• New pangenome graphs made using exclusively Saudi and Japanese samples give new genetic insights on these two populations  

A new study by researchers at King Abdullah University of Science and Technology (KAUST), Tufts University, and the Japan Institute for Health Security (JIHS) provides pangenome graphs of Saudi and Japanese populations. The information gained is expected to benefit precision medicine and clinical genetics for these underrepresented populations in pangenome databases.  

Researchers and clinicians use the pangenome as a reference to examine the DNA of an individual or groups. Much like how a map informs someone where they are relative to a location, a pangenome helps researchers determine how an individual's DNA differs from genetic patterns found across a whole population.  

The first human pangenome was reported in 2023. However, it depends heavily on the people from which the DNA samples were taken, none of whom were of Arab or Japanese descent, meaning it was constructed without representation from almost 10% of the world's population. Other groups were also excluded, which is why scientists are building pangenomes using samples from subpopulations, as these pangenomes are expected to be more reliable baselines for those groups.   

"Up to 12% of patients with genetic disorders go undiagnosed due to reliance on reference genomes that don’t reflect their population’s genetic background. By constructing population-specific pangenome graphs, we improve variant calling and help close this diagnostic gap,” said Malak Abedalthagafi, Professor and Chair of the Department of Pathology and Laboratory Medicine at Tufts Medical Center and one of the lead authors of the study. Variant calling is how experts like her determine differences between an individual's DNA with the sample genomes used in the graphs.   

“Having worked on the Saudi genome for several years, contributing to this project marks a meaningful step in my commitment to advancing representation in genomics and ensuring precision medicine serves diverse populations,” she added.  

KAUST Professor Robert Hoehndorf, another author of the study and member of the KAUST Center of Excellence for Smart Health, explained that building the graphs, which the study calls JaSaPaGe (Japanese Saudi PanGenome), using samples from two distinctive populations provides an opportunity to study the impact of differences between the reference used and the population studied, offering new health insights.  

"Japan and Saudi Arabia are pretty much at the opposite ends of Asia and have been separated for a long time. It gave us a chance to study the effects of population-specific pangenome graphs on variant calling when populations do not match," he said. 

Yosuke Kawai of the JIHS and another author of the study concurs, adding there are clinical benefits to be gained for the two populations.  

"The joint development of a population-specific pangenome graph for the Japanese and Saudi Arabian populations addresses a critical gap in global genomic representation. By integrating diverse data from both countries, we have created a powerful resource that not only improves variant detection accuracy but also holds great potential for advancing precision medicine tailored to each population’s unique genetic landscape." 

The study can be read in Scientific Data.