david sexton biogen

david sexton biogen
November 1, 2020

Taking this massive amount of raw data, over a petabyte of data from 500,000 individuals complexities around the traditional ecosystem that Biogen had and it needs to move to the cloud. One is that we needed to be able to partition the data heavily based on genetic location to really be able to query this quickly as well as do vertical table splitting, essentially vertical partitioning to be able to query fast enough because there’s so much metadata across 11,000 columns. There are 22 centers across the United Kingdom with over 500,000 volunteers, and this is one of the largest and most detailed population studies ever undertaken. And so those made real time interaction with the data quite difficult. They’ve been able to find a number of variants in about six different genes that have a significant impact on human lifespan. ", David Sexton Senior Director of Genome Technology and Informatics, Biogen. There are a lot of different fields, over 3500 different phenotypic fields that are there. And so that was incredibly important as we build this entire system together and provided it out to the authorized researchers that were part of the UK Biobank Consortium. When we look at why this is hard, if you’re processing a few samples, it’s actually not that hard to do yourself in the cloud. Seeking a cloud-first solution, Biogen partnered with Databricks, an Amazon Web Services (AWS) Advanced Technology Partner in the AWS Partner Network (APN) and an AWS Life Sciences Competency Partner, to design a software solution stack that harnessed AWS to analyze the data efficiently and securely. David Sexton Senior Director, Genome Technology and Informatics, Biogen. Frank holds a PhD and Masters of Science in Computer Science from UC Berkeley, and a Bachelor’s of Science with Honors in Electrical Engineering from Stanford University.

See the complete profile on LinkedIn and discover David’s connections and jobs at similar companies.

So how is Biogen leveraging the UK Biobank data? So there’s one piece, which is an uptrend piece where you look at preparing the high quality data set. View David Sexton’s profile on LinkedIn, the world's largest professional community.

And so now I will turn it over to John to talk about scaling the UK Biobank data using DNA Nexus’s Titan and Apollo products. We’ve accelerated that and paralyze that out using Spark. “Because all groups were already using AWS infrastructure,” says Sexton, “it was very easy to move data via bucket to each group that had an Amazon Virtual Private Cloud to use the data.” With the insights gleaned from data processed by its AWS stack, Biogen was able to reposition its drug portfolio based on genomic evidence, identify new drug targets, and further uncover important insights into the biological basis of neurodegenerative diseases like Alzheimer’s and Parkinson’s. Our data infrastructure had challenges in not having enough storage capacity and data center. So when you go ahead and do that full cross, you can be looking at running billions of billions of regression tests to associate this data together. We really break this up into two different pieces.

Dublin, CA. View David Sexton’s profile on LinkedIn, the world's largest professional community. He is also involved in industry efforts within the Pistoia Alliance to promote FAIR data practices in life sciences research. Databricks, an AWS Advanced Technology Partner in the APN and an AWS Life Sciences Competency Partner, offers a unified data analytics platform that enables data teams to collaborate with data engineering and data science tools to accelerate data-driven innovation. United States.

So the UK Biobank is the premier data set for associating disease to genetics in the world right now. So they’ve been able to go ahead and reposition and reprioritize their drug portfolio. We are using human genetic evidence to rank our drug portfolio. And for a research environment, it’s also quite important that you actually use the tools that are particularly important and relevant view. Amazon Elastic Compute Cloud (Amazon EC2) provides the backbone for data analysis and maintaining the stack in the AWS Cloud; Amazon Simple Storage Service (Amazon S3) provides a scalable storage solution for the project’s expanding petabytes of data; and Amazon Virtual Private Cloud (Amazon VPC) provides robust security.

And they’ve been able to use the Databricks platform to do a really deep dive into these workflows. David Sexton works in the industry of Drug Manufacturing & Research, Pharmaceuticals, Healthcare. David has 4 jobs listed on their profile. Greater Pittsburgh Region.

What is David Sexton’s direct phone number? The ability to focus only on exceptions and in the science and not having to deal with cloud optimizations and such is also quite important. Biogen is a life sciences company dedicated to eradicating neurological diseases. You really need to bring the tools and the researches to the data. Large scale genomics datasets like the UK Biobank are revolutionizing how pharmaceutical companies identify targets for therapeutic development. – Good evening to those of you who are joining the session. Prior, John was CPO at Vantiq, delivering intelligent systems in the IoT space, and co-founder, CTO, and CPO at Model N (NYSE: MODN) where he led the Global Products group and drove technical strategy. Previously, David was the Head of Genome Informatics at Novartis Institutes of Biomedical Research where he led the group responsible for all genomic information systems at Novartis. So with the GWAS pipelines, what this is is essentially a statistical kernel that takes every single genomic variants in the data set and the phenotypes that we’re interested in, and goes ahead and performs some sort of a statistical test to see if these two are associated. On the so called phenotypic side which might be demographic information, health information, clinical information that might come from medical records. View David Sexton’s profile on LinkedIn, the world's largest professional community. David Sexton Senior Director Genome Technologies and Informatics at Biogen Greater Boston Area 500+ connections David has 2 jobs listed on their profile. David Sexton. If you have questions, or would like information on sponsoring a Data + AI Summit, please contact organizers@spark-summit.org. Prior to joining Databricks, Frank was a lead developer on the Big Data Genomics/ADAM and Toil projects at UC Berkeley, and worked at Broadcom Corporation on design automation techniques for industrial scale wireless communication chips. I’m the head of Genome Technology and Informatics at Biogen. It has been pioneering neuroscience and biotechnology since 1978, and its portfolio currently spans 60 target treatments across eight diseases.

Another important aspect is to keep this all secured in our environment, we’ve integrated the Spark hive meta store into our platform access control model to really control the security of the massive data set. So this is a long term study of genetic predisposition and environmental exposure to the development of disease. And so this is the core aspect and the core engine that’s powering Apollo, is a Spark based engine. David is a Senior Director, Genome Technology and Informatics at Biogen. And ultimately, the Biogen team has been able to deliver a lot of success. That is a wide data set. Watch the AWS on-demand webinar and hear from David Sexton, the Senior Director of Genome Technology and informatics at Biogen, and Frank Nothaft, Technical Director, Health and Life Sciences at Databricks about the challenges of the project and the solution that enabled Biogen team to significantly accelerate variant annotation of massive genomic datasets and ramp up the sequencing …

I’ll show that in a second. John Ellithorpe, PhD, is the Executive Vice President & Chief Product Officer at DNAnexus. David holds a Bachelor of Science in Molecular and Cellular Sciences and a Master's degree in Computer Information Systems.

We see a tight integration coming up as their Spark team underpower many of the different technologies in this space. If I’m looking at, let’s say, a common continuously distributed variable like height, this could be something like a linear association between every single genomic variants and every single phenotype. The participants of the UK Biobank Consortia Regeneron, and GSK sequence the first 50,000 samples, and all 500,000 participants are to be sequenced in 2020.

Greater Boston. So what we did is that this is built using the Apollo technology, which takes the high quality data sets that are being processed out of Titan and combines it with structured data, that is the health assessment data, and provides you an ability to interact with it in a variety of ways. David is a Senior Director, Genome Technology and Informatics at Biogen.

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