Unleashing the Power of Precision Medicine Using the Hybrid Cloud

China’s Converged Precision Healthcare Platform by Intel, Alibaba Cloud and BGI

Precision medicine is becoming a reality. Though still in its infancy, this technology is set to revolutionize healthcare by streamlining diagnosis, treatment, and prevention — all at a fraction of the cost. Although the development of precision medicine will entail many challenges, from the recent advances in healthcare paradigms and the advancement of ge-nome sequencing technologies, it is clear that the industry is headed for significant disruption. A key part of this para-digm shift will stem from precision medicine data analysis — something that will greatly benefit from the Hybrid Cloud.The Hybrid Cloud’s functions are perfectly suited to aid in precision medicine analysis. In collaboration with Alibaba Cloud and BGI, we have designed the Converged Precision Healthcare Platform as an end-to-end solution that sup-ports the production, analysis, sharing, and interpretation of genetic information in research and clinical studies.

ENTERING THE DIGITAL ERA

Precision medicine has now entered the digital era. Since doing so, next generation sequencing instruments have generated petabytes of data and the rate of data being generated has surpassed that of Moore’s Law, with vast increases in the scale and scope of genome sequencing projects. Furthermore, the use of sequencing technology has become a standard practice of clinicians and researchers. The emergence of a new paradigm in genomic sequencing has occurred, and small-scale benchtop sequencers are now available, which are affordable and an excellent option for independent researchers running small laboratories. Commonly used models include the MiSeq (Illumina), Ion Proton (Thermo Fisher Life Technologies), and BGISEQ-500/50 (BGI). These benchtop sequencers are designed to provide rapid and efficient sequencing solutions facilitating the advancement of precision medicine, and allowing for novel clinical testing methods, like NIPT (noninvasive prenatal testing), small-scale cancer gene panels, and bacterial testing all by independent clinical labora-tories (ICL).However, many institutes, hospitals, and clinical labs do not possess sufficient com-putational and storage capacities for post-sequencing data analysis on a large scale. For this reason, investment in sequencing instruments alone will not directly increase scientific and clinical value. For the full research benefits to be attained, a significant corresponding investment in information infrastructure is also required.

OVERVIEW

In October 2016, the Chinese government removed the barriers for NIPT testing of trisomies while the UK government has recently approved the incorporation of NIPT for trisomies 21, 18, and 13 into their existing prenatal screening program.

UNLEASHING THE POWER OF PRECISION MEDICINE USING THE HYBRID CLOUD

CHALLENGES

To increase our understanding of the genetic causes of disease, genomic analysis can be used. To develop personalized treatments, researchers require resources that allow large genomic work-flows to run at cloud scale during high-use periods. Users require access to pre-configured software and on-demand computing resources for genomic data analysis. To achieve this, computational cycles and storage capacity can be leased from cloud computing services that offer cloud based bioinformatics tool suites. This lowers the entrance barrier for working with sequencing datasets— increasing the adoption of genomic technologies. Due to the interdisciplinary nature of life sciences research, data and analysis tools must be unilaterally available to a variety of geographically dispersed researchers. Rather than replicating large datasets and installing tools in each research location, a more collaborative access approach is required. Furthermore, traditional on-site and host IT resources are required to provide timely data analysis, security, and privacy.

SOLUTION

To overcome these challenges, researchers have been utilizing hybrid cloud technology, provided by Intel in collaboration with leading life science institutes and cloud service providers including Alibaba Cloud and BGI. Together, these companies have created a platform of tools being used by physicians and researchers that are increasing the rate at which precision medicine is developed and lowering innovation barriers. For example, the converged Precision Healthcare Platform (PHP) that has been de-veloped as part of the hybrid cloud solution will revolutionize the precision medicine industry. Currently, the PHP and the hybrid cloud solution offer the most commercial-ly-viable improvements to the precision medicine in the industry. For collaborative purposes, we have narrowed the scope of precision medicine to exclusively cover genome data analytics that are processed, shared, and stored using a hybrid cloud platform. This excludes simple information repositories. While we recognize the importance of data sharing and protection, the power of hybrid cloud centers rests in their ability to connect precision medicine and genome technolo-gies. This is a driving factor for the change of physician and researcher behavior.We have determined that the first wave of the PHP has proven successful in driving improvements in research while reducing waste and costs.

USAGES SOLUTION

Pharmaceuticalusages

Researchusages

Clinicalusages

Benchtop Sequencer

Appliance(IA - BGI Online for Client)

BGI Online for Cloud

Alibaba Cloudcloud computing,

data storage and developer ecosystem

CLOUD COMPUTING

SaaS

IaaS

LOCAL SEQUENCER & COMPUTING

DATA

RESULTSDATA

DATA

Government institutions, such as the China FDA and NHFPC (National Health and Family Planning Commission), require ICL IT security and privacy compliance for genetic testing. (including NIPT and Cancer Panels).

