BGI Group

BGI, currently known as the BGI Group, formerly known as the Beijing Genomics Institute, is a Chinese genome sequencing company, headquartered in Shenzhen, Guangdong, China.
It was formed in 1999 to participate in the Human Genome Project as a genetics research center. It also sequences genomes of other animals, plants and microorganisms. The company has morphed from a research institute that decoded the DNA of pandas and rice plants into a company active in animal cloning, health testing, and contract research, while its earlier non-profit research has been continued by the Beijing Institute of Genomics, Chinese Academy of Sciences.
History.
Wang Jian, Yu Jun, Yang Huanming and Liu Siqi created BGI in September 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, after which 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, the Chinese Academy of Sciences founded the Beijing Institute of Genomics in cooperation with BGI, with Yang Huanming as its first director. BGI Hangzhou and the Zhejiang University also 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 modeled 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 non-profit organization by the Shenzhen government. 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 Illumina HiSeq 2000 gene-sequencing machines, which was backed by US$1.5 billion in "collaborative funds" over the next 10 years from the China Development Bank. By the end of the year, they reportedly had a budget of $30 million. In 2010, BGI Americas was established with its main office in Cambridge, Massachusetts, USA, and BGI Europe was established in Copenhagen, Denmark. By 2018, they were expanded with offices and laboratories in Seattle and San Jose in USA, and London in the UK, as well were founded BGI Asia Pacific with offices in Hong Kong, Kobe (Japan), Bangkok (Thailand), Laos, Singapore, Brisbane (Australia) and many others.
In 2011 BGI reported it employed 4,000 scientists and technicians, and had a $192 million in revenue. BGI did the genome sequencing for the deadly in three days and released it under an open license. Since 2012, it has started to commercialize its services, having investments from China Life Insurance Company, Citic's Goldstone Investment, Jack Ma's Yunfeng Capital, and SoftBank China Capital. That year they also launched their own scientific journal, "GigaScience", partnering with BioMed Central to publish data-heavy life science papers. 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. In the same year, the BGI was roughly valued at $820 million.
In 2015, they signed a collaboration with the Zhongshan Hospital' Center for Clinical Precision Medicine in Shanghai, opened in May 2015 with a budget of ¥100 million. They are reportedly being involved as a sequencing institution in China's US$9.2-billion research project for medical care which will last for 15 years. In May 2017, was announced formation of West Coast Innovation Center, co-located in Seattle and San Jose, on the first location planned to work on precision medicine and feature collaborations with University of Washington, the Allen Institute for Brain Science, the Bill & Melinda Gates Foundation, and Washington State University, while on the second's already existing laboratory with 100 employees to develop the next-generation sequencing technologies. In May 2018, was reached an agreement with Mount Sinai Hospital (Toronto), Canada, for first installation of BGISEQ platforms in North America.
The BGI Group subsidiary, BGI Genomics, had made initial public offering in July 2017 at Shenzhen Stock Exchange, raising ¥547 million ($80.7 million), with company's first-day valuation set at over $1.15 billion. In 2018, the BGI was reportedly 85.3% owned by Wang Jian, and the group owns 42.4% of its main unit BGI Genomics. The reported market value for BGI Genomics in July 2018 was around $5 billion, as is of another subsidiary, MGI Tech, specialized in developing and manufacturing technology, which IPO of a stake of about 20% for $1 billion is scheduled for 2019 in Hong Kong.
Current research projects.
Human genetics.
Human Genome Project.
An international project launched in 1990 and declared complete in 2003. They joined in 1999 and provided 1% of the workload.
International HapMap Project.
An international project launched in 2002 and declared complete in 2009. They provided 10% of the workload.
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.
1000 Genomes Project.
An international project to establish a detailed catalogue of human genetic variation launched in 2008 and declared complete in 2015.
International Cancer Genome Project.
An international project launched in 2008.
1000 Rare Disease Project.
An international projected jointly initiated with Children's Hospital of Philadelphia in 2011. With it were discovered genes and mutations associated with rare diseases, which was reported in more than 20 scientific publications. They also "co-developed a clinical whole exome diagnostic test offered through CHOP pathology since 2012". They again collaborated in 2017 when CHOP's Children's Brain Tumor Tissue Consortium was joined by BGI's China National GeneBank.
Cognitive Genomics Project.
A project called the Cognitive Genomics project focused on the research of the genetic basis of intelligence was announced in August 2012. American physicist Stephen Hsu joined as a scientific adviser and was one of the project's leaders. It was done on 2,200 samples mostly from the United States, out of which 1,600 were of individuals who participated in the Study of Mathematically Precocious Youth and reportedly have IQs over 160, collected by American psychologist and geneticist Robert Plomin. Other than publishing a new improved version of the popular Genome Wide Association Study tool PLINK, the project was never completed and the lead researchers moved to the US to set up the company Genomic Prediction which provides advanced genetic testing for IVF.
