Whitepaper: Discriminating copy number variation from heterogeneous samples using the S3™ Cell Sorter and the QX200™ Droplet Digital™ PCR System

By combining technologies such as flow cytometry, cell sorting, and digital PCR highly accurate and more specific results can be attributed to cell populations of interest vs. the bulk heterogeneous populations…

Many biological samples are composed of mixtures of physiologically different cell types. These include stem cell cultures, tumor samples, and blood.

Understanding the genetic makeup of a subpopulation within these samples may provide valuable clues about the characteristics of the sample and, by extension, the organism. For example, identifying and characterizing rapidly growing subpopulations within a tumor may reveal the metastatic potential of the cancer. Measuring potentially interesting genetic properties, such as copy number, mutation status, or transcript abundance, is confounded in a mixed sample by competing signals. In stem cell cultures, the pluripotent cells grow alongside differentiated cells, feeder cells, and stromal cells. In some stem cell cultures, the pluripotent cells represent a minority of the total cells within the culture. Accurately measuring transcript abundance within a subpopulation of cells requires separation from the heterogeneous population, or the use of a calibrator, a pair of genes that can be used to determine the relative abundance of each cell type. However, applying a calibrator to mixed cell measurements comes with a host of assumptions that may or may not be valid for that particular culture. Therefore, the most effective way to obtain reliable data from the mixed culture is to sort the cells of interest prior to performing the measurement.