Countdown to AGBT 2018

We can’t wait for the annual Advances in Genome Biology and Technology (AGBT) meeting, taking place February 12-15 in Orlando! We are excited to join hundreds of industry leaders in the sunshine to exchange ideas about the latest advances in DNA sequencing technologies, new approaches to leveraging multi-omic datasets, and their widespread applications in healthcare.

If you’re headed to AGBT, join us for coffee (or a cocktail!) and discussion on how the DNAnexus team can work with you to integrate multi-omic data into your research, discovery, and development pipeline. Email us to schedule a meeting.

DNAnexus Events

Passport Party

Tuesday, February 13th 9:00pm-11:00pm  
Hilton Suite #1865  

Stop by our suite Tuesday night during the Passport Party to celebrate novel scientific developments at DNAnexus from deep learning applications to leveraging multi-omic data in research and development.

Posters

Poster #117: Dot: A New Interactive Dot Plot Viewer for Comparative Genomics
Presenter: Maria, Nattestad, PhD, Scientific Visualization Lead
Presentation Time: Tuesday, February 13th, 1:00pm-2:30pm

Comparing genome assemblies to genomes of related species is crucial to understanding differences between organisms across the tree of life. Dot plots are excellent tools to visualize genome-genome alignments, however traditional dot plots are static images that limit detailed investigation. We are excited to present Dot, our interactive dot plot viewer that enables scientists to visualize genome-genome alignments in order to evaluate new assemblies and perform exploratory comparative genomics.

Poster #105: How Well Can We Phase the Diploid Human Genome Using FALCON-Unzip?
Presenter: Chai Fungtammasan, PhD, Scientist  Presentation Time: Tuesday, February 13th, 1:00pm-2:30pm

Long read sequencing technology has allowed researchers to create de novo assemblies with impressive continuity, which has increased the number of reference genomes available. As a roadmap to personal genome assembly and phasing, we assess the phasing accuracy of FALCON-Unzip in human using trio information. We performed a de novo assembly of the son in the Ashkenazi trio using the data from Genome in a Bottle Consortium, concluding that the FALCON-Unzip algorithm can be used to create the long and accurate haplotype for human, and characterizes the underperformed area for future improvement.

Poster: A CLIA NGS Visual Process Monitoring for QC and Analytical Evaluations
Presenter: David Ross, CareDx

Visual data analytics (VDA) are powerful tools to efficiently develop, implement and monitor processes. VDA can rapidly provide deep analytic capabilities. We detail how VDA tools help evaluate and monitor our clinical-grade NGS assay. This assay, AlloSure®, is for the detection of donor-derived cell-free DNA (dd-cfDNA) to measure transplanted organ injury. A higher percentage of dd-cfDNA is indicative of active rejection of the allograft. The bioinformatic pipeline for the analysis is uploaded from MiSeqs into DNAnexus and then result files are downloaded to local database systems for QC, result presentation to the CLIA lab and further cross-functional analysis. Much of the cross-functional analysis and data exploration i accomplished in Tableau. The Tableau workbooks facilitate analysis of development QC, and assay status. The flow of information is immediate, visual and purpose-built for the user group and individual.

Talks Featuring the DNAnexus Platform

Joint Variant Calling on >200,000 Exome Sequences with GLnexus  
Presenter:
Mike Lin, PhD, VP Research & Development, DNAnexus

Date/Time: Tuesday, February 13th, 7:30pm-7:50pm
Track: Computational Biology

Abstract

The vast human cohorts now being sequenced present increasing opportunities for improved genetic variant discovery by leveraging information from a whole cohort to refine conclusions about each individual. We consider the problem of joint calling, where Genomic Variant Call Format (gVCF) data, representing initial variant calls for single samples, are evaluated together to generate a multi-sample project VCF (pVCF). The pVCF provides a matrix of refined and harmonized variant calls for the whole cohort, informed by allele frequencies and error patterns observed therein. In contrast to initial gVCF generation, which is readily parallelized across samples, joint calling into pVCF presents acute scale and representation challenges for modern population sequencing projects. This is done using our new system for joint calling on large cohorts, called GLnexus.

