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The invention concerns a new method of detecting a rare product of a directed genetic alteration of a cultured cell. The method is applicable to any method of making the alteration. The method comprises sequentially using polymerase chain reaction (PCR) using an allele specific primer to preferentially amplify sequences containing one of the two linked alterations, coupled with a second technique that detects the second change in the PCR product. The second method may comprise restriction digestion, conventional DNA sequencing or pyro-sequencing. Experiments indicate that alterations as rare as one correctly altered copy in 10, 000 cells can be detected using the methods provided.