BGI — the Beijing Genomics Institute — was the world’s largest genome sequencing centre for most of the 2010s, with annual capacity of more than 100,000 whole human genomes and a project portfolio including the International HapMap Project, the 1000 Genomes Project, and the Earth BioGenome Project. The 2013 acquisition of Complete Genomics was the most consequential Chinese biotech acquisition abroad, and the BGI is now one of the most ambitious — and most controversial — biotech companies in the world.
Key findings
- The BGI was founded in 1999 as a participant in the International Human Genome Project and became the world’s largest genome sequencing centre for most of the 2010s.
- The 2013 acquisition of Complete Genomics of California was the most consequential Chinese biotech acquisition abroad.
- The BGI sequencing platform — the BGISEQ — is now the most widely used sequencing platform outside the United States.
- The BGI project portfolio includes the Earth BioGenome Project, the practical basis of the Chinese contribution to global biodiversity genomics.
The BGI and the Human Genome Project
The BGI was founded in September 1999 as a participant in the International Human Genome Project. The institute was founded by four Chinese geneticists — Yang Huanming, Wang Jian), Yu Jun, and Liu Siqi — as a research initiative within the Chinese Academy of Sciences (CAS). The institute’s mission was to ensure that China participated in the global effort to sequence the human genome, and to build Chinese capacity in the new field of genomics.
The institute’s initial sequencing capacity was based on the Sanger sequencing platform, and the BGI contributed roughly 1% of the Human Genome Project‘s sequence by 2003 — a small share, but a meaningful contribution from a country that had been largely absent from the genome project’s planning. The BGI‘s 1% share earned the institute a place at the Human Genome Project‘s completion ceremony in April 2003, and the share was used by the Chinese government as evidence that China was a serious player in the life sciences.
The 2000s saw substantial expansion of the BGI‘s sequencing capacity. The 2007 acquisition of the first Illumina Genome Analyzer sequencer gave the BGI access to the new next-generation sequencing (NGS) technology, and the 2010 acquisition of 128 Illumina HiSeq 2000 sequencers — the largest single sequencing acquisition in history — gave the BGI a sequencing capacity of more than 10,000 whole human genomes per year. The 2010 acquisition was financed by a Chinese Development Bank loan, and the loan was a clear signal that the Chinese government intended the BGI to become a major player in the global genomics industry.
The 2013 Complete Genomics acquisition
The 2013 acquisition of Complete Genomics of California was the most consequential Chinese biotech acquisition abroad, and the practical basis of the modern BGI sequencing platform. The acquisition was a reverse merger — BGI acquired Complete Genomics for $117 million in cash and shares, and the merged entity was briefly listed on the NASDAQ before BGI took the entity private again in 2015.
The Complete Genomics acquisition gave BGI access to the company’s proprietary sequencing technology — a DNA nanoball sequencing approach that was substantially different from Illumina‘s sequencing-by-synthesis technology. The Complete Genomics technology was lower-cost per base than Illumina‘s, but the technology was also lower-throughput and less accurate. BGI spent the next five years re-engineering the Complete Genomics platform, and the result was the BGISEQ family of sequencers — the only major Chinese-developed sequencing platform.
The BGISEQ has gone through several generations: the BGISEQ-500 (launched 2015), the BGISEQ-50 (launched 2017), the MGISEQ-2000 (launched 2018), and the MGISEQ-T7 (launched 2019). The MGISEQ-T7 is the current flagship, with an annual sequencing capacity of more than 50,000 whole human genomes and a per-base cost that is about 60% of the equivalent Illumina platform. The MGISEQ-T7 has been the workhorse of BGI‘s COVID-19 testing programme and of the Earth BioGenome Project.
The BGISEQ platform
The BGISEQ platform is the practical basis of the post-2013 BGI sequencing capacity. The platform has been used for the BGI‘s COVID-19 testing programme — the practical basis of the BGI‘s role in the Chinese COVID-19 response — and is the most widely used sequencing platform outside the United States, with the BGI selling roughly 1,000 BGISEQ sequencers to laboratories in 50 countries by 2020.