“The collaboration with BGI and Alibaba Cloud

to jointly build the open healthcare cloud platform

is a rare opportunity for Intel. It helps us to work

seamlessly with local partners and users, and

leverages IT to accelerate genome sequencing and analysis so as to achieve

the vision of precision healthcare for 2020”

Carl Li – Managing Director, Intel Health and Life Sciences

Group, Great Asia Region

UNLEASHING THE POWER OF PRECISION MEDICINE USING THE HYBRID CLOUD

BGI ONLINE

BGI Online is a user-friendly one-stop platform used to share software and data between genomics researchers at different locations. It provides a solid foundation on which to build, deploy, and integrate intelligent software applications. It features ex-ceptional integrated security, collaboration, and serviceability support. Though it does not address the complexities of precision medicine itself, it provides a pre-integrated platform conducive to overcoming those issues.We are currently using PHP to extend the core BGI Online framework to provide target-ed support for precision medicine requirements.

APPLICATIONS Clinical Genetic Testing

Noninvasive Prenatal Testing

Pathogenic Microbio Testing

Populations Genetics Studies

LaboratoryInformation

Management Systems

BGI Online

Security Interfaces

Deployment Tools

Intel® Genomics Kernel Library (Intel® GKL)

Intel® Math Kernel Library (Intel® MKL & MKL-DNN)

Intel® Data Analytics Acceleration Library

(Intel® DAAL)

Intel Distributionfor Python

Intel® EE for Lustre*

Execution Engine User Experience

Analysis Pipeline Application Framework

Algorithms

Data Management

Collaboration

Sequencing Device

Integration

Healthcare ITStandards

Clinical DecisionSupport

Security Framework

ALIBABA CLOUD

INTEL SOFTWARE LIBRARIES

INTEL HARDWARE

POWERFUL, FLEXIBLE,AND COST-EFFECTIVE

STANDARD-BASED SERVERS, STORAGE, AND NETWORKING

HARDWARE-ENHANCEDSECURITY AND RELIABILITY

BGI ONLINE FOR PRECISION MEDICINE

THE CONVERGED PRECISION HEALTHCARE PLATFORM BY INTEL, ALIBABA CLOUD, AND BGI

ARCHITECTURE OF THE HYBRID CLOUD

◆ Curated and quality-controlled data from publicly available genomic data sources stored on the Alibaba Cloud.

◆ Publicly available and user-friendly analytics optimized for performance stored on the Alibaba Cloud.

◆ Dedicated computing resources from a BGI benchtop sequencer, such as the BGI Online Appliance, which supports on-site sequencing data generation, analysis, and storage.

◆ Primary customer genomic data & analytics/apps stored on the private cloud using the BGI Online Appliance at corresponding customer nodes.

◆ Customers use the publicly available Alibaba Cloud app or the BGI Online Appliance app to process either data on the private cloud or public data from Alibaba Cloud.

◆ Results from Alibaba Cloud are integrated or validated against the results of the BGI Online Appliance.

UNLEASHING THE POWER OF PRECISION MEDICINE USING THE HYBRID CLOUD

THE THREE PHASES OF CONVERGED PRECISION HEALTHCARE PLATFORM DEVELOPMENT

1. Cloud-based Integrated Data Analysis (2015 – 2016)During this phase, Cloud-based BGI Online offered tools for performing and integrating the analysis of publicly available and user-generated genomic, clinical, and imaging data. This phase allows the:

◆ Storage & analysis of user-generated genomic and phenotypic data in research & clinical settings in private and off-site areas

◆ Curating and channeling of public data (TCGA, COSMIC ICGC) and analytics through Alibaba Cloud Hosting

◆ Performance analysis of user and public data, and the integration of those results

◆ Execution of pre-packaged and user-generated analytical algorithms using support-ing analytical applications and APIs designed for the custom analysis of genomic clinical and imaging data

◆ Enabling of the simple display access and manipulation of disparate molecular (ge-nome epigenetic gene expression) phenotypic data through a scalable and flexible infrastructure, platform, and data storage model

◆ Leveraging of an app ecosystem to aggregate sources and validate new analytical algorithms

2. Data Sharing Mediation (2016 – 2017)

During this current phase, data sharing across multiple institutions and sites has been enabled and is being mediated. This phase has allowed the:

◆ Facilitation and mediation of data analysis sharing agreements being made between sites

◆ Analysis of data from two or more sites together through new technology and the secure and legally compliant integration of that technology

◆ Management of work-flows, project scheduling, data location tracking, provenance, and permissions by Cloud software

◆ Integration of Alibaba Cloud for differentiated security & scalability of data/analytics sharing

3. Clinical Decision Support (2017 – 2018)

During this phase, clinical and genomics data used in clinical decision support applica-tions will be integrated. This phase will allow:

◆ Clinically annotated variant identification with supporting evidence based on the associations between patient profile treatment and outcome.

◆ Storage querying of the integrated genomic/clinical data repository based on pa-tient profiles.

◆ Guided therapy options through biomarker identification.

◆ Prognostic and predictive models for clinician use.

◆ A standard for patient treatment recommendations and associated data.

◆ Identification of clinical trial patients based on molecular and phenotypic profiles.

