Genomics Core Facility

The Genomics Core Facility at the Icahn Institute and Department of Genetics and Genomic Sciences is a CLIA-certified laboratory, which houses both our basic and translational genomics research. Our researchers leverage cutting-edge technologies and next-generation sequencing capabilities for research and clinical applications. We help investigators and clinicians analyze samples, identify genetic variants contributing to disease risk, and reveal complex mechanisms involved in human disease.

Our capabilities include:

  • Massively parallel sequencing with the Illumina HiSeq 4000, HiSeq 2500, and MiSeq
  • Single molecule sequencing with the Pacific Biosciences RS II
  • Ion Proton for development of whole-exome and whole-genome sequencing using LifeTech's sequencing chemistry for rapid-turnaround NGS sequencing
  • Ion PGM for targeted research and clinical assays with high throughput, intermediate length reads, and rapid turnaround time
  • Next-generation sequencing library preparation from RNA and DNA
  • Genotyping, gene expression profiling, and epigenetics using the high-throughput Illumina BeadArray platform
  • Real-time PCR using the Roche LightCycler 480 System

To submit requests for Illumina sequencing and sample preparation, please use our Genomics Core Facility Online Request Portal (please note: this link can only be accessed using on-campus computers). Print a copy of your confirmation email and include it with your samples to be dropped off to the Genomics Core Monday-Thursday from 2-4 pm. 

Submission Forms For Other Services

For those interested in our services, our Illumina Sequencing and Pacific Biosciences Sequencing submission forms can be accessed using the links provided. If the table sample rows are insufficient, please submit a complete sample list using an Excel-compatible file and the same column headers as shown on the original submission form. Please email your completed forms to john.holt@mssm.edu. Printed forms, with fund number signed by the principle investigator, must be included when submitting your sample.

Illumina BeadArray Submission
Monday – Wednesday from 3 – 5 PM
All Samples: Pooja Sandhuria
Illumina BeadArray Form

DNA/RNA QC Service
Monday – Thursday from 2 – 4 PM
All Samples: Genomics Core Facility 13-02
QC Service Request Form

Shipping Address
Genomics Core Facility
Department of Genetics and Genomic Sciences
Icahn Medical Institute at Mount Sinai
1425 Madison Avenue, Room 13-02
New York, NY 10029

Technology Platforms

Our laboratories have a number of technology platforms available for use. 

Our five sequencers are as follows:

  • The Illumina HiSeq 2000: A second generation sequencer with a capacity of 120-150M reads of 100 nt in length. Libraries may be sequenced from one or both ends.
  • Illumina MiSeq: A "personal" second generation sequencer based on HiSeq chemistry with a capacity of 12-15M reads in 24 hours.
  • Pacific Biosciences RS: A third generation single molecule sequencer with read lengths up to 6kb.
  • Applied Biosystems 3730xl: A 96 capillary dye-terminator sequencer.
  • Applied Biosystems 7900HT: A real-time thermocycler for quantitative PCR and end-point allele discrimination for use by GGS department members

Our microarray-based SNP and transcriptomics instruments include:

  • The Illumina HiScan, which is the most advanced bead-array reader on the market for high-density SNP detection, mRNA-profiling, and methylation microarrays.
  • The Illumina BeadXPress, a medium density, custom SNP detection platform.

Our sample preparation instruments include:

  • Covaris LE220 Focused-ultrasonicator with AFA technology: a versatile system engineered for high throughput pre-analytical sample processing.
  • Two TECAN liquid handling robot: Automated Bead Array hybridization and washing.
  • Three Agilent BioAnalyzer: A microfluidics-based platform for sizing, quantification, and quality control of DNA and RNA--crucial for preparing libraries for Illumina sequencing.
  • Agilent Bravo: A sample preparation of Illumina sequencing libraries using SPRI magnetic bead technology.
  • Beckman BioMek FX liquid handling robot: An automated Sanger sequencing reaction cleanup and real-time PCR plate set-up.

Our primary storage and computing capacity is built to gather real time data coming from second and third generation sequencers, to carry out primary analysis and to distribute data to users. It has the following features:

  • Primary Storage: 100 TB high-performance parallel file system with N/2 redundancy
  • RAM: 96 GB per node
  • Processing: 192 cores at 3.46 GHz each
  • Average demultiplexing (or primary) pipeline run-time for a 100bp paired-end run : 2-3 hours
  • Each sequencing machine is directly connected to the Server via a 1 Gigabit network mount

Minerva, our high-performance computing (HPC) infrastructure, features:

  • 7,680 Advanced Micro Devices (AMD) 2.3 GHz Interlagos cores
  • 120 Dell C6145, 2 blade chassis nodes in six cabinets
  • 64 compute cores in four sockets and 256 gigabytes (GB)s of memory per node
  • 30 terabytes (TB) of RAM
  • Interconnected with Mellanox Quad Data Rate (QDR 40 Gbps) Fat-Tree Infiniband
  • 1.5 petabytes (PB) of DataDirect Networks (DDN) SFA10K high-speed storage (600 disk drives in two cabinets), 10 GB/s
  • Dual 10 Gigabit Ethernet links to the Sinai campus network

Our current bioinformatics support includes:

  • Analysis of basic sequence quality and run parameter QC using Illumina CASAVA software, and SMART software.
  • Alignment of genome/exome/ chromatome sequence with reference genome using CASAVA and BWA pipelines.
  • Secondary analysis of genome/exome sequences using GATK pipeline, output will include a list of SNPS, SNVs, and indels.
  • Alignment of RNA-Seq data by TopHat analysis pipeline.
  • Analysis of transcriptome expression profile using Cuff Link software.
  • Model-based analysis of ChIP-Seq data (MACS).
  • Research project driven tertiary analysis and collaboration with our faculty.