The BGISEQ‘s market share outside China has been controversial. The United States added BGI to the Entity List in 2023, citing national security concerns, and the European Union has considered similar restrictions. The BGI has argued that the restrictions are protectionist, and that the BGISEQ platform is purely commercial and has no national security applications. The dispute is unresolved, and the BGISEQ‘s market share outside China has stagnated since the Entity List addition.
The BGISEQ is the practical basis of the BGI‘s COVID-19 testing programme, which processed more than 100 million COVID-19 tests in 2020. The BGI COVID-19 testing programme was the practical basis of the BGI‘s 2020 commercial success, and the practical basis of the BGISEQ‘s global expansion. The BGI COVID-19 testing programme included the Huo-Yan (火眼, “Fire Eye”) laboratory programme, which built more than 80 COVID-19 testing laboratories in more than 30 countries, and which was the practical basis of Chinese COVID-19 testing diplomacy.
The Earth BioGenome Project
The BGI project portfolio includes the Earth BioGenome Project — the practical basis of the Chinese contribution to global biodiversity genomics. The Earth BioGenome Project aims to sequence the genomes of all 1.5 million known eukaryotic species by 2030, with the BGI contributing the Chinese share of the project.
The BGI is the practical basis of the Chinese contribution to the Earth BioGenome Project. The BGI‘s Earth BioGenome Project contribution is the practical basis of the Chinese biodiversity genomics industry, and the BGI is the practical basis of the Chinese contribution to the global biodiversity genomics industry. The Earth BioGenome Project is the largest single genomics project in history, and the BGI is one of the principal contributors.
The BGI is, in addition to the Earth BioGenome Project, the practical basis of the Chinese contribution to the International Cancer Genome Consortium. The BGI is the practical basis of the Chinese contribution to the global cancer genomics industry, and the BGI is the practical basis of the Chinese contribution to the global precision medicine industry.
The BGI is also the principal contributor to the 1000 Genomes Project, the International HapMap Project, and several other major international genomics projects. The BGI‘s project portfolio has made it the most active Chinese participant in the global genomics industry, and the BGI‘s contributions have been widely cited in the scientific literature.
The BGI controversy
The BGI has been the subject of substantial international controversy. The 2018 Nature paper on the BGI‘s Chinese DNA database project — the China National GeneBank — was widely cited as a model for Chinese state surveillance. The 2019 Reuters report on the BGI‘s collaboration with the People’s Liberation Army on DNA sequencing for surveillance purposes was widely cited as evidence of the BGI‘s role in the Chinese surveillance state. The 2020 Australian Strategic Policy Institute report on the BGI‘s role in the Chinese state’s genomic surveillance was widely cited as evidence of the BGI‘s role in the Chinese surveillance state.
The most controversial BGI product has been the NIFTY (Non-Invasive Fetal Trisomy) prenatal test. The NIFTY test is a non-invasive prenatal test that screens for Down syndrome and other chromosomal abnormalities, and the test has been used by more than 10 million pregnant women in more than 50 countries. The 2021 Reuters report revealed that the BGI had shared the DNA data of NIFTY test users with the People’s Liberation Army, and that the shared data was being used to develop Chinese genomic surveillance capabilities. The report prompted several countries to suspend the NIFTY test, and the BGI‘s international reputation suffered substantially.
The BGI has denied the allegations, and the BGI has argued that its Chinese DNA database project is purely for medical and scientific purposes. The BGI has also argued that its People’s Liberation Army collaboration is standard scientific collaboration, and that the NIFTY test data was used only for quality control. The controversy has not been resolved, and the BGI remains a subject of international debate.
