Beijing Genomics Institute

History

Wang Jian, Yu Jun, Yang Huanming and Liu Siqi created BGI in November 1999 in Beijing, China as a non-governmental independent research institute in order to participate in the Human Genome Project as China's representative. After the project was completed, funding dried up. So BGI moved to Hangzhou in exchange for funding from the Hangzhou Municipal Government.

In 2002, BGI sequenced the rice genome which was a cover story in the journal Science. In 2003 BGI decoded the SARS virus genome and created a kit for detection of the virus. In 2003, BGI Hangzhou and the Zhejiang University founded a new research institute, the James D. Watson Institute of Genome Sciences, Zhejiang University. The Watson Institute was intended to become a major center for research and education in East Asia modelled after the Cold Spring Harbor Laboratory in the US.

In 2007 BGI’s headquarters relocated to Shenzhen as "the first citizen-managed, non-profit research institution in China". Yu Jun left BGI at this time purportedly selling his stake to the other 3 founders for a nominal sum. In 2008, BGI-Shenzhen was officially recognized as a state agency. In 2008, BGI published the first human genome of an Asian individual.

In 2010 BGI Shenzhen was certified as meeting the requirements of ISO9001:2008 standard for the design and provision of high-throughput sequencing services, The same year BGI bought 128 sequencing machines and claimed to be the world's largest genome center.

In 2010 it was reported that BGI would receive US$1.5 billion in “collaborative funds” over the next 10 years from the China Development Bank. In 2010, BGI Americas was established with its main office in Cambridge, Massachusetts and BGI Europe was established in Copenhagen.

In 2011 BGI reported it employed 4,000 scientists and technicians. BGI did the genome sequencing for the deadly 2011 Germany E. coli O104:H4 outbreak in three days under open licence.

In 2013 BGI reported it had relationships with 17 out of the top 20 global pharmaceutical companies and advertised that it provided commercial science, health, agricultural, and informatics services to global pharmaceutical companies. That year it bought Complete Genomics of Mountain View, California, a major supplier of DNA sequencing technology, for US$118 million.

The institute has described itself as partly private and partly public, receiving funds both from private investors and the Chinese government. The laboratory was also the Bioinformatics Center of the Chinese Academy of Sciences.

Key achievements

Yan Huang Project

Started in 2007 and named after two Emperors believed to have founded China’s dominant ethnic group, BGI planned in this project, to sequence at least 100 Chinese individuals to produce a high-resolution map of Chinese genetic polymorphisms. The first genome data was published in October 2007. An anonymous Chinese billionaire donated $10 million RMB (about US$1.4 million) to the project and his genome was sequenced at the beginning of the project.

Diabetes-associated Genes and Variations Study (LUCAMP) Cancer Genome Project

Nine Danish universities and institutes will collaborate with BGI in this targeted resequencing project.

BGI explores associated genome and gene variation in complexes diseases in large-scale studies primarily using two methods: PCR-based resequencing of candidate genes and exon-capture-based whole exome resequencing.

Cognitive Research Lab

The Cognitive Research Lab at BGI is working with Stephen Hsu on a project to discover the genetic basis of human intelligence.

1,000 Plant and Animal Reference Project

BGI is leading an international collaboration to sequence 1,000 plants and animals of economic and scientific import within two years. It has pledged an initial US$100 million to start the program.

BGI has already sequenced genomes of 20 species of animals and 9 species of plants—sometimes for multiple individuals, such as 40 silkworms 19713493, and has an equal number underway as of March 2010.

Three Extreme-Environment Animal Genomes Project

In 2009 BGI-Shenzhen announced the launch of three genome projects that focus on animals living in extreme environments. The three selected genomes are those of two polar animals: the polar bear and emperor penguin, and one altiplano animal: the Tibetan antelope.

International Big Cats Genome Project

In 2010, BGI, Beijing University, Heilongjiang Manchurian tiger forestry zoo, Kunming Institute of Zoology, San Diego Zoo Institute for Conservation Research in California, and others announced they would sequence the Amur tiger, South China tiger, Bengal tiger, Asiatic lion, African lion, clouded leopard, snow leopard, and other felines. BGI would also sequence the genomes and epigenoms of a liger and tigon. Since the two reciprocal hybrids have different phenotypes, despite being genetically identical, it was expected that the epigenome might reveal the basis of such differences. The project aim was to significantly advance conservation research and was auspiciously announced for the Chinese year of the Tiger.

Results were reported in 2013 for the genomes of the Anur tiger, the white Bengal tiger, African lion, white African lion and snow leopard.

Symbiont Genome Project

A jointly funded project announced March 19, 2010, BGI will collaborate with Sidney K. Pierce of University of South Florida and Charles Delwiche of the University of Maryland at College Park to sequence the genomes of the sea slug, Elysia chlorotica, and its algal food Vaucheria litorea. The sea slug uses genes from the algae to synthesize chlorophyll, the first interspecies of gene transfer discovered. Sequencing their genomes could elucidate the mechanism of that transfer.

Ten Thousand Microbial Genomes Project

http://english.cas.cn/Ne/CASE/200908/t20090805_44705.shtml

Bioinformatics technology

De novo sequencing requires aligning billions of short strings of DNA sequence into a full genome, itself three billion base pairs long for humans.

BGI’s computational biologists developed the first successful algorithm, based on graph theory, for aligning billions of 25 to 75-base pair strings produced by next-generation sequencers, specifically Illumina’s Genome Analyzer, during de novo sequencing. The algorithm, called SOAPdenovo, can assemble a genome in two days and has been used to sequence an array of plant and animal genomes.

BGI’s 500-node supercomputer processes 10 terabytes of raw sequencing data every 24 hours from its current 30 or so Genome Analyzers from Illumina. The annual budget for the computer center is US$9 million.

SOAPdenovo is part of "Short Oligonucleotide Analysis Package" (SOAP), a suite of tools developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis. Built for the Illumina sequencers' short reads, SOAPdenovo has been used to assemble multiple human genomes (identifying an eight kilobase insertion not detected by mapping to the human reference genome) and animals, like the giant panda.