Research Cytogenetics

Function

Research Cytogenetics provides services to assist cancer research investigators at Fox Chase Cancer Center and the other Temple University campuses in research projects that require karyotyping, molecular cytogenetic analysis and DNA copy number/aCGH analysis at a reasonable cost. The following services are provided:

• Cell line species verification
• Modal chromosome number analysis
• Karyotyping of embryonic stem cells, blood, bone marrow, solid tumors, and cell lines from human, mouse and rat
• Gene or viral integration mapping by 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
• aCGH (array comparative genomic hybridization) using Agilent's DNA microarray-based technology

Description

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

The Affymetrix GeneChip System uses 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. We use 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.

The Genomics Facility has 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. For formalin-fixed paraffin-embedded (FFPE) tumor samples, the Research Cytogenetics Unit also has considerable experience in the use of Affymetrix’ OncoScan CNV Plus Assay, a whole-genome copy number microarray-based assay that enables the detection of copy number variations (CNVs) such as copy number gain and loss, loss of heterozygosity (LOH), copy neutral loss of heterozygosity (cnLOH), ploidy, allele specific changes, break point determination, mosaicism, clonal heterogeneity, and chromothripsis.

The Agilent DNA Microarray platform is used for aCGH studies of murine tumors or tumor-derived cell lines. We have also used this platform successfully for formalin-fixed paraffin-embedded (FFPE) samples. 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. Cytogenetics and chromosome microarray analysis 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.