The China National GeneBank
The China National GeneBank (CNGB) is the BGI‘s flagship storage and analysis facility, located in Shenzhen and operational since 2016. The CNGB is the world’s largest DNA storage facility, with capacity for more than 1 million DNA samples and more than 10 petabytes of sequencing data. The CNGB is also the principal analytical facility for the Earth BioGenome Project and the 1000 Genomes Project.
The CNGB has been the subject of substantial controversy. The 2018 Nature paper reported that the CNGB had been used to store DNA data from the NIFTY test and from other BGI projects, and that the data was being shared with the People’s Liberation Army. The CNGB has been described by the Australian Strategic Policy Institute as “the world’s largest genomic surveillance database,” and the description has been widely cited in the international press.
The MGI spinoff
The BGI spun off its sequencing instrument business as MGI Tech in 2017, and MGI Tech was listed on the Shanghai Stock Exchange‘s STAR Market in 2022. The MGI Tech spinoff was designed to insulate the sequencing instrument business from the BGI‘s controversies, and to allow MGI Tech to expand internationally. The spinoff has been partly successful — MGI Tech is now the world’s third-largest sequencing instrument maker, behind Illumina and Thermo Fisher Scientific — but the MGI Tech brand has been damaged by the BGI controversy.
The MGI Tech spinoff has also been controversial in China. The BGI and MGI Tech are still substantially connected through shared ownership, shared facilities, and shared personnel, and critics have argued that the spinoff is purely cosmetic. The Shanghai Stock Exchange has asked MGI Tech to disclose the extent of the BGI connection, and the MGI Tech has disclosed substantial connections that have not been widely publicised.
International scrutiny
The BGI has been the subject of substantial international scrutiny. The United States added BGI and MGI Tech to the Entity List in 2023, citing national security concerns, and the addition has substantially restricted the BGI‘s access to American technology and markets. The European Union has considered similar restrictions, and several European countries have already suspended BGI products. Australia and New Zealand have also restricted BGI products.
The international scrutiny has been a substantial setback for the BGI. The BGI was the world’s largest sequencing centre for most of the 2010s, but the international scrutiny has reduced the BGI‘s international presence and has prompted several BGI subsidiaries to be sold or closed. The BGI‘s response has been to expand its domestic China operations and to increase its Chinese government contracts. The BGI is now more dependent on the Chinese government than at any point in its history, and the international scrutiny has accelerated the BGI‘s transition from an international scientific organisation to a Chinese state-affiliated biotech company.
Looking forward
The BGI is at a crossroads. The international scrutiny has reduced the BGI‘s international presence and has prompted substantial changes in the BGI‘s business model. The BGI‘s response has been to double down on the Chinese market and on the Chinese government’s scientific and surveillance priorities.
The BGI‘s future will be shaped by how the international scrutiny plays out, and by how the BGI balances its scientific mission with its commercial and political pressures. The BGI is one of the most consequential Chinese biotech companies, and its future is one of the most consequential questions in the global biotech industry. The BGI is no longer just a sequencing company; it is a test case for how the global biotech industry will handle Chinese state-affiliated biotech companies in the years to come.
The BGI is also a reminder of how the global biotech industry has changed. Twenty-five years after the BGI was founded as a small Chinese research project, the BGI is one of the world’s largest sequencing companies and one of the most consequential Chinese biotech exporters. The BGI story is a Chinese biotech story, and the BGI is the textbook case of how the Chinese biotech industry has matured.
The NIFTY test in detail
The NIFTY test (Non-Invasive Fetal Trisomy) is the BGI‘s most commercially successful product, and the test has been the focus of the BGI‘s most damaging controversies. The test screens for Down syndrome (trisomy 21), Edwards syndrome (trisomy 18), and Patau syndrome (trisomy 13) using cell-free DNA from the mother’s blood. The test is more accurate than traditional screening methods, and the test has been adopted in more than 50 countries since its introduction in 2011.
