precision Medicine World Conference (PMWC) took place in January in Mountain View, California, and offered attendees the opportunity to learn about innovative technologies, initiatives, and clinical case studies that are catalyzing the adoption of precision medicine in the clinic. DNAnexus was pleased to host a panel to discuss scalable infrastructure/platforms integrating next-generation sequencing (NGS) and other data (e.g. phenotypic) to power discovery and analysis in pharma and the clinic. Learn more below and watch the panel discussion.

Moderator: DNAnexus, Brady Davis, Chief Strategy Officer

 

Panelists:
AstraZeneca/MedImmune – David Fenstermacher, VP BioInformatics

Sutter Health – Greg Tranah,  Director, CPMC Research Institute, Adjunct Professor Dept. of Epidemiology & Biostatistics, UCSF

 Carol Franc Buck Breast Cancer Center at UCSF– Laura Esserman, Director

City of Hope – Sorena Nadaf, SVP & CIO

 

Abstract:

Health care providers increasingly require multi-omic datasets, including phenotypic data informed by genomic data. Such data needs to be obtained in an economically sustainable way and made available on an agile user-friendly platform so that these data may inform clinical care and lead to health improvements.

Pharmaceutical companies are interested in obtaining datasets containing phenotypic/clinical and genomic information generated from patient cohorts of specific disease areas. Such datasets can help pharma researchers identify drug targets or find biomarkers, validate hypotheses related to the interaction of genomics with disease or with specific therapies, and identify candidate populations for future clinical trials. Payers are also interested in the outcomes related to new discoveries and therapies in order to reimburse for these treatments.

This discussion focuses on how healthcare provider organizations, pharmas and payers are working toward solving these complex and challenging problems from a technical and business model perspective.