PCR Fingerprinting for Detection of Deleted or Amplified Sequences in Human Cancer

Genomic fingerprinting is one of several methods for screening human genome to identify genetic alterations in cancer cells. Arbitrarily primed polymerase chain reaction (AP-PCR) is a PCR-based genomic fingerprinting method (1 ). In AP-PCR, a single oligonucleotide is used to initiate DNA synthesis from sites along the template with which it matches only imperfectly. PCR is performed under a low stringent condition in the initial five cycles to permit hybridization of arbitrary primers to various sequences dispersed throughout the human genome. This is followed by 30-35 cycles of PCR under high stringent condition, so that only the best matches of the initial annealing events are further amplified. By controlling the stringency of the initial cycles, 50-100 distinct DNA fragments can be amplified from the human genome by a single PCR. When those fragments are size fractionated by gel electrophoresis, a representative sample of cell genome is visualized by staining or autoradiography as a genomic fingerprint. Because of the arbitrary nature for designing a primer and the low stringent condition for hybridization of a primer, DNA fragments are simultaneously amplified from various chromosomal regions in a single PCR. By comparison of AP-PCR genomic fingerprints of DNA from tumors and normal tissues, deleted and amplified DNA sequences in cancer cells have been detected and cloned (2 -5 ). Intensities of deleted and amplified DNA fragments are decreased and increased, respectively, by AP-PCR.