Ca. Crouse et al., ANALYSIS AND INTERPRETATION OF THE HLA DQ-ALPHA 1.1 WEAK-SIGNAL OBSERVED DURING THE PCR-BASED TYPING METHOD, Journal of forensic sciences, 39(1), 1994, pp. 41-51
The Perkin-Elmer (PE) AmpliType DQ alpha Forensic Kit is currently ava
ilable for amplification and typing of a polymorphic region in the Hum
an Leukocyte Antigen (HLA) DQ alpha DNA sequence. Following amplificat
ion of the DQ alpha region with the PE kit, typing strips are processe
d. These strips contain immobilized DNA probes designed to distinguish
six possible HLA DQ alpha alleles. It has been observed in this labor
atory and others that in a single source DNA sample, it is possible to
detect a weak signal on the 1.1 specific allele dot when the samples'
genotype clearly does not contain the 1.1 allele. It has been suggest
ed that a potential source of this weak-signal is the non-specific amp
lification of a HLA DX alpha gene sequence. To demonstrate the relatio
nship of the DX alpha gene to the 1.1 nonspecific signal, we designed
biotinylated DX alpha PCR primers specific for a 178 bp region in whic
h the amplified product spans the homologous DQ alpha region encompass
ing the DNA probes present on the typing strips. DX alpha DNA sequence
s from various DQ alpha genotypes were amplified and hybridized to DQ
alpha typing strips. We have demonstrated that DX alpha PCR products d
o not always hybridize to the 1.1 probe on the typing strips. Sequence
analysis of DX alpha PCR products show that this region is polymorphi
c which may explain why the occurrence of the ''1.1 weak-signal'' is u
npredictable. We have further analyzed the effect of DNA template conc
entration for the DQ alpha amplification protocol and have shown that
regulation of PCR input DNA optimizes the amplification and typing pro
tocols for HLA DQ alpha alleles and minimizes the potential observatio
n of the ''1.1 weak-signal.''