HLA genotyping of 5,000- and 6,000-year-old ancient bones in Japan

We used polymerase chain reaction (PCR)-based DNA typing to identify HLA class II alleles of two individuals from ancient human remains. Genomic DNAs were isolated from two ancient human skeletons excavated from the Sanganji and Kitakogane sites in the main and northern islands of Japan, respectively. They were archaeologically estimated to be approximately 5,000 and 6,000 years old respectively, representing the remnants from the Jomon era. High molecular weight DNA was extracted by the standard proteinase K-phenol extraction method followed by purification with a Centricon-30 micro concentrator. Several rounds of PCR successfully gave rise to amplification of the HLA-DRB1 and -DQA1 genes. The PCR-restriction fragment length polymorphism (PCR-RFLP) and sequencing based typing (PCR-SBT) methods revealed that those ancient individuals possessed the DRB1 and DQA1 alleles which are highly prevalent among the modern north Asian as well as Japanese populations.