Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes

Pangenome projects have enhanced our understanding of human genomic and genetic diversity, but repetitive regions are still challenging to assemble and yet medically important. Here we generate 20 near-complete haplotypes from 10 Japanese male individuals using three complementary long-read and long-range datasets and construct a pangenome graph from these haplotype-resolved assemblies. All haplotypes achieve an N50 value exceeding 100 Mbp for gapless contigs. We substantially improve the average reconstruction rate of complete haplotypes from 46.8% and 52.8% in two previous pangenome graphs to 91.2% within 30 segmentally duplicated complex regions. Furthermore, we identify complete minor haplotypes in the KIR and SMN regions that are absent in those previous pangenome graphs. We find putatively biased gene conversion events occurring in only one direction around the SMN and beta-defensin (DEFB) genes, implying non-random evolution in these regions. Our study contributes to the growing body of pangenomic data, offering a more refined view of human genomic diversity involving complex segmental duplications. A Japanese human pangenome graph built from near-complete genomes brings medically important blind spots of the human genome into focus, revealing hidden diversity in complex genomic regions related to immunity and disease.