Beijing Genomics Institute
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This article appears to be written like an advertisement. (March 2013) |
| Industry | Genome sequencing |
|---|---|
| Number of locations | Hong Kong, Hangzhou, Beijing, China; Boston, USA; Copenhagen, Denmark |
BGI (Chinese: 华大基因; pinyin: Huádà Jīyīn), known as the Beijing Genomics Institute prior to 2008, is one of the world’s premier genome sequencing centers.[1]
History [edit]
BGI was created in 1999. Initially it participated in the Human Genome Project as China's representative.[2] After the project was completed BGI moved to Hangzhou in exchange for funding from the local government. The Rice genome was sequenced in 2002 which became a cover story in Science. In 2003 the SARS virus was sequenced and a detection kit quickly created. Later the first Asian genome was sequenced. In 2010 BGI dramatically expanded its sequencing capacity.[3]
BGI states that in 2007 "the organization’s headquarters relocated to Shenzhen and founded the first citizen-managed, non-profit research institution in China". In 2008, "BGI-Shenzhen was officially recognized as a state agency."[4]
In October 2003, The Beijing Genome Institute Hangzhou (Zhejiang) branch and Zhejiang University founded a new research institute, the James D. Watson Institute of Genome Sciences, Zhejiang University. The Watson Institute is intended to become a major center for research and education in East Asia modeled after the Cold Spring Harbor Laboratory.
BGI Shenzhen received certification for meeting ISO9001:2008 requirements for design and provision of high-throughput sequencing services.[5]
BGI will receive US$1.5 billion in “collaborative funds” over the next 10 years from the China Development Bank.[6]
In 2010, BGI Americas was established and set up its main office in Boston. BGI Europe was established in Copenhagen.
In 2011 the BGI had 4,000 scientists and technicians with numbers predicted to increase.[1]
BGI states that it has collaborations with fifteen out of the top twenty global pharmaceutical companies.[7] BGI provides commercial science, health, agricultural, and informatics services.[8]
The Institute has both a private and a public character. It receives funds both from private investors and the Chinese government. The laboratory is also the Bioinformatics Center of the Chinese Academy of Sciences.
Key achievements [edit]
- First to de novo sequence and assemble mammalian[9] and human genomes with short-read sequencing (so-called "next generation sequencing")[10]
- Sequenced the first ancient human’s genome[11]
- Sequenced the first diploid genome an Asian individual,[12] as part of the Yan Huang project
- Initiated building a sequence map of the human pan-genome, estimated to contain 19-40 million bases not in the human reference genome[13][14]
- Contributed 10% of sequence information for the International HapMap Project
- BGI's first project was contributing 1% of the Human Genome Project’s reference genome and was the only institute in the developing world to contribute
- Produced proof-of-principle study for sequencing the microbiome of the human digestive system, an estimated 150 times larger than the human genome[15][16]
- Key sequencing center in the 1000 Genomes Project
- First Chinese institution to sequence the Severe acute respiratory syndrome (SARS) virus, just hours after the first sequencing of the virus by Canadians[17]
- Key player in the analysis of the 2011 E. coli O104:H4 outbreak[18]
- Sequenced 40 domesticated and wild silkworms, identifying 354 genes likely important in domestication.[19]
- Sequenced the first giant panda genome,[9] equal in size to the human genome, in less than 8 months[20] 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.[9]
- Key player in the Sino-British Chicken Genome Project
- As of 2010[update], plant genomes sequenced include rice, cucumber, soybean, and Sorghum. Animal genomes sequenced include silkworm, honey bee, water flea, lizard, and giant panda. An additional 40 animal and plant species and over 1000 bacteria had also been sequenced.[2][19][21]
- 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.[22]
Current research projects [1] [edit]
Human genetics [edit]
Yan Huang Project [edit]
Named after two Emperors believed to have founded China’s dominant ethnic group,[23] BGI plans to sequence at least 100 Chinese individuals to produce a high-resolution map of Chinese genetic polymorphisms.[24] The first genome sequenced is of an anonymous Chinese billionaire who donated $10 million RMB to the project.[24] And the first YanHuang genome project is named "YanHuang 1",whose genome data is published on http://yh.genomics.org.cn.
