Comprehensive, Genome-Wide Epigenetic Fingerprinting by Replication Profiling

This is a procedure for typing cells (cancer cells, stem cells, any kind of cells) based upon the order of replication of chromosome segments. In brief, cells from any source are pulse-labeled with 5-bromo-2deoxyuridine, sorted into early and late S-phase of the cell cycle by flow cytometry and the DNA replicated in each temporal compartment of S-phase is differentially labeled and hybridized to a DNA array consisting of evenly spaced probes from the entire genome. Using customized algorithms, the resulting data (ratio of each probe sequence replicated in early vs. late S-phase) can be converted into a form that can segment the genome and identify the order of replication of chromosome segments characteristic for a cell type. An alternative, if the cell line is difficult to label metabolically, is to sort cells into S-phase and G1-phase populations, hybridize differential labeled DNA from these sorted populations, and determine the ratio of each probe sequence in S vs G1. This provides similar data that can be evaluated by the same computational conversion.

Advantages:

• More comprehensive (covers the entire genome)
• Less expensive (covers the entire genome for less than 1/20th what is needed for existing profiling methods)
• Much easier to interpret- the informative data for each cell line is distilled down to combinations of only about 1,000-2,000 segments of the genome that uniformly identify each cell type
• Measures very different properties of cells than any other method
• Focuses the analysis on the proliferating population of cells, which is particularly useful for stem cell and cancer technologies.