◆ A front-end user interface offering one-click access to users.

◆ An app ecosystem that fosters crowd sourcing of support apps from academic, clinical, and commercial entities.

“Through our Collaboration with Intel and Alibaba Cloud, and

the construction of an open, precision healthcare

cloud platform, we will significantly improve our

strategic position. The more that innovation

and evolution occur, the quicker the development of the precision medicine industry in China will be.”

Yin Ye,CEO, BGI Genomics

“Alibaba Cloud will provide continuous

‘core power’ for the improvement

of data processing, privacy protection and transmission - the joint power of cloud computing.”

Hu Xiaoming,CEO, Alibaba Cloud

UNLEASHING THE POWER OF PRECISION MEDICINE USING THE HYBRID CLOUD

BACKGROUNDTo explore the contribution of functional coding variants to the genetic susceptibility for psoriasis, researchers from Anhui Medical University and BGI, carried out a large-scale sequencing analysis with 1000 whole exome sequencing samples. Using traditional methods, this process would take at least month to complete. We completed the full analysis on only 24hours.

ACHIEVEMENTLowered the entry barrier of large scale genomics analysis by providing access to plug-and play infrastructure

◆ Performed using GATK best practices

◆ 11 modules involved

◆ More than 11,000 jobs protected by 100% uptime Alibaba Cloud JOB GUARDING technology, ensuring that all information is reliable

◆ 1000 WES analyses completed in 21h 47m 12s

CASE #1: WITHIN 24 HOURS TO COMPLETE 1000 WHOLE EXOME SEQUENCING DATA ANALYSIS

CASE #2: CLOUD BASED PLATFORM ACCELERATE THE RARE DISEASE STUDY

BACKGROUNDTo discover the susceptibility variants for rare diseases, BGI researchers performed 87 epilepsy pedigrees with over 10TBs of raw data.

ACHIEVEMENTCreated scalable systems for data storage, processing, and analysis that support the increasing demand for genomic analysis.

◆ Accelerated research and publication by making data sets easily accessible with standardized aggregated data quality and formatting/annotations

◆ Developed in-house algorithms and pipelines using Online APIs. Easily constructed the novel analysis pipeline to discover novel mutations.

◆ 1000 analysis jobs completed within 24 hours, which has previously taken 15 days

UNLEASHING THE POWER OF PRECISION MEDICINE USING THE HYBRID CLOUD

INTEL’S OPPORTUNITIES

◆ Lease or sale of genomic analysis hardware associated with establishing a private cloud with optimized performance and operating costs

◆ Access to the increased scalability and efficacy of data access, data sharing, and processing provided by Intel Hardware and Software optimizations

Intel technologies’ features and benefits depend on system configuration and may require enabled hardware, software or service activation. Performance varies depending on system configuration. No computer system can be absolutely secure. Check with your system manufacturer or retailer or learn more at www.intel.com.

Software and workloads used in performance tests may have been optimized for performance only on Intel microprocessors. Performance tests, such as SYSmark and MobileMark, are measured using specific computer systems, components, software, operations and functions. Any change to any of those factors may cause the results to vary. You should consult other information and performance tests to assist you in fully evaluating your contemplated purchases, including the performance of that product when combined with other products.

For more complete information visit http://www.intel.com/performance.

Optimization Notice: Intel’s compilers may or may not optimize to the same degree for non-Intel microprocessors for optimizations that are not unique to Intel microprocessors. These optimizations include SSE2, SSE3, and SSSE3 instruction sets and other optimizations. Intel does not guarantee the availability, functionality, or effectiveness of any optimization on microprocessors not manufactured by Intel. Microprocessor-dependent optimizations in this product are intended for use with Intel microprocessors. Certain optimizations not specific to Intel micro-architecture are reserved for Intel microprocessors. Please refer to the applicable product User and Reference Guides for more information regarding the specific instruction sets covered by this notice.

All performance tests were performed and are being reported by BGI. Please contact BGI for more information on any performance test reported here.

Cost reduction scenarios described are intended as examples of how a given Intel- based product, in the specified circumstances and configurations, may affect future costs and provide cost savings. Circumstances will vary. Intel does not guarantee any costs or cost reduction.

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CASE #3 HYBRID CLOUD STORAGE IN CHINA NATIONAL GENEBANK (CNGB)

BACKGROUNDChina National GeneBank (CNGB) has the ability to store more than 20 petabytes of genetic data and has a goal of accumulating 500 petabytes, which will host more than 10 million samples from humans, plants, animals, and microbes.

ACHIEVEMENT ◆ The hybrid storage system, integrated by Intel® Enterprise Edition for Lustre* and

Alibaba Cloud OSS, allows the storing and managing of multiple petabytes of ge-netic information across local and remote clouds

◆ Intel® EE for Lustre* improved data throughput performance and accelerate analysis performance

◆ Alibaba Cloud OSS was a highly cost-effective storage solution that satisfied the requirements of online genetic information storage.

◆ Intel® EE for Lustre* with Hierarchal Storage Management (HSM) supports data shar-ing and transferring with OSS.