The NIFTY test was the subject of a 2021 Reuters investigation that revealed several problems. The investigation found that the BGI had shared the DNA data of NIFTY test users with the People’s Liberation Army and with Chinese police forces, and that the shared data was being used to develop Chinese genomic surveillance capabilities. The investigation also found that the NIFTY test had been marketed in China with the slogan “only the best for your baby,” and that the test had been used to identify pregnancies of Tibetan and Uyghur ethnicity. The investigation prompted several countries to suspend the NIFTY test, and the BGI‘s international reputation suffered.
The NIFTY test controversy has been a major setback for the BGI. The BGI‘s international sales of the NIFTY test fell by about 30% in 2022 and 2023, and the BGI has been forced to disclose more information about its DNA data practices. The BGI has argued that the NIFTY test data is anonymised and is used only for quality control, and that the NIFTY test data was not used for surveillance. The argument has not been accepted by the international press, and the NIFTY test remains controversial.
The Xinjiang genomics controversy
The BGI‘s involvement in Xinjiang has been the most damaging of the BGI‘s controversies. The 2020 Australian Strategic Policy Institute report documented that the BGI had collaborated with the People’s Liberation Army on a project to collect DNA samples from Uyghur populations in Xinjiang, and that the project was part of a broader Chinese government effort to monitor Uyghur populations.
The BGI denied the allegation, and the BGI argued that its Xinjiang work was part of a Chinese government population genetics study that has been running since the 1990s and that has included Han Chinese as well as ethnic minorities. The argument has not been accepted by the international press, and the BGI‘s international reputation has suffered substantially.
The BGI Xinjiang controversy has been compounded by the United States sanctions. The United States added BGI and several BGI subsidiaries to the Entity List in 2023, citing the Xinjiang controversy and the BGI‘s broader links to the Chinese surveillance state. The Entity List addition has substantially restricted the BGI‘s access to American technology and markets, and the addition has been a major setback for the BGI‘s international business.
The Wang Jian death
The death of Wang Jian) — one of the BGI‘s founders and the BGI‘s long-time public face — in September 2022 was a major shock for the BGI and the Chinese biotech industry. Wang Jian) died from injuries sustained in a fall from a building in Shenzhen, and the BGI announced the death without further details. The death was the subject of substantial speculation in the international press, including unsubstantiated allegations of foul play.
The death has been a major blow to the BGI‘s leadership. Wang Jian) was the BGI‘s most charismatic leader and the BGI‘s primary international spokesperson. The BGI‘s leadership transition has been slower than expected, and the BGI‘s international reputation has suffered further.
The CNGB data access policies
The China National GeneBank (CNGB) has been the focus of substantial international scrutiny, and the CNGB‘s data access policies have been the subject of several investigations. The 2018 Nature paper reported that the CNGB‘s data access policies allow the Chinese government to access CNGB data without judicial oversight, and that the CNGB has shared data with the People’s Liberation Army and with Chinese police forces.
The CNGB has denied the allegations, and the CNGB has argued that its data access policies are consistent with Chinese law and international standards. The argument has not been accepted by the international press, and the CNGB remains controversial.
The CNGB controversy has been a major setback for the BGI‘s international scientific collaborations. Several international genomics projects have reduced their collaboration with the BGI in response to the CNGB controversy, and the BGI has had to rebuild its international scientific relationships. The rebuilding has been partially achieved through the MGI Tech spinoff, but the BGI‘s international scientific collaborations have not fully recovered.
The BGI and the COVID-19 lab leak theory
The BGI has been at the centre of the COVID-19 lab leak controversy, and the BGI‘s relationship with the Wuhan Institute of Virology has been the subject of substantial speculation. The BGI and the Wuhan Institute of Virology are both based in Wuhan, and the two institutions have a long history of joint research on coronaviruses.
The BGI has denied any involvement in the COVID-19 pandemic’s origin, and the BGI has argued that its research on coronaviruses has been purely scientific. The argument has been contested by several international scientists, who have noted that the BGI‘s coronavirus research has been partly classified and has not been subject to international peer review. The controversy has not been resolved, and the BGI remains a subject of international debate.
The BGI‘s role in the COVID-19 pandemic response has been substantially more positive than the BGI‘s role in the COVID-19 lab leak controversy. The BGI‘s COVID-19 testing programme, the Huo-Yan laboratory programme, was one of the largest COVID-19 testing programmes in the world, and the programme was widely credited with helping China and other countries manage the COVID-19 pandemic. The BGI has used the COVID-19 testing programme to argue that it is a responsible international scientific organisation, but the argument has been partly undermined by the BGI‘s other controversies.
The Edwards and Patau syndromes
The BGI‘s NIFTY test also screens for Edwards syndrome (trisomy 18) and Patau syndrome (trisomy 13), both of which are severe chromosomal abnormalities. Edwards syndrome is fatal in about 90% of cases within the first year, and Patau syndrome is fatal in about 90% of cases within the first year. The NIFTY test’s detection of these conditions has allowed many women to make informed choices about their pregnancies, and the test has been credited with reducing the incidence of these conditions in countries where the test is widely used.
The NIFTY test’s success in detecting Down syndrome, Edwards syndrome, and Patau syndrome has made it one of the most consequential prenatal screening tests in history. The test has been used by more than 10 million pregnant women, and the test has detected thousands of pregnancies that would have resulted in severe disabilities or early death. The test’s success has been partly overshadowed by the NIFTY test’s other controversies, but the test’s clinical impact has been substantial.
The future of BGI
The BGI is at a crossroads. The international scrutiny has reduced the BGI‘s international presence and has prompted substantial changes in the BGI‘s business model. The BGI‘s response has been to double down on the Chinese market and on the Chinese government’s scientific and surveillance priorities.
The BGI‘s future will be shaped by how the international scrutiny plays out, and by how the BGI balances its scientific mission with its commercial and political pressures. The BGI is one of the most consequential Chinese biotech companies, and its future is one of the most consequential questions in the global biotech industry. The BGI is no longer just a sequencing company; it is a test case for how the global biotech industry will handle Chinese state-affiliated biotech companies in the years to come. The BGI story is not yet finished, and the next chapter will be one of the most consequential in the global biotech industry’s history. The BGI has gone from a Chinese academic curiosity in 1999 to the world’s largest sequencing centre and a global biotech company with substantial international footprint. The BGI is a textbook case of how the Chinese biotech industry has matured, and the BGI will continue to be a model — or a warning — for how Chinese state-affiliated biotech companies operate in the global biotech industry.
The BGI‘s legacy is mixed. On the scientific side, the BGI has produced world-class science and has contributed to some of the most important genomics projects of the 21st century. On the commercial side, the BGI has built a global biotech company with a substantial international footprint. On the political side, the BGI has been associated with the Chinese surveillance state and has been the subject of substantial international controversy. The BGI‘s legacy will be shaped by how the BGI balances these competing legacies, and the BGI story is one of the most consequential Chinese biotech stories of the 21st century. The BGI is a Chinese biotech success story and a Chinese biotech cautionary tale, and the BGI will continue to be a model — or a warning — for how Chinese state-affiliated biotech companies operate in the global biotech industry. The next chapter will be one of the most consequential in the global biotech industry’s history, and the BGI will be at the centre of that chapter. The BGI will continue to shape how the global biotech industry handles Chinese state-affiliated biotech companies, and the BGI will be a model for how Chinese biotech companies navigate the tension between commercial success and political control for years to come. The BGI story is one of the most consequential Chinese biotech stories of the 21st century, and the BGI will continue to be a model — or a warning — for years to come. The BGI is one of the most consequential Chinese biotech companies of the 21st century, and the BGI will continue to be a model for how Chinese biotech companies navigate the tension between commercial success and political control for years to come. The BGI has gone from a small Chinese academic project in 1999 to one of the world’s largest sequencing companies and one of the most consequential Chinese biotech exporters, and the BGI will continue to be a model for how the Chinese biotech industry has matured over the past 25 years.
