Genome sequencing technologies have lowered costs and increased data output at a much faster rate than traditional hardware refresh cycles can service effectively. With lowered costs, more biomedical research and clinical operations are integrating sequencing into a larger portion of their projects, compounding an already tough problem for IT operations. When Regeneron committed to using Next Generation Sequencing technology for biopharmaceutical research, the decision was made to keep the server room empty and deliver all genomic analysis and storage services using AWS and DNAnexus. We review the consequences of this decision, illustrating how basic AWS core services are game-changers in the design and operation of a scientific infrastructure at scale. We show how Amazon S3 changes the storage performance equation, discuss the impact of new instance types on the cost of genomic analysis, and explain how secure collaboration enables Regeneron to advance biopharmaceutical research techniques and support the future of genomic medicine.

1. November 13, 2014 | Las Vegas, NV
Angel Pizarro, Amazon Web Services |Omar Serang, DNAnexus | Jeffrey Reid, RegeneronPharmaceuticals

4. Facilities
Physical security
Compute infrastructure
Storage infrastructure
Network infrastructure
Virtualization layer (EC2)
Hardened service endpoints
Rich IAM capabilities
Network configuration
Security groups
OS firewalls
Operating systems
Applications
Proper service configuration
Auth & acct management
Authorization policies
+ =
Customer/Partner
• Re-focus your security professionals on a subset of the problem
• Take advantage of high levels of uniformity and automation
First global public cloud provider to achieve certification for security & quality management system

5. EC2
10.0.2.12
AWS region –VPC network isolation
AZ A
AZ B
VPC 10.0.0.0/16
SN 10.0.1.0/24 (DMZ)
SN 10.0.2.0/24 (Private)
(23.20.103.11)
Internet
EC2
10.0.1.11
Internet GW Service
Virtual Gateway

6. AWS system entitlements
Roles
Root Account
Multi-factor authentication
Groups
Administrators
Developers
Applications
Alyson
Anand
Tomcat
Jim
Shandra
Xiao
Susan
Reporting
Console

7. You get to choose whocan do whatin your AWS environment and from where
Manage and operate
US EAST
A
VPC
Internet GW Service
Virtual Gateway
B
S
M
(EIP)
(EIP)
AWS account owner (master)
Network & security
Researcher
Operations
EMR

8. Amazon EBS
Amazon S3
•HTTPS
•Server-side encryption of each object
•AWS-managed keys
•Customer-managed keys
•End-to-end secure network traffic
•Whole volume encryption
•AWS-managed keys
•Encrypted incremental snapshots
•Minimal performance overhead (utilizes Intel AES-NI)

9. •RecordsAPI calls, no matter how those API calls were made (console, SDK, CLI)
•Who did what and when and from what IP address
•Logs saved to Amazon S3
•Includes Amazon EC2, Amazon EBS, Amazon VPC, Amazon RDS, IAM, AWS STS, and Amazon Redshift
•Be notifiedof log file delivery by using the Amazon Simple Notification Service (Amazon SNS)
•Aggregate log information across services into a single S3 bucket
•Out of the box integration with log analysis tools from AWS partners including Splunk, AlertLogic, and SumoLogic

10. Virtual Private
Cloud
AWS Cloud
Amazon
S3
Amazon
EBS
IAM
CloudTrail

12. DNAnexus is a platform-as-a-service for genome informatics. In production now with over 20% of the high throughput sequencing installations globally.
Enables collaboration and datasharing within a secure and compliant environment that helps attract new users. Creates a “Network Effect” for genomics.
Platform launched in 2013. Located in Silicon Valley.

13. Baylor College of Medicine
x
14,691
INDIVIDUAL
GENOMES
x
430TB
ANALYTIC
DATA
x
3.3M
CORE-HOURS
x
20,800
CORES
x
300+
RESEARCHERS
1 customer. 1 project. 1 week.

14. x
GEISINGER
x
REGENERON
$30B pharma company focused on cholesterol, oncology, and rheumatoid arthritis
$3.5B health care
provider for 3M patients

22. Amazon S3: the center of the universe

23. Amazon EC2: job manager and payloads

24. Amazon EC2: application services

25. Leveraging the AWS detailed billing report

26. VPC + Dx: connecting partners

27. DNAnexus: connecting science

31. Samples (extracted DNA)
1.4M Sample BioBank
Library Prep Automation
Illumina HiSeq Fleet
Data

32. Data QC

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37. http://bit.ly/awsevals