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EYE ON CHINA
BGI contributes genome sequencing and bioinformatics expertise
BGI, the world’s largest genomics organization, has announced that 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. 

XiaosenGuo, 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.”

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