Shared Resource Spotlight: Molecular Cytogenetics

Shan Zha is the director of the Molecular Cytogenetics Shared Resource at the Herbert Irving Comprehensive Cancer Center

The Molecular Cytogenetics Shared Resource (MCSR) at the Herbert Irving Comprehensive Cancer Center (HICCC) provides a wide range of technology platforms and services – from classical cytogenetics and high throughput imaging analyses to sequence-based assessment of DNA damage and repair. It also provides two specialized microscope systems, Miseq sequencer as well as analytic platforms, to bring advances in genomic instability technology to HICCC members.

The MCSR provides both reagents and the how-to for SKY, FISH analyses in mammalian cells, as well as specialized repetitive sequences – including telomere (both leading and lagging strand) and ribosomal DNA FISH. The service can be customized from all-inclusive (sample preparation to quantification) to reagents/instrument only. We have metasystem working station (open to trained investigators) that can be used for the automatic scan of metaphase phase/interphase nuclei, DNA damage foci, and semi-automatic acquisition and quantification. The software has been trained to recognized gH2AX, RPA, and RAD51 foci, and can be trained to recognize and quantify other foci or nuclear patterns in the cells. The slide loaders can accommodate 8 slides at a time and take <15 minutes to scan the entire slide. The pattern recognition-based quantification system relieves the post-doc and students from tedious foci counting and provides consistent and objective results.

We provide high throughput genomic translocation analyses, including high throughput sequence analyses that are low-cost (~ 50 dollars per library with over 1000 junctions) and have the ability to multiplex (30 libraries per run and > 1000 junctions per libraries). The platform can also be customized for analyzing gene editing products, BCR/TCR diversification, and serve as a platform to measure DNA double-strand break repair capacity in your favorite cells and tissues. The Miseq instrument in the SR is open for trained users for other applications.

Our cell biology platform and the pattern recognition platform has contributed to several member research projects. Our SR has worked with Drs. Richard Baer and Jean Gautier to analyze DNA damage foci (Molecular Cell, Baer Lab) and develop new tools to examine actin derived clustering of DNA breaks (Nature, Gautier Lab). The specialized FISH – including telomere FISH and rDNA Fish –have made it possible to examine those critical, yet highly repetitive genomic regions. We used them to uncover the important roles of ATR in repetitive regions (Nature Communications, Zha lab).

There are two new additions to the core – 1) quantitative analyses for rDNA copy number and instability, together with fluoresces-based quantitative analyses for telomere length. This is a dark matter that has escaped detection in mammalian cells, and we would like to help researchers see them with our new probes and assays; 2) semi-automatic analyses for the comet assay. This is a new analytic module that will expand the current pattern analyses to comet assay.