DNAnexus is going “virtual”! — Bio IT World 2020

Bio-IT World Virtual Booth

LIVE NOW! Visit the Wicked Smart digital experience: including webinars, expert demos, curated content, and super swag.

When we realized we wouldn’t be able to attend the Boston Bio IT World Conference and Expo in person, we came up with the next best thing: A virtual booth.

Webinars

Explore Millions of Clinico-Genomic Data Points from UK Biobank
April 23, 2020, 10 a.m. PT 

Did you know that another load of whole exome sequencing data will be released by the UK Biobank soon? That’s millions of clinico-genomic data points, in a single dataset. Will you be ready to mine it? This webinar will introduce you to Apollo™ for UK Biobank, an analytics solution purpose-built for researchers looking to explore and analyze genomic and phenotypic data together, at scale – and at lightning speed. You can learn how to explore possible correlations across population-wide genomic and phenotypic data; easily create and compare the genetic and phenotypic features of custom cohorts; investigate characteristics of a cohort of individuals who carry the same genetic variant; and quickly conduct sophisticated, iterative analyses of cohort data using the embedded JupyterLab environment.

Rapid Exploration of Oncology Clinico-Genomic Data from TCGA
May 14, 2020, 10 a.m. PT

Mining large scale multidimensional oncology datasets like the The Cancer Genome Atlas (TCGA) to identify novel diagnostic, prognostic, and treatment response markers remains a huge endeavor for researchers, and easy identification of TCGA cohorts that meet clinical inclusion criteria poses significant challenges to clinician researchers and bioinformaticians.

We can help. Learn how our Apollo platform can enable you to explore expansive TCGA clinical data elements with the Apollo Cohort Browser; identify, compare, and save cohorts of TCGA individuals that meet key phenotypic criteria; and launch detailed analysis of genomic features of TCGA cohorts using the embedded Apollo JupyterLab environment.

Live Demo

Powering Precision Medicine and Targeted Genome-Based Therapies with DNAnexus Titan 
April 28th, 2020, 10 a.m.

Pharmaceutical companies are rushing to unlock the power of next-generation sequencing genomics to advance precision medicine. With the size and scope of research initiatives growing rapidly, pharma is experiencing scalability, reliability, and productivity challenges with their internally-built systems. To handle the higher volumes of multi-omics data and to get more strategic value out of analysis pipelines requires a centralized, cloud-based data analysis solution to fuel scientific advancement.

Join us for an interactive live demo to learn how DNAnexus Titan eliminates bottlenecks in development and production systems with a unified platform that brings data and pipelines together for streamlined analysis. 

Presenters:
Ben Busby, Principal Scientist 
Darren Ames, Solutions Science Director  

White Papers

Want to learn more about compliance in the Cloud? We’ve compiled some useful information about security, privacy and quality for your genomic analysis, as well as how to navigate the odyssey of big genomics in biopharma R&D to deliver genomics-based precision medicine. Explore lots of other handy info sheets that describe our products, use cases and FAQs

Free Stuff

Probably the most popular feature of any conference booth, our digital version doesn’t disappoint, with some wicked smart swag, while supplies last. Fill in a quick survey for your chance to get free tee shirts and/or totes. Totes cool!

Bioinformaticians for Good: DNAnexus Aids in Open Science Collaborations In Fight Against Coronavirus

Sequestered in bedrooms, kitchens, and makeshift office spaces around the world, a virtual army of bioinformatic enthusiasts has banded together to do their bit in the battle against coronavirus.

These data doyens are working behind the scenes to build the tools and infrastructure scientists need to better understand and respond to the virus that is currently ravaging the world. They are helping to overcome current obstacles to research, and they are coming up with brand new solutions to a number of challenges related to drug discovery, development, and delivery.

They are gathering online for “hackathons,” which are essentially grassroots, sprint-like design events in which groups of experts (usually in small teams) compete or collaborate intensively over a number of days to solve technical challenges.

Dozens of hackathons devoted to COVID-19 are being launched worldwide, involving thousands of scientists, including many from DNAnexus.

Principal scientist Ben Busby is helping to coordinate several of the events, a role he is familiar with after helping to organize more than 40 hackathons in his former job as genomics outreach coordinator at NCBI.

Hackathons are great ways to generate new ideas, foster intense learning and facilitate data sharing and collaboration among people who would never have met otherwise, he said.

“And the DNAnexus Platform is a great data integration and collaboration solution, especially since it already has security built in,” Busby said.

COVID-19 Biohackathon

April 5-11, 2020

COVID-19 Biohackathon Logo

Hundreds of scientists and bioinformaticians have already signed up for this week-long event, organized by an international team of established biohackers. 

Using video conferencing, e-mail, Slack messaging, wikis, and source code repositories, teams will work together to address more than 20 topics.

Among them is a project to create a coronavirus “pangenome.” This would involve collecting genomic data for SARS-CoV-2 and the five other types of coronavirus known to infect humans (SARS-CoV, HKU1, NL63, OC43 and 229E), and coming up with data comparison and visualization programs in order to help researchers answer questions like: What virulence factors do SARS and CoV have in common? What proteins influence virulence, and are we likely to see a new strain emerge that is even more virulent?

hackseqRNA: COVID-19 Ultra-hackathon

April 4, May 2, May 22-24

RNAseq Hackathon Logo

In this peer-led hackathon, participants are encouraged to propose projects and organizers will help recruit a team of interdisciplinary RNA biologists, bioinformaticians, statisticians, computer scientists, and developers to turn the idea into a reality.

