Amplification and detection of a Y‐chromosome DNA sequence by fluorescence in situ polymerase chain reaction and flow cytometry using cells in suspension

A procedure for amplifying and detecting nucleic acid sequences in situ using cells in suspension and flow cytometry has been developed. The process involves the use of the polymerase chain reaction (PCR) and a fluorescent in situ hybridization (FISH) protocol developed in our laboratory to detect the amplified PCR product. For these studies, a Y‐chromosome specific repeat DNA sequence was amplified. Daudi cells, a B‐cell lymphoma culture line established from a male, was used as a positive control and HL‐60, a promyelocytic leukemia culture line established from a female, was used as a negative control. During the in situ PCR process cellular autofluorescence (noise) increases causing markedly reduced detection sensitivity of the probe (signal) bound to the amplified product within the positive cells. An autofluorescence reduction circuit was applied which was integrated into a standard bench top flow cytometer to reduce this noise, thereby producing a 10‐fold increase in detection sensitivity of the signal. Without the application of the autofluorescence reduction circuit, the positive control histogram distribution was virtually indistinguishable from the negative control sample distributions. After autofluorescence reduction, the data showed that the Y‐chromosome DNA was only amplified in the Daudi cells subjected to the complete in situ PCR protocol. This increased sensitivity also provided direct detection of the Y‐chromosome repeat sequence, albeit exhibiting less signal compared to the amplified target after the in situ PCR. © 1995 Wiley‐Liss, Inc.