AB050. Building population-specific reference genomes: a case study of Vietnamese reference genome
Part 2: Symposium

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

Nguyen Dai Thanh1, Pham Thi Minh Trang1, Dang Thanh Hai1, Nguyen Ha Anh Tuan2, Le Si Quang3, Bui Quang Minh4, Dao Quang Minh5, Pham Bao Son1, Le Sy Vinh1

1VNU University of Engineering and Technology, Hanoi, Vietnam; 2Instituto Superior Tecnico, Lisbon, Portugal; 3Wellcome Trust Center for Human Genetics, Oxford University, Oxford, UK; 4Center for Integrative Bioinformatics Vienna, University of Vienna, Wien, Austria; 5Hanoi University of Science and Technology, Hanoi, Vietnam

Abstract: 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.

Keywords: Reference genome; human genomes; genotype; Vietnamese

Cite this abstract as: Thanh ND, Trang PT, Hai DT, Tuan NH, Quang LS, Minh BQ, Minh DQ, Son PB, Vinh LS. Building population-specific reference genomes: a case study of Vietnamese reference genome. Ann Transl Med 2015;3(S2):AB050. doi: 10.3978/j.issn.2305-5839.2015.AB050

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