The hackathon entails one-day coding ‘sprints’ to develop hackseqRNA projects and lay the ground-work for research efforts, followed by a final three-day push to bring each project to completion.

Among the projects to be tackled: Using RNA sequencing data to better understand how coronaviruses react with the immune system, how different drugs work within the system, and whether personalized treatments might be developed based on individual patients’ responses.

Amplifying High Impact Potential Research for Novel Coronavirus

April 4-5

Coronavirus High Impact Research Logo

Organized by the non-profit group Research to the People and Stanford University, this hackathon involves several initiatives, from tapping into wearable devices like FitBit and Apple Watch to track infectious diseases and predict the onset of symptoms, to using computational models to simulate the effectiveness of potential coronavirus therapies.

Busby will be leading a team exploring novel genomics research directions for COVID-19, including the potential for using HLA typing to determine a person’s (or population’s) predisposition to COVID-19 severity. A kind of genetic test used to identify certain variations in a person’s immune system, HLA (short for human leukocyte antigen) typing is currently used to identify which people can safely donate bone marrow, cord blood, or an organ to a person who needs a transplant.

Busby’s team will investigate any correlations between HLA types and an individual’s susceptibility to coronavirus, as well as the severity of their reactions when infected. They may also look at potential epidemiological ramifications based on geographic distributions of HLA types. This research will help to lay the groundwork for the HLA COVID-19 Project.

Seeding New Science

Although the projects may not result in complete, polished solutions, they will help seed new science, which can be just as valuable, Busby said.

“This could be a really good opportunity to think about precision medicine in infectious diseases, something that’s been largely ignored before now,” he added. “Treatments would be way more effective if you knew your immune type. It could also help in the assessment of personal susceptibility and risk.”

Busby also notes that even if the current COVID-19 pandemic subsidies, the virus — or others like it — will likely re-emerge.

“Having responses ready when it does re-emerge would be very helpful, but we have to start now,” he said. “Our contribution to the ‘all hands on deck’ coronavirus call is to build an infrastructure so that we will be able to respond in a much better, far more constructive, way.”

Doubling Down on Next Generation Sequencing: How TwinStrand Biosciences and DNAnexus Work Together

In the majority of cancer patients, the first sign that something is wrong is finding an already well-established tumor. But what if we could detect cancer at the first sign that the immune system is unable to correct it, when there are only a few cancer cells present? This is one of the challenging problems that TwinStrand Biosciences hopes to solve with their error correction technology, Duplex Sequencing™.

While current next generation sequencing (NGS) methods positively impact how we conduct research and discovery and stratify patients into disease categories, they aren’t yet sensitive enough to detect a small number of cancer cells among millions of healthy cells in the blood. Nor are they sensitive enough to detect the rare mutations induced by carcinogen exposure.  And this is where the TwinStrand Duplex Sequencing Technology™ comes in.

The many steps involved in a typical NGS workflow — DNA isolation, fragmentation, amplification, etc. — can all introduce technical errors. Likewise, different sequencing platforms possess idiosyncratic differences that might also introduce errors. The goal of any NGS run and associated bioinformatic pipeline is to correct the error and separate the “noise” from true signal. However, TwinStrand takes error detection to a whole new level through use of their proprietary error correction technique that detects and masks technical errors with much greater sensitivity by examining and comparing both strands of a DNA sequence.

Twinstrand NGS Pipeline

Typical sources of error in next generation sequencing (NGS)

Duplex Sequencing™ is an ultra-high accuracy sequencing method that overcomes the limitations of Next-Generation Sequencing by independently tracking both strands of individual DNA molecules. The paired sequences are compared to eliminate technical errors affecting only one strand, revealing ultra-low frequency biological mutation signal. Using a combination of proprietary biochemistry and cloud-based informatics, Duplex Sequencing greatly increases the resolution of NGS by reducing error rates from about 1-in-100 with standard NGS to below 1-in-10 million.

Duplex Sequencing can be used on any Illumina® sequencing platform. While early cancer detection and testing for residual disease make for natural applications of the technology, TwinStrand anticipates that the technology will be used to detect the emergence of antibiotic or antiviral resistance, occupational or environmental exposure to carcinogens, fetal abnormalities in non-invasive prenatal testing (NIPT), and in crime scene forensics. 

Indeed, with the wide array of suitable applications, TwinStrand hopes to make their technology as accessible as possible — even to those with little NGS experience or bioinformatics expertise. One of the ways they’ve done this is by implementing their analytic pipeline on the DNAnexus Platform and making the platform available to their customers. When a sequencing run is complete, users can easily upload it to a DNAnexus TwinStrand Portal where the TwinStrand Biosciences analytical pipeline can be run. Then, users can access the results as well as share the data to collaborate with other users. Offering their pipeline on DNAnexus as part of their Duplex Sequencing assays made it easy for TwinStrand to deploy a complete kit-plus-informatics solution from the initial R&D on the pipeline through the final commercialization of the technology.

TwinStrand launched their technology with four new assays at the Advances in Genome Biology and Technology (AGBT) conference on Marco Island, FL, February 23-26. Specifically, they presented the use of their technology to measure residual disease in acute myeloid leukemia (AML MRD) and mutagenesis in human, mouse, and rat models. For more information contact info@twinstrandbio.com.