The 1000 genomes project [edit]
Ancient Human Genome [edit]
The International Cancer Genome Project [edit]
1,000 Mendelian Disorders Project [edit]
Diabetes-associated Genes and Variations Study (LUCAMP) Cancer Genome Project [edit]
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 [edit]
The Cognitive Research Lab at BGI is working with Stephen Hsu on a project to discover the genetic basis of human intelligence.[25]
Animals and plants [edit]
1,000 Plant and Animal Reference Project [edit]
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.[26]
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.[27]
Genome10K Project [edit]
Three Extreme-Environment Animal Genomes Project [edit]
http://www.genomics.cn/en/research.php?type=show&id=330
Large-scale transcriptome sequencing projects [edit]
1K Insect Transcriptome Evolution (1KITE) Project [edit]
The International Giant Panda Genome Project [edit]
The Ant Genome Initiative [edit]
The cucumber Genome Initiative [edit]
The Orchid Genome Project [edit]
Silkworm Re-sequencing Project [edit]
Soybean genome re-sequencing Project [edit]
International Big Cats Genome Project [edit]
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.[28]
The project will significantly advance conservation research and was auspiciously announced for the Chinese year of the Tiger.[29]
Symbiont Genome Project [edit]
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.[30]
Microorganisms [edit]
Metagenomics of Human Intestinal Tract (MetaHIT) [edit]
Ten Thousand Microbial Genomes Project [edit]
http://english.cas.cn/Ne/CASE/200908/t20090805_44705.shtml
Epigenetics [edit]
Human genome DNA methylation [edit]
Methylome map in silkworm [edit]
Bioinformatics technology [edit]
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[14] 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.[31]
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[10][11][12] (identifying an eight kilobase insertion not detected by mapping to the human reference genome[32]) and animals, like the giant panda.[9]
See also [edit]
References [edit]
- ^ a b Lone Frank, High-Quality DNA, Apr 24, 2011, The Daily Beast, http://www.thedailybeast.com/newsweek/2011/04/24/high-quality-dna.html
- ^ a b The dragon's DNA, Jun 17th 2010, The Economist, http://www.economist.com/node/16349434
- ^ Kevin Davies, The Bedrock of BGI: Huanming Yang, March 23, 2012 | Bio-IT World, http://www.bio-itworld.com/BioIT_Article.aspx?id=109651
- ^ About BGI, BGI, http://en.genomics.cn/navigation/show_navigation.action?navigation.id=95
- ^ "BGI". Retrieved 29 March 2010.
- ^ "BGI to Receive $1.5B in 'Collaborative Funds' Over 10 Years from China Development Bank | In Sequence | Sequencing | GenomeWeb". Retrieved 29 March 2010.
- ^ Pharma and Biotech Services Introduction, BGI, http://en.genomics.cn/navigation/show_navigation.action?navigation.id=1618
- ^ Industry, BGI, http://en.genomics.cn/navigation/show_navigation.action?navigation.id=92
- ^ a b c d Li, R.; Fan, W.; Tian, G.; Zhu, H.; He, L.; Cai, J.; Huang, Q.; Cai, Q. et al. (2009). "The sequence and de novo assembly of the giant panda genome". Nature 463 (7279): 311–317. Bibcode:2010Natur.463..311L. doi:10.1038/nature08696. PMID 20010809.
- ^ a b Li, R.; Zhu, H.; Ruan, J.; Qian, W.; Fang, X.; Shi, Z.; Li, Y.; Li, S. et al. (2009). "De novo assembly of human genomes with massively parallel short read sequencing". Genome Research 20 (2): 265–272. doi:10.1101/gr.097261.109. PMC 2813482. PMID 20019144.
- ^ a b Rasmussen, M.; Li, Y.; Lindgreen, S.; Pedersen, J. S.; Albrechtsen, A.; Moltke, I.; Metspalu, M.; Metspalu, E. et al. (2010). "Ancient human genome sequence of an extinct Palaeo-Eskimo". Nature 463 (7282): 757–762. doi:10.1038/nature08835. PMID 20148029.
