AB050. Building population-specific reference genomes: a case study of Vietnamese reference genome

• Published in: Annals of translational medicine 2015-09, Vol.3 (Suppl 2)
• Main Authors: Thanh, Nguyen Dai, Trang, Pham Thi Minh, Hai, Dang Thanh, Tuan, Nguyen Ha Anh, Quang, Le Si, Minh, Bui Quang, Minh, Dao Quang, Son, Pham Bao, Vinh, Le Sy
• Format: Article
• Language: English
• Subjects: Part 2: Symposium
• ISSN: 2305-5839; 2305-5839
• DOI: 10.3978/j.issn.2305-5839.2015.AB050

The human reference genome is an essential tool for studying human genomes. The standard reference genome is constructed from genomes of a few donors. The 1,000 genomes project has revealed a huge amount of genetic differences between diverse populations. It is therefore naturally questioned whether the standard reference genome can work well for all human genome studies or population-specific reference genomes are needed accordingly. In this paper, we present a pipeline for constructing and evaluating a population-specific reference genome. The pipeline was examined on building the Vietnamese reference genome from 100 Kinh Vietnamese genomes obtained from the 1,000 genomes project. Experiments showed that the resulting Vietnamese reference genome was better than the standard reference genome at analyzing Vietnamese genomic data. It helped improve the quality of short reads mapping and genotype calling for Vietnamese genomes. The pipeline is applicable for building and evaluating other population-specific reference genomes.