Structural Variation Across Human Populations and Families in >23,000 Whole-Genomes 
Presenter: Will Salerno, PhD, Human Genome Sequencing Center, Baylor College of Medicine  
Date/Time: Tuesday, February 13th, 3:00pm-3:20pm
Track: Plenary Session

Abstract

While the impact of small variation in well-characterized genomic regions is still being realized, it is clear that clinical-quality understanding of the full spectrum of genetic disease requires accurate assessment of large, complex variants across the entire genome for populations that span phenotypic space, including gender and ethnicity. Such structural variants (SVs) pose specific challenges with respect to detection accuracy, validation, allele reconciliation and the cost of these methods. Here we address these challenges and present the aggregation of multiple SV methods applied to whole-genome sequencing across a large human population and families.

dd-cfDNA, a Transplant Biomarker in Clinical Diagnostics – From Discovery to Clinical Practice  
Presenter: Marica Grskovic, Associate Director, R&D, CareDx
Date/Time: Thursday, February 15th, 3:30pm-3:50pm
Track: Plenary Session

PMWC 2018: Leveraging Multi-Omic Datasets in Discovery & Clinical Trials

The Precision Medicine World Conference kicks off next week at the Computer History Museum in Mountain View, California. The program traverses innovative technologies, thriving initiatives, and clinical case studies that enable the translation of precision medicine into direct improvements.

Please join us for a lively panel discussion around scalable infrastructure/platforms that integrate next-generation sequencing (NGS) and other data (e.g. phenotypic) to power discovery in Pharma and the clinic.

Title: Scalable NGS Infrastructure/Platforms
Talk Details: Track 1 – Monday, January 22 at 10:30am
Moderator: Brady Davis, Chief Strategy Officer, DNAnexus

Panel Speakers:

  • 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 (“Pharmas”) 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 session will focus on how both healthcare provider organizations, Pharmas and Payers are working toward solving these complex and challenging problems from a technical and business model perspective.

 

PAG 2018: A Focus on Genome Assembly

The DNAnexus team is headed to San Diego, January 13-17, for the largest gathering of Ag-Genomics scientists in the world! The International Plant & Animal Genome Conference brings together over 3,000 leading genomic scientists in plant and animal research to discuss recent advancements, ongoing projects, and future studies in the field. Learn more about PAG and register here.

Visit DNAnexus in booth #431 to learn how we can be your partner for complex genome assembly, structural variation analysis, and physical mapping to achieve complete and accurate views of all types of genomic variation. Join our activities listed below, or email us to schedule a member of our team at the conference.

Demo Hour with PacBio

Transforming De Novo Assembly
Tuesday, January 16th, 10:00am-10:30am
DNAnexus Booth #431

Stop by our booth to learn how to leverage PacBio’s FALCON and FALCON-Unzip tools on DNAnexus for streamlined genome assembly. Bioinformaticians from PacBio and DNAnexus will be available to answer questions.

DNAnexus Workshops

The Data Backbone for the Vertebrate Genome Consortia
Tuesday, January 16th, 1:30pm-3:40pm
Sunset – Meeting House

Brett Hannigan, PhD, Director of Scientific Partnership, will discuss how the Vertebrate Genomes Project at the Sanger Institute leverages DNAnexus to access approved tools, pipelines, and datasets generated by the consortia.

An Interactive Dot Plot Viewer for Comparative Genomics
Wednesday, January 17th, 11:45am-12:00pm
Digital Tools and Resources Program – California Room

Maria Nattestad, PhD, Scientific Visualization Lead, will debut Dot, our interactive dot plot viewer that enables scientists to visualize genome-genome alignments in order to evaluate new assemblies and perform explorative comparative genomics.

Dot will also be presented as a poster (PO104) Monday, January 15th from 10:00am-11:30am in the Grand Exhibit Hall.