Dot Hybridization

 

From the pattern of probes that the amplified DNA binds to, a potential DNA type, also called a genotype, can be inferred. 

DQ alpha typing strips look like this before any types are obtained:

 

 

 The invisible dot to the right of the number 1, has a DNA probe for the 1-allele (variation) for DQ alpha.  The invisible dot to the right of the 2 has a DNA probe for the 2-allele and so on.  The 1-allele itself has variations, the 1.1,1.2 and 1.3 subtypes, also called alleles.  Notice that the typing strip has no specific dot or probe for the 1.2 subtype.  Also, the typing strip can't distinguish between the 4.2 and 4.3 subtypes and there is a single dot for these.  It is quite possible that there exist DQ alpha alleles that would be undetected by the typing strip and alleles that may be further subtypes of the alleles that the strip does detect.

 Here are some examples of how the strips are read: 

 

 

This last example brings up an important issue with DQ alpha typing.  The 1.2 allele is actually the second most common allele in most populations.  This means there will be frequent situations where the 1.2 allele may be present but undetected as in the last example.  An obvious question is:  Why not just have a specific probe for the 1.2 allele?  The answer is that the typing strip already maximizes the probing of a relatively short stretch of DNA.  That is, the DQ alpha locus itself is only about 240 base pairs long.  The multiple probe typing strip was probably about the best that could be done in terms of detecting multiple alleles of this small locus in a single typing step.  

Historicall, DQ alpha was often the first PCR-based test that forensic labs used.  Actually, the DQ alpha system is quite different from the majority of PCR applications in the scientific community.  This will be explained in more detail below.