Because DQB1 is the best single genetic marker for T1D, it is the gene most often used to identify individuals with a high risk of developing disease. However, risk estimates based on DQB1 alone are less precise than those based on the combination of alleles at both the DQA1 and DQB1 loci. These combinations are called haplotypes, and reflect the specific alleles on each of the two chromosomes. Not all haplotypes (i.e., chromosomes) with DQB1*0201 or *0302 also have high risk DQA1 alleles. Thus, DQB1 and DQA1 typing provide more accurate risk estimates than those based on DQB1 alone. However, it is also more expensive. For that reason, most screening is based only on DQB1.

The two DQA1-DQB1 haplotypes that are most strongly associated with T1D are DQA1*0501-DQB1*0201 and DQA1*0301-DQB1*0302. That is, chromosomes with DQB1*0201 and DQA1*0501 confer a higher risk for T1D than chromosomes with DQB1*0201 but some other DQA1 allele (not *0501). Similarly, chromosomes with DQB1*0302 and DQA1*0301 confer a higher risk for T1D than chromosomes with DQB1*0302 and another DQA1 allele (not *0301).