Allegations of genetic surveillance in Xinjiang.
In 2019, it was reported that a BGI subsidiary, Forensic Genomics International, had created a WeChat-enabled database of genetic profiles of people across the country. In July 2020, it was reported that BGI returned a Paycheck Protection Program loan following media scrutiny. The same month, the United States Department of Commerce's Bureau of Industry and Security placed two BGI subsidiaries on its Entity List for assisting in alleged human rights abuses due to its genetic analysis work in Xinjiang. BGI responded to the listing stating they "do not condone and would never be involved in any human-rights abuses" and stating that they were puzzled by the decision as the "subsidiary mentioned was established in November 2016 and has not carried out actual business"
Animals and plants.
1000 Plant Genome Project.
Named the 1000 Plant Genomes Project (1KP), this was an international project launched in 2008 and declared complete in 2015. The final results were published in Nature in 2019. In 2010, BGI has announced it will contribute US$100 million to large-scale sequencing projects of plants and animals. In 2018 it was announced that the 1KP project was being succeeded by the 10KP project to sequence 10,000 plant species to a high (chromosome level) quality.
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. The Tibetan antelope genome was published in 2013, the polar bear in 2014, and the Emperor and Adelie penguin genomes in 2014.
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. It was announced at the time that BGI would also sequence the genomes and epigenomes 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. The liger and tigon projects were never carried out, but results were reported in 2013 for the genomes of the Amur tiger, the white Bengal tiger, African lion, white African lion and snow leopard.
Symbiont Genome Project.
A jointly funded project announced on 19 March 2010, BGI announced it would 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. This work was eventually completed presenting the genome assembly with a total length of 557 Mb.
Earth BioGenome Project.
An international project initiated with the Smithsonian Institution and other partners in 2018, to sequence DNA of the 1.5 million known eukaryotic species on the planet.
Microorganisms.
Ten Thousand Microbial Genomes Project.
The project was started on 1 August 2009, with the mission to sequence 10,000 microbes within 3 years. It includes sequencing industrial, agricultural, medical microorganism and many others. It is done in collaboration with many institutes, universities and enterprises, including Biotechnology Research Institute of the Chinese Academy of Agricultural Sciences and the Tianjin Institute of Industrial Biotechnology of Chinese Academy of Sciences.
Collaboration with the Chinese military.
In January 2021, Reuters reported that BGI has worked with the People's Liberation Army and affiliated institutions such as the National University of Defense Technology on efforts to enhance soldiers' strength and other projects.
COVID-19.
On August 25, 2020, Reuters reported that about 3,700 people in Sweden were told in error that they had the coronavirus due to a fault in a COVID-19 testing kit from BGI Genomics. Despite being the 5th test to be given WHO Emergency Use Listing, and getting top marks in sensitivity tests in a Dutch study independently validating commercially available tests. BGI Genomics defended the product, blaming differences in thresholds used between labs looking at very low levels of the virus.
Bioinformatics technology.
In 2010, the institute 500-node supercomputer processed 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 was US$9 million. In the same year, 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 assemble an array of plant and animal genomes.
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.
Up until 2015, BGI had released BGISEQ-100, based on Thermo Fisher Scientific's Ion Torrent device, and BGISEQ-1000, based on similar technology by Complete Genomics, for both of which received an approval from the CFDA for a NIFTY (Non-invasive Fetal Trisomy Test) prenatal test. In October 2015, BGI launched BGISEQ-500, a larger desktop sequencing system, which received an approved registration as a medical device a year later by the CFDA. It reportedly received more than 500 orders for the system and run over 112,000 tests until late 2016. The China National GeneBank, opened by BGI and Chinese Government in September 2016, has 150 instruments of the system. The BGISEQ-500 was developed as a sequencing platform capable of competing with Illumina's platforms with its quality and reduced price. In November 2016, BGI launched BGISEQ-50, a miniature version of desktop sequencer. In 2017, BGI began offering WGS for $600. In October 2017, MGI Tech, a subsidiary of BGI, launched two new sequencers MGISEQ-2000 and MGISEQ-200 (later renamed as DNBSEQ-G400 and DNBSEQ-G50), while a year later DNBSEQ-T7.
Patent infringement lawsuits.
In 2019, competitor Illumina, Inc. filed multiple patent infringement lawsuits against BGI. In response, BGI has filed patent infringement lawsuits against Illumina alleging violations of federal antitrust and California unfair competition laws.