- ^ a b Wang, J.; Wang, W.; Li, R.; Li, Y.; Tian, G.; Goodman, L.; Fan, W.; Zhang, J. et al. (2008). "The diploid genome sequence of an Asian individual". Nature 456 (7218): 60–65. doi:10.1038/nature07484. PMC 2716080. PMID 18987735.
- ^ Li, R.; Li, Y.; Zheng, H.; Luo, R.; Zhu, H.; Li, Q.; Qian, W.; Ren, Y. et al. (2009). "Building the sequence map of the human pan-genome". Nature Biotechnology 28 (1): 57–63. doi:10.1038/nbt.1596. PMID 19997067.
- ^ a b "To Start Building 'Human Pan-Genome,' BGI De Novo Assembles Two Genomes from Illumina Data | In Sequence | Sequencing | GenomeWeb". Retrieved 29 March 2010.
- ^ Qin, J.; Li, R.; Raes, J.; Arumugam, M.; Burgdorf, K. S.; Manichanh, C.; Nielsen, T.; Pons, N. et al. (2010). "A human gut microbial gene catalogue established by metagenomic sequencing". Nature 464 (7285): 59–65. doi:10.1038/nature08821. PMID 20203603.
- ^ "International Team Catalogs Microbial Genes in the Human Gut | GenomeWeb Daily News | Sequencing | GenomeWeb". Archived from the original on 7 March 2010. Retrieved 29 March 2010.
- ^ Enserink, M. (2003). "SARS IN CHINA: China's Missed Chance". Science 301 (5631): 294–296. doi:10.1126/science.301.5631.294. PMID 12869735.
- ^ German Teams, BGI and Life Technologies Identify Deadly European E.coli Strain, March 23, 2012 | Bio-IT World, http://www.bio-itworld.com/news/06/02/2011/German-teams-BGI-Life-Technologies-Identify-E-coli-strain.html
- ^ a b Xia, Q.; Guo, Y.; Zhang, Z.; Li, D.; Xuan, Z.; Li, Z.; Dai, F.; Li, Y. et al. (2009). "Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)". Science 326 (5951): 433–436. doi:10.1126/science.1176620. PMID 19713493.
- ^ Cyranoski, D. (2010). "Chinese bioscience: The sequence factory". Nature 464 (7285): 22–24. doi:10.1038/464022a. PMID 20203579.
- ^ Huang, S.; Li, R.; Zhang, Z.; Li, L.; Gu, X.; Fan, W.; Lucas, W.; Wang, X. et al. (2009). "The genome of the cucumber, Cucumis sativus L". Nature Genetics 41 (12): 1275–1281. doi:10.1038/ng.475. PMID 19881527.
- ^ BGI Shenzhen Ranked 4th of Top 10 Institutions in NPI 2010 China, BGI, http://www.bgisequence.com/home/newsandevents/news/bgi-shenzhen-ranked-4th-of-top-10-institutions-in-npi-2010-china
- ^ "Chinese scientists sequence 1st volunteer's genome". Retrieved 29 March 2010.
- ^ a b "BGI Offers Next-Gen Sequencing Service, Kicks Off 100-Genome Sequencing Project | In Sequence | Sequencing | GenomeWeb". Retrieved 29 March 2010.
- ^ Stephen Hsu is New Director of Research for MSU:
- ^ Fox, J.; Kling, J. (2010). "Chinese institute makes bold sequencing play". Nature Biotechnology 28 (3): 189–191. doi:10.1038/nbt0310-189c. PMID 20212469.
- ^ http://www.ldl.genomics.cn/page/index.jsp
- ^ "BGI to Sequence Tiger, Lion, and Leopard Species This Year | In Sequence | Sequencing | GenomeWeb". Archived from the original on 28 February 2010. Retrieved 29 March 2010.
- ^ "BGI". Archived from the original on 17 February 2010. Retrieved 29 March 2010.
- ^ "BGI". Retrieved 29 March 2010.
- ^ Petsko, G. A. (2010). "Rising in the East". Genome Biology 11 (1): 102. doi:10.1186/gb-2010-11-1-102. PMC 2847708. PMID 20156314.
- ^ "BGI Uses New Short-Read Algorithm to Assemble Panda Genome as Proof of Concept for Human Genome | BