Microwave denaturation or ethanol fixation yields superior results for apolipoprotein E genotyping from paraffin-embedded human brain

Tissue processing procedures of paraffin-embedded materials have been investigated for employing PCR gene amplification of disease-related genes. The apolipoprotein E (ApoE) gene is a major risk factor or susceptibility gene for late-onset familial and sporadic Alzheimer's disease (AD). To resolve which methods might be most suitable for detecting specific genotypes of interest, we compared the tissue processing procedures for determining ApoE genotypes using DNA extracted from ordinary processed paraffin-embedded brain tissue and PCR. The samples were obtained from 75 individuals including normal subjects, patients with AD, Lewy body disease (LBD) and other neurological diseases, The ApoE genotype was determined most reliably and consistently in microwave (MW)-denatured (96.8%) or 70% ethanol (EtOH)-fixed (95.0%) tissues compared to tissues fixed in 10% neutral buffered formalin (63.3%) or Bouin's fixative (59.1%). The age of the sample and the post-mortem interval did not affect the results. Consistent with previous studies, the ApoE-ε4 allele frequency was significantly increased in patients with AD (38.0%, p < 0.01) or LBD (34.4%, p < 0.01) compared with normal control subjects (10.4%). We conclude that ApoE genotyping can be performed most reliably on MW-denatured or EtOH-fixed denatured paraffin-embedded brain tissues.