Yang Huanming and others 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 2007 BGI’s headquarters relocated to Shenzhen as "the first citizen-managed, non-profit research institution in China". 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 2011 BGI reported it employed 4,000 scientists and technicians.
In 2013 BGI claimed 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.
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.
First to de novo sequence and assemble mammalian and human genomes with short-read sequencing (so-called "next generation sequencing")
Sequenced 40 domesticated and wild silkworms, identifying 354 genes likely important in domestication.
Sequenced the first giant panda genome, equal in size to the human genome, in less than 8 months Sequencing revealed that the giant panda, Ailuropoda melanoleura, has a frameshift mutation in a gene involved in sensing savory flavors, T1R1. The mutation might be the genetic reason why the panda prefers bamboo over meat. However, the panda also lacks genes expected for bamboo digestion, so its microbiome might play a key role in metabolizing its main source of food.
Key player in the Sino-British Chicken Genome Project
Sends unsolicited bulk email to more scientists than any other company of its size, ignoring requests to desist.
Nature in 2010 ranked BGI Shenzhen as the fourth among the ten top institutions in China with all the others being universities and the Chinese Academy of Sciences. The ranking was based on articles in Nature research journals. There were similar results for other tops journals.
In 2014, BGI was reported to be producing 500 cloned pigs a year to test new medicines.
Named after two Emperors believed to have founded China’s dominant ethnic group, BGI plans to sequence at least 100 Chinese individuals to produce a high-resolution map of Chinese genetic polymorphisms. The first genome sequenced is of an anonymous Chinese billionaire who donated $10 million RMB to the project. And the first YanHuang genome project is named "YanHuang 1",whose genome data is published on http://yh.genomics.org.cn.
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.
Animals and plants
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[update]. Visit the project's website to monitor progress, see the species planned to be sequenced, and apply to join the effort.
Three Extreme-Environment Animal Genomes Project
BGI, Beijing University, Heilongjiang Manchurian tiger forestry zoo, Kunming Institute of Zoology, San Diego Zoo’s Institute for Conversation Research in California, and others will sequence the Amur tiger, South China tiger, Bengal tiger, Asiatic lion, African lion, cloud leopard, snow leopard, and other felines. BGI will also sequence the genomes and epigenoms of a liger and tigon. Since the two reciprocal hybrids have different phenotypes, despite being genetically identical, it is expected that the epigenome may reveal the basis of such differences.
The project will significantly advance conservation research and was auspiciously announced for the Chinese year of the Tiger.
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.
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.
^ abRasmussen, M.; Li, Y.; Lindgreen, S.; Pedersen, J. S.; Albrechtsen, A.; Moltke, I.; Metspalu, M.; Metspalu, E.; Kivisild, T.; Gupta, R.; Bertalan, M.; Nielsen, K.; Gilbert, M. T. P.; Wang, Y.; Raghavan, M.; Campos, P. F.; Kamp, H. M.; Wilson, A. S.; Gledhill, A.; Tridico, S.; Bunce, M.; Lorenzen, E. D.; Binladen, J.; Guo, X.; Zhao, J.; Zhang, X.; Zhang, H.; Li, Z.; Chen, M.; Orlando, L. (2010). "Ancient human genome sequence of an extinct Palaeo-Eskimo". Nature463 (7282): 757–762. doi:10.1038/nature08835. PMID20148029.edit