A team led by Dr. XU Shuhua from CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health of the Chinese Academy of Sciences recently created a genome variation resource/database, PGG.SNV, which archives 265 million single nucleotide variations (SNVs) across 220,147 present-day genomes and 1,018 ancient genomes, including 1,009 newly sequenced genomes, representing 977 global populations. The study was published online in Genome Biology.

PGG.SNV significantly improve the coverage of Asian populations which are significantly under-represented in other available database such as GnomAD. Compared with the available database, another unique feature of the PGG.SNV is that it provides estimation of population genetic diversity and evolutionary parameters.

Despite Asia is the largest and most populous of earth's continents, most of the genomic studies have been conducted in Europe and America. Accordingly, currently available human genome variation resources are based on populations of European ancestry.

PGG.SNV documents more genomes and represents a much more comprehensive genomic diversity of worldwide populations by including 16 ethnic groups, especially many indigenous groups living in East Asia and Southeast Asia whose genomes have not been sequenced before. With a comprehensive catalogue of genetic variants and annotations.

Besides, PGG.SNV documents 1,018 ancient genomes that represent time periods from the 430,000 years before the present day up to the early 20th century, and compares them with contemporary human genomes, allowing researchers to understand the evolutionary trajectory of genetic variants as well as gene flow or introgression events.

Furthermore, this database enables studies of variants that are rare or not existing in well-studied populations and provides the population prevalence of variants in various populations with little ancestral bias and further guides Mendelian-inherited disease mapping studies by improving interpretations of putative causal loci for Mendelian diseases. It will help advance the understanding of the biological meaning of the human genome sequence in light of human evolution.

PGG.SNV provides a web-based user interface to access data. PGG.SNV has also embedded a web-based tool for the generation of figures after users have uploaded their own analyses. In addition, users can query variants using a mobile application (App) by linking to the WeChat official account named PGGbase.

The study was funded by the grants from CAS, the National Natural Science Foundation of China, the National Key Research and Development Program and Science and Technology Commission of Shanghai Municipality.