Research at Fox Chase »Research Facilities »Genetic Research

Joseph R Testa, PhD Director Jianming Pei, MD Manager

Cancer Prevention Pavilion, Room P3011 215-728-2898 Joseph.Testa@fccc.edu Jianming.Pei@fccc.edu

Function

The Research Cytogenetics and Genomics Facility (RCGF) assists Fox Chase Cancer Center (FCCC) investigators in research projects that require karyotyping, molecular cytogenetic analysis, and DNA copy number analysis at a reasonable cost. The Facility provides the following services:

• cell line species verification;
• modal chromosome number analysis;
• chromosome karyotypic analysis of embryonic stem (ES) cells, blood, bone marrow, solid tumors, and cell lines of human, mouse and rat;
• fluorescence in situ hybridization (FISH); interphase FISH; chromosome painting and multiplex-FISH (M-FISH);
• DNA copy number and loss of heterozygosity (LOH) analysis using the Affymetrix GeneChip System (for human samples); and
• aCGH (array comparative genomic hybridization) using Agilent's DNA microarray-based technology (for murine or human samples).

Description

The Cytogenetics Unit provides classical cytogenetic and molecular genetic services, as well as high-resolution DNA copy number analysis for the detection of genomic imbalances, including chromosomal deletions and amplifications. The classical cytogenetics and microarray-based copy number analysis are complementary to clarify a genetic change due to either a rearrangement or copy number alteration or both.

The Affymetrix Microarray system has greatly expanded the capabilities of the Research Cytogenetics and Genomics Facility. The Affymetrix GeneChip System provides high-density GeneChip arrays that facilitate high-resolution whole genome scans; and multiple probe sets provide highly accurate and automated genotype and sequence calling, reducing the need for manual quality control. GeneChip Mapping Arrays enable scientists to conduct large-scale linkage analysis, as well as whole genome association and DNA copy number studies at high throughput and at a low cost per data point. In recent weeks, we have established the use of the platform's newest Genome-Wide Human SNP Array 6.0, which contains more than 1.8 million markers for genetic variation, including more than 906,000 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The SNP Array 6.0 represents more genetic variation on a single array than any other available product and provides the highest physical coverage of the genome. Importantly, we have developed profiling software that permits DNA copy number changes to be portrayed beside ideograms of individual chromosomes for easy recognition of specific sites of genomic imbalance. Profiling separate CNV data and SNP data from the SNP Array 6.0 chips permits us to differentiate genomic alteration due to germ line CNV versus somatic genetic imbalances. The RCGF Facility uses the Agilent DNA Microarray platform for aCGH studies of murine tumors or tumor-derived cell lines. This platform can also be used for human tumors, if needed. We currently use the Agilent Mouse Genome CGH Microarray 244A chip featuring about 235,000 mouse sequences, which has five times more coverage than the original 44K format. The Facility provides users with aCGH profiles plotted beside individual chromosomes using Agilent CGH Analytics software. We provide user-friendly chromosome-tabbed MS Excel array result files, and we help investigators in array data mining and summarizing DNA copy number data using in-house software to generate heatmap-style and bar-style frequency plots.

The Laser Capture Microdissection Facility