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One application of multiplex PCR is microdeletion screening. This can be applied to the X and Y chromosomes (male genomic DNA) or to hybrid cell lines (rodent-human) containing one copy only of a human chromosome of interest.
Figures below show a few examples of multiplex PCR screening reactions for microdeletions on human chromosome Y.
Fig. 43. Y-chromosome microdeletion screening reactions of 12 male genomic DNA samples (yellow) using multiplex mixture B (5 loci) and of 11 DNA samples (green) using multiplex mixture A (7 loci). DNA samples 1, 2, 9, 10 and 12 (yellow) and 1 and 2 (green) show deletion of some loci tested (lack of amplification products).
Fig. 44. Y-chromosome microdeletion screening reactions of 16 male genomic DNA samples (yellow) using multiplex mixture D (5 loci). DNA samples 10, 11, 12, and 13 show deletion of some loci tested. Gel separation was done at high voltage, in about 3-4 hours. See also Fig. 45 for comparisons.
Fig. 45. Y chromosome deletion screening using esentially the same DNA samples and primer mixture D as in Fig. 44 above. Only the order of the samples on the gel was somewhat changed. Gel separation was done overnigtht (16 hours) at low voltage. Products appear much more diffuse but result interpretation can be easily done.