Herbert Irving Comprehensive Cancer Center
Flash Section

Molecular Cytogenetics and Epigenetics

Murty Vundavalli, Ph.D., Co-Director

Molecular Cytogenetics and Epigenetics

Murty Vundavalli, Ph.D., Co-Director

Ben Tycko, M.D. Ph.D., Co-Director
Ganchimeg Ishdorj, Ph.D., Manager

The Molecular Cytogenetics & Epigenetics Shared Resource uses the iLab Core Management System for service requests and billing. Before you can request services, you must log into iLab and be approved as a lab member. To access iLab, go to https://cumc.corefacilities.org and log in with your UNI and password.

More information for users, PIs, and Financial Managers can be found here.

Molecular Cytogenetics Service

The Molecular Cyto- and Epi-genetics facility provides karyotypic (G-banding) and molecular cytogenetic (SKY and FISH) characterization of human and mouse tumor cells with efficient turnaround times, utilizing state of-the-art technologies.
Services include:


  • G-banded karyotyping of human cancer and non-cancer cells
  • FISH analysis using a variety of DNA probes (locus and gene specific, region-specific, and chromosome painting) on a variety of human and mouse cell types and tissue samples, including cell lines, primary tissues from frozen or paraffin section, and tissue microarrays.
  • Spectral karyotype (SKY) analysis of human and mouse primary tumors and cell lines.

These services are provided to the researchers after initial discussions regarding the requirements for cell and tissue specimen preparations to best facilitate the required testing. The molecular cytogenetics service also provides technical assistance on custom design and preparation of probes for FISH.

Epigenetics Service

The epigenetics shared resource provides DNA methylation analysis through targeted sequencing. The technology that is currently in place uses the Fluidigm Access Array system for targeted Next Generation Sequencing (NGS) of bisulfite treated DNA on the Illumina MiSEQ platform. Whole genome bisulfite sequencing on HiSeq is also available on a more limited first-come-first serve basis. The epigenetics service also provides technical assistance on custom design of their projects, as well as advice on outsourcing of whole genome methylation by Illumina Infinium 450K methylation arrays and deep bisulfite sequencing.

Services include:

  • Bisulfite treatment of DNA samples
  • Targeted bisulfite PCR primer design
  • Fluidigm 48x48 targeted bis-PCR and sequencing sample preparation
  • MiSeq sequencing of bisulfite treated targeted sequencing libraries
  • Analysis of the bis-seq data
  • HiSeq whole genome bis-seq on a limited basis
  • Advice and help with project design and, where necessary, outsourcing for large-scale projects

Before using the service, read the Sample Submission Instructions. Please note that DNA should not be dropped off unless previously arranged with the facility.

Researchers are encouraged to initiate discussions regarding their project plans with the service staff in order to best facilitate proper DNA sample preparation, target region details, and the pipeline of data generation.