The Genomics Core Facility at the Icahn School of Medicine at Mount Sinai currently operates a diverse world-class next generation sequencing platform (NGS) suite directed by Robert Sebra, Ph.D. alongside Associate Director, Kristin Beaumont, Ph.D. (single cell molecular biology & sequencing), and Assistant Director, Mike Beaumont, Ph.D (physiology and functional validation) who guide sequencing/molecular and single cell technologies. Since 2013, the team has successfully published 120 collaborative high-impact publications and has played an ample role in submitting dozens of grants which have been funded across various disease foci including cancer, inherited disease, structural variation, infectious disease and innovative technology development.
The facility's NGS suite includes the following platforms: 2 Illumina HiSeq2500, 2 MiSeq, 2 NovaSeq, 3 NextSeq550, 2 Illumina MiniSeqs, 1 PacBio RSII system, 1 PacBio Sequel instruments, 2 PacBio Sequel II instruments, 3 Ion S5XL instruments, 2 PGM Sequencers, 4 10X Genomics Chromium instruments, 1 Oxford Nanopore GridIon configuration, and 3 Ion Chefs from Ion Torrent/Thermo-Fisher. The combination of various sequencing equipment facilitates a broader range of clinical and scientific applications through the generation of flexible and robust data across a variety of genetic loci of varying complexity. Beyond bulk DNA and RNA sequencing methods, the lab also has equipment and expertise centered on single cell and low-input characterization using 1 Berkeley Lights Beacon system, 4 Chromium 10X Genomics instrument, 2 MissionBio Tapestri system and one CelSee Genesis platform. With this equipment, single cells can be isolated from viable tissue with the capacity of tens of thousands of cells per day from individual samples followed by a variety of molecular methods for sequencing purposes, post amplification. Current example projects include characterization of single cells derived from various patient tumor biopsies across primary and metastatic sites to better understand tumor heterogeneity, as well as characterization of single cells isolated from various regions of brain, heart, and other tissues for discovery and characterization of niche functional populations. The team is comprised of 31 staff and faculty harbored in a >4500 sq ft innovation laboratory inclusive of instrumentation, wet bench, and cell biology space, including a BSL2 lab and the basic science lab.
High Performance Computing (HPC) cluster: A central High-Performance Computing (HPC) facility with 1.5 Petabyte storage capacity called “Minerva” is available for secondary and tertiary data analysis. The Minerva cluster consists of 120 Dell C6145 two blade chassis totaling 7,680 cores (64 cores per node) with 70 teraflop peak speed, interconnected through a Quad-Data Rate (QDR, 40Gbps) InfiniBand network. Each compute node is equipped with at least 256 GB of memory, with one 1-TB high-memory node. The hardware accessible for analysis is optimized for parallel jobs that are CPU bound such as NGS read mapping, as well as parallel jobs such as Bayesian network reconstruction that are memory bound. In addition, the high-speed InfiniBand interconnects enable jobs requiring substantial shared memory, such as all-by-all comparisons of splice-form specific RNAseq results to generate isoform-specific co-expression networks. Minerva is connected to the Genomics Core cluster and Mount Sinai network via dual 10 GB Ethernet links. GridFTP enabled nodes are also available for fast data transfers to external sites. Access to ISMMS computational resources is restricted by firewalls and external access is provided through secure shell/ftp with two-factor authentication.
The software and programming environments offered on Minerva are the best of breed, and include community standards such as Linux and MPI. The cluster runs resource managers and schedulers to balance job workload, optimized to process as many jobs as possible for the highest overall machine utilization, job throughput and job success rate. Minerva is operated with over 95% uptime, using scalable and reproducible configuration management techniques. Long-term archival storage is provided by a high-capacity Tivoli Storage Manager (TSM) system and protects against data loss. One copy of the tapes is kept off-site (New Jersey) and one stays onsite at Mount Sinai. All data on the tapes are encrypted. In accordance with Sinai policy, tapes are kept for at least six years.
The Minerva file system provides extensive data capacity (approximately 14 PB of storage overall) for high performance storing and accessing research data, based on IBM Spectrum Scale (formerly known as GPFS). Minerva file system is made of different storage tiers to ensure the users will benefit of the maximum performance and it’s mounted on about 600 nodes including a flash pool of 264 TB. The Technology Development laboratory has a dedicated allocation of 670 TB for various projects in parallel.