Benchmark and Advance Computational Methods for Targeted Strain Detection

The second Mosaic Community Challenge: Strains #2 is now live! 

In order to develop biotherapeutic products that are based on live strains of commensal bacteria, we need to be able to accurately detect and track how these product strains perform in patients after they are administered. Being able to accurately detect specific strains, given that there may be closely related strains in the sample, is the first step towards characterization of biotherapeutic products in terms of their dosage and efficacy.

Strains Challenge #2 is a slightly different problem than the first Strains Challenge. Strains #1 is looking at advancing methods to profile a sample at the strain-level, whereas Strains #2 is a targeted study to track the presence of certain known strains in a sample. Learn more and sign up to participate here.

Webinar: Introduction to Strains #2 Challenge 

Date: Wednesday, February 21st
Time: 10:30am PST (1:30pm EST)

Join us for an introduction to the Strains #2 challenge, and hear the challenge sponsors discuss how you can participate and contribute to the improvement of strain-level microbial analysis.

Tri-Con 2018: Leveraging the Cloud to Power Multi-Omics Research

The Molecular Medicine Tri-Conference kicks off next week in downtown San Francisco. Bringing together over 3,700 attendees, Tri-Con is one of the world’s leading international events in the field of drug discovery, development, and diagnostics. The program is fully-loaded with presentations highlighting advancements in cancer research, big data, molecular diagnostics, precision medicine, rare disease, human microbiome, and more.

Please join us for our presentations during the Converged IT & The Cloud program and the Microbiome-Based Precision Medicine Symposium. Can’t make it to our talks? Email us to schedule a meeting with a member of our team.

Title: The Infrastructure Requirements for Geno-Pheno Analysis on a Massive Scale
Speaker: Omar Serang, Chief Cloud Officer, DNAnexus
Talk Details: Monday, February 12th at 3:55pm – Moscone South Convention Center
Program: Converged IT & The Cloud

Abstract:

Learn how Biopharmas are delivering on the promise of precision medicine by leveraging genomics in R&D. A comprehensive security and privacy framework is required to provide auditability, data immutability and versioning to reproduce research. Learn about the necessary infrastructure to scale geno-pheno analysis, while maintaining stringent security and compliance controls.

 

Title: Mosaic, a Cloud-Based Community Platform for the Acceleration of Translational Microbiome Science
Speaker: Michalis Hadjithomas, Microbiome Lead, DNAnexus
Talk Details: Thursday, February 15th at 12:15pm, Hilton San Francisco – Union Square
Program: Microbiome-Based Precision Medicine Symposium

Abstract:

Mosaic provides a collaborative space where researchers can implement and compare microbiome methods through community challenges. The “Strains” series of challenges encourages the improvement of strain-level performance of bioinformatic tools. “Standards” addresses experimental and computational sources of variability in metagenomic analyses to promote accurate and reproducible NGS-based microbiome profiling. Learn more and get started at http://mosaicbiome.com/.

 

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