Genomic Medicine Center Facilities

The Genomic Medicine Center's capital equipment and software tools provide support for the Center's achieving and maintaining Clinical Laboratory Improvement Amendments (CLIA) certification and College of American Pathology (CAP) laboratory accreditation as well as support for a variety of research activities. The collection of sequencers and robots allows the Center to process more than 20 terabases of data per week.

Equipment features

• Illumina Sequencer Suite
  • NovaSeq 6000
  • Next Seq 2000
  • MiSeq (2)

• Pacific Biosciences Sequel IIs (2)
• Hamilton NGS Star liquid handling robots (2)
• Perkin Elmer liquid handling robots
  • Sciclone
  • Janus

• Perkin Elmer Chemagen, automated system to extract nucleic acids 
• 10X Chromium System (2)
• Fluidigm C1
• Nanocellect WOLF cell sorter
• Agilent Fragment Analyzer (2)
• Agilent Femto Pulse
• Agilent TapeStation
• Agilent Bioanalyzer
• Tecan Spark Fluorescence plate reader
• Qubit Fluorometer (2)
• Life Technologies QuantStudio 12k Flex real time PCR detection system
• Covaris LE220 Plus 96-well plate DNA sonication system
• Diagenode Megarupter 3 DNA fragmentation system
• Sage ELF electrophoresis system
• Sage BluePippin electrophoresis system

Genetics laboratory

The Clinical Molecular Genetics Laboratory is a full-service diagnostic laboratory operated by the Department of Pathology and Laboratory Medicine, which collaborates extensively with the Genome Medicine Center.

Cloud compute infrastructure

The Genomic Medicine Center works with Microsoft and DNAnexus to migrate computational infrastructure to the Microsoft Azure cloud. An Azure ExpressRoute connection provides dedicated, high-capacity and low-latency connection to resources in the Azure cloud.  Computational analysis pipelines are being migrated to the DNAnexus genomics cloud platform, and workflows are run in DNAnexus using community standard bioinformatics domain specific languages (such as the Common Workflow Language and containerization technologies such as Docker) to enable environment-independent, reproducible analysis methods that can be easily shared.

The cloud platform allows researchers to take advantage of a diverse range of hardware configurations including large RAM servers, GPUs and the ability to scale resources up and down as dictated by needs. The Azure cloud provides scalable storage that will accommodate the 3+ petabytes of data hosted by the Center currently and provide an easy mechanism to grow with the Center’s needs.

With this capability, the Genomic Medicine Center provides a robust, secure, user-friendly and highly scalable analytical environment for researchers that features:

• Researcher access to their own data through the DNAnexus platform (where they access best practice workflows and toolsets developed and deployed by the bioinformatics team in the Genomic Medicine Center)
• Computationally intense analyses executed through the DNAnexus web interface, empowering researchers without dedicated bioinformatics personnel to perform much of their own data analysis
• Common workflows (such as alignment and variant detection for individuals and cohorts, variant annotation, bulk and single cell RNA analysis, WGBS and differential methylation identification) for human genomics studies with support for other model organisms including mouse, rat and zebrafish
• Additional workflows and tools developed for core Genomic Medicine Center projects as they become available
• Visualization tools and consoles for interactive data analysis
• Secure data access as well as a mechanism for per-PI/project cost tracking and auditing

On-premise compute infrastructure

The Genomic Medicine Center's computer resources are located within a dedicated data center with environmental controls, 8 tons of air conditioning, conditioned power, hospital emergency back-up power and substantial UPS capability. 

Other data center features

• 2308-core Linux compute cluster with 13TB of DDR3 RAM
• Head node (48-core Intel Xeon e5-2650 v4 CPU, 128 GB RAM and 200GB SATA drive)
• General purpose compute server (12-core Intel Xeon X5670, 256 GB RAM, 1TB SATA hard drive)
• Web servers (48-core Intel Xeon e5-2650 v4 CPU, 256GB RAM, 200GB SATA drive)
• Database server (20-core Intel Xeon Silver 4114 CPU, 196 GB RAM, three 1.9TB SSDs in RAID 5)
• Database server (16-core Intel Xeon E5-2640 v3, 256GB RAM, 6TB SSD RAID 5)
• Data Direct Networks Grid Scalar 7K with 3.8 PB usable capacity
• Data Direct Networks Web Object Scaler (WOS) with 2.7PB usable capacity
• 3 x Illumina DRAGEN Bio-IT servers (48 core Intel Xeon Gold 6126 CPU, 256GB RAM, 2TB SATA hard drive, XILINX DRAGEN FPGA accelerator card)
• RStudio, JupyterLab, R-Shiny server (48 core Intel Xeon e5-2650 v4, 1TB RAM)
• RStudio, JupyterLab, R-Shiny server (80 core Intel Xeon Gold 6138, 1 TB RAM)