System and method of genomic profiling

A method of identifying aberrations in a variable cancer cell genome sample, comprising:

• obtaining a cancerous tumor sample comprising normal and abnormal cells;
• creating a suspension of de-agglomerated nuclei of the cells suitable for flow sorting;
• sorting the nuclei into a plurality of fractions based at least on a quantification of genetic material in the nuclei;
• extracting the genetic material from at least a portion of the sorted nuclei;
• differentially labeling the extracted genetic material and a reference sample;
• hybridizing the labeled extracted genetic material and reference sample on a feature comparative genomic hybridization array;
• and,
• comparing the labeled extracted genetic material with the labeled reference sample to infer aberrations unique to the labeled extracted genetic material.