Whole-genome seqencing of an Okhotsk human skeleton from Hamanaka 2 site, Rebun Island, northern Japan

In 2013, an ancient human skeleton (NAT002) of the prehistoric Okhotsk culture was excavated from Rebun Island, northern Japan. Some bones of this individual were affected by severe hyperostosis, suggesting SAPHO syndrome. To investigate the genetic features of this individual, we extracted genomic DNA from 3rd molars and performed whole genome sequencing. As a result of sequencing for 18 NGS libraries, the high-coverage genome data was obtained. The typical deamination pattern and sufficiently low modern DNA contamination rate were observed, ensuring the DNA authenticity. The mtDNA haplotype of NAT002 was assigned to haplogroup G1b, which is commonly observed among the modern North Asian populations. Results of outgroup f3 test, PCA, and ADMIXTURE analysis indicated that NAT002 was genetically close to the modern Lower Amur populations. The fact suggest the past human migration from the Lower Amur region to the northern part of the Japanese archipelago. HLA typing indicated that NAT002 possessed HLA-B40 allele, which has been reported as one of the risk factors of ankylosing spondylitis, reactive arthritis, and undifferentiated spondyloarthritis. These disease are classified into seronegative arthritis as well as SAPHO syndrome.The Data Access Committee of the National Bioscience Database Center (NBDC) approved that this personal genetic data were made published according to NBDC data sharing guidelines (http://humandbs.biosciencedbc.jp/).