PHEMI Central Precision Medicine Edition

A unified view of the genotype and phenotype

 

PHEMI Central Precision Medicine Edition is a big data management system for genotypic and phenotypic information at the whole genome level, purpose-built for privacy, performance, and governance

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Our customers in precision medicine have told us they need two key things: a unified view of genotypic and phenotypic information at the whole genome level, and the ability to query that data at speed. With PHEMI Central Precision Medicine Edition, customers get interactive performance across the genotype and phenotype at scale, independent of the amount and types of data in the system. PHEMI offers a ready-to-use environment for collection, curation, and analysis of clinical data and billions of genomic observations while protecting privacy.

Precision Medicine Edition

PHEMI Central Precision Medicine Edition allows you to:

  • Centralize Data from Silos: Collect all organizational data assets scattered across different applications and databases into a central repository where it is annotated, indexed, and made available for analysis, reporting, sharing, and collaboration.
  • Curate and Prepare for Analytics: Automatically index imported genomic, reference, and phenotype files for sub-second query performance for common access patterns. With support for a keyword, graph, and geospatial indexes you have the flexibility to catalog and find just the data you need—at speed.
  • Collaborate with Confidence: Share data with researchers, physicians, geneticists, and collaborators knowing that privacy, security, and access rules are universally and consistently enforced for each user and data element, reducing the risk of data breach.

  • Scale Economically: Leverage proven Hadoop big data technology, so you can scale performance and capacity using commodity servers and inexpensive disk drives, lowering your overall cost of ownership by 60% compared to a traditional data warehouse approach. Moreover, built-in fault-tolerance capabilities keep your system up and running when a hard drive or an entire node fails. PHEMI Central Precision Medicine Edition eliminates a common bottleneck in the high-throughput genomics pipeline by speeding up ingestion, indexing, and annotation of VCF/gVCF files.
  • Simplify Your Bioinformatics Infrastructure: Eliminate proliferation of databases and isolated data sources, multiple bolt-on data management software packages, and specialized hardware. Data analytic workloads run in situ on the PHEMI cluster, without transferring large volumes of data to an external system, protecting privacy and delivering faster performance.

Key Benefits

  1. Enrich and annotate genomic data from multiple sources.
  2. Consolidate data silos.
  3. Enable collaboration across researchers, clinicians, and other authorized users.
  4. Enforce privacy, security, and data sharing policies.
  5. Eliminate performance bottlenecks.
  6. Free up scarce IT resources.
  7. Adapt to quickly changing requirements.
  8. Use standard analytics tools.
  9. Shorten your implementation time by leveraging the simplicity of PHEMI Central Precision Medicine Edition.

Get Performance at Scale

  • VCF Import: 86 sec/VCF
  • gVCF Import: 77 sec/gVCF
  • Query by RCV Accession: <1 sec
  • Query by Gene + Depth + Tumor Status: <1 sec
  • Query by CHR1 + 0/1 + experiment ID + Depth + Site: 34 sec

Ingest and query performance measured on a dataset with 13 billion variant observations on an 18 node cluster with 192 CPU cores, 640GB RAM, and 10GbE interconnect

GWAS VisualizationGenome Wide Association Study (GWAS) against 212 genomes on a modest 4 data node cluster in Azure Cloud takes 1 hour 35 min.

 

Integrate with Your Infrastructure

PHEMI Central Precision Medicine Edition integrates with your existing bioinformatics and data center infrastructure. Users are authenticated against your existing AD or LDAP drectory. Standard interfaces allow you to quickly and easily work with your existing tools and remain confident that as new tools evolve, PHEMI Central Precision Medicine Edition will seamlessly adapt.

Choose Your Deployment Type

PHEMI Central Precision Medicine Edition is available preinstalled on Oracle Big Data Appliance, as on-premise software, or as a managed cloud service, depending on your IT preferences.

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See PHEMI Central Precision Medicine Edition in Action

Contact us for a live demo of the PHEMI Central Precision Medicine Edition, or to discuss your precision medicine data management needs.