Kulmanov Maxat, Ashouri Saeideh, Liu Yang, Abdelhakim Marwa, Alsolme Ebtehal, Nagasaki Masao, Ohkawa Yasuyuki, Suzuki Yutaka, Tawfiq Rund, Tokunaga Katsushi, Katayama Toshiaki, Abedalthagafi Malak S, Hoehndorf Robert, Kawai Yosuke
Computer, Electrical and Mathematical Sciences & Engineering (CEMSE) Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, Saudi Arabia.
KAUST Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, Saudi Arabia.
Sci Data. 2025 Aug 12;12(1):1316. doi: 10.1038/s41597-025-05652-y.
The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here we present JaSaPaGe, a pangenome graph reference for Saudi Arabian and Japanese populations, both of which have been significantly underrepresented in previous genomic studies. We constructed JaSaPaGe from high-quality phased diploid assemblies which were made utilizing PacBio high-fidelity long reads, Nanopore long reads, and Hi-C short reads of 9 Saudi and 10 Japanese individuals. Quality evaluation of the pangenome graph by variant calling showed that our pangenome outperformed earlier linear reference genomes (GRCh38 and T2T-CHM13) and showed comparable performance to the pangenome graph provided by the Human Pangenome Reference Consortium (HPRC), with more variants found in Japanese and Saudi samples using their population-specific pangenomes. This pangenome reference will serve as a valuable resource for both the research and clinical communities in Japan and Saudi Arabia.
在基因组分析中选择参考序列至关重要，因为它是所有下游分析的基础。最近，泛基因组图被提议作为一种整合多个个体单倍型的数据模型。在此，我们展示了JaSaPaGe，这是一个针对沙特阿拉伯和日本人群的泛基因组图参考，在之前的基因组研究中，这两个人群的代表性都严重不足。我们利用9名沙特人和10名日本人的PacBio高保真长读长、纳米孔长读长和Hi-C短读长构建了高质量的分阶段二倍体组装体，从而构建了JaSaPaGe。通过变异检测对泛基因组图进行质量评估表明，我们的泛基因组优于早期的线性参考基因组（GRCh38和T2T-CHM13），并且与人类泛基因组参考联盟（HPRC）提供的泛基因组图表现相当，使用其特定人群的泛基因组在日本和沙特样本中发现了更多变异。这个泛基因组参考将成为日本和沙特阿拉伯研究和临床社区的宝贵资源。
