October 31, 2012, Cambridge, MA, and Shenzhen, China – BGI, the world's largest genomics organizations, announced today it is among 101 research organizations comprising the 1000 Genomes Project Consortium that has successfully constructed an integrated map of genetic variation from 1,092 human genomes, providing an invaluable resource for researchers to better understand the contribution of genetics to diseases. The latest study was published as an Advance Online Publication in Nature.
As an international public-private consortium, the 1000 Genomes Project Consortium reported in 2010* that, in sequencing the whole genomes of 179 individuals, it had detected over 95% of variants at 5% frequency. However, some lower-frequency variants that are enriched for potentially functional mutations and exhibit increased levels of population differentiation remain to be characterized.
Significantly, in this latest study, the consortium provided a more comprehensive and accurate integrated haplotype map, including 38 million SNPs, 1.4 million bi-allelic indels, and 14,000 more large deletions. This data set captured up to 98% of variants at 1% frequency in populations, making available powerful approaches for researchers to conduct sequencing-based disease studies in order to benefit human health.
The study is highly innovative in its design. Using a combination of low-coverage whole-genome and exome targeted sequencing, researchers sequenced the genomes of 1,092 individuals from 14 populations drawn from Europe, East Asia, sub-Saharan Africa, and the Americas. To construct the integrated map, they also developed methodologies to combine information across multiple algorithms and diverse data resources.
As one of the participating organizations, BGI contributed sample collection, sequencing, identification of genome variations, among other activities. In sample collection, BGI was responsible for all Chinese samples, including Han Chinese in Beijing (CHB), Han Chinese South (CHS) populations. For whole genome sequencing, 8 in 14 populations and 272 individuals were sequenced on BGI's sequencing platforms. For exome targeted sequencing, 11 in 14 populations and 375 individuals were sequenced by BGI. In data analysis, BGI participated in the detection of small InDels and large deletions. Also, BGI contributed additional efforts in sequencing coordination, data quality control, among others.
Xiaosen Guo, Project Manager from BGI, said, "This work presents a higher resolution human genetic variation map, especially including the low frequency mutation sites, for researchers worldwide to better explore the relationship between phenotype and genotype in human genetic disease studies. Thus, it is a major milestone in human genome research, not only for the 1000 Genomes Project, but also for broader human disease research."
Jun Wang, Executive Director of BGI, said, "This is another major breakthrough toward the achievement of personalized human medicine using next-generation sequencing technologies. The data obtained in this study are freely and publicly accessible to research communities all over the world. They provide an invaluable resource for researchers to better conduct genome-wide association studies and other medical research studies in the future."
* A map of human genome variation from population scale sequencing, Nature. 2010 October 28; 467(7319): 1061.
BGI was founded in 1999 with the mission of being a premier scientific partner to the global research community. The goal of BGI is to make leading-edge genomic science highly accessible through its investment in infrastructure that leverages the best available technology, economies of scale, and expert bioinformatics resources. BGI, which includes both private non-profit genomic research institutes and sequencing application commercial units, and its affiliates, BGI Americas, headquartered in Cambridge, MA, and BGI Europe, headquartered in Copenhagen, Denmark, have established partnerships and collaborations with leading academic and government research institutions as well as global biotechnology and pharmaceutical companies, supporting a variety of disease, agricultural, environmental, and related applications.
BGI has established a proven track record of excellence, delivering results with high efficiency and accuracy for innovative, high-profile research which has generated over 250 publications in top-tier journals such as Nature and Science. These accomplishments include sequencing one percent of the human genome for the International Human Genome Project, contributing 10 percent to the International Human HapMap Project, carrying out research to combat SARS and German deadly E. coli, playing a key role in the Sino-British Chicken Genome Project, and completing the sequence of the rice genome, the silkworm genome, the first Asian diploid genome, the potato genome, and, most recently, have sequenced the human Gut metagenome, and a significant proportion of the genomes for 1,000 genomes. For more information about BGI please visit www.genomics.cn or www.bgiamericas.com.
Public Communication Officer
Joyce Peng, Ph.D.
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