eprintid: 1608
rev_number: 14
eprint_status: archive
userid: 21
dir: disk0/00/00/16/08
datestamp: 2016-05-26 06:26:37
lastmod: 2016-05-26 06:29:19
status_changed: 2016-05-26 06:26:37
type: conference_item
metadata_visibility: show
creators_name: Nguyen, Dai Thanh
creators_name: Pham, Thi Minh Trang
creators_name: Dang, Thanh HaI
creators_name: Nguyen, Ha Anh Tuan
creators_name: Le, Si Quang
creators_name: Bui, Quang Minh
creators_name: Dao, Quang Minh
creators_name: Pham, Bao Son
creators_name: Le, Sy Vinh
creators_id: sonpb@vnu.edu.vn
creators_id: vinhls@vnu.edu.vn
title: Building population-specific reference genomes: A case study of Vietnamese reference genome
ispublished: pub
subjects: IT
divisions: fac_fit
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 1000 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 1000 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. For the first time the Vietnamese reference genome, which is now available for further Vietnamese genome studies, was successfully built.
date: 2015-10-08
date_type: published
full_text_status: none
pres_type: paper
pagerange: 97-102
event_title: KSE: the 2015 International Conference on Knowledge and Systems Engineering
event_location: Ho Chi Minh city, Vietnam
event_dates: 8-10 October 2015
event_type: conference
refereed: TRUE
citation:   Nguyen, Dai Thanh and Pham, Thi Minh Trang and Dang, Thanh HaI and Nguyen, Ha Anh Tuan and Le, Si Quang and Bui, Quang Minh and Dao, Quang Minh and Pham, Bao Son and Le, Sy Vinh  (2015) Building population-specific reference genomes: A case study of Vietnamese reference genome.  In: KSE: the 2015 International Conference on Knowledge and Systems Engineering, 8-10 October 2015, Ho Chi Minh city, Vietnam.