Gap-PCR provides a simple technique that can definitively identify gene deletion mutations, provided the breakpoint sequences are known, using two primers complimentary to the sense and antisense strand in the DNA regions that flank the deletion. For small deletions of less than one kilobase in size, the primer pair will generate two products, the smaller fragment arising from the deletion allele. For larger deletions, the distance between the two flanking primers is too great to amplify the normal allele and the only product obtained is from the deletion allele. In these cases the normal allele is detected by amplifying across one of the deletion breakpoints, using a third primer complimentary to part of the deleted sequence near to the flanking normal DNA sequence.

The technique is the standard method for diagnosis of the 3.7kb and 4.2kb a⁺-thalassaemia deletion genes, the five common a^o-thalassaemia deletions, various b-thalassaemia deletions, and a number of db-thalassaemia and HPFH deletions, including Hb Lepore and Hb Kenya. A protocol is also described for diagnosis the anti3.7 triple a-globin gene allele. Most laboratories find the amplification of the b-globin gene cluster deletions is more robust and technically easier than the amplification of the a-globin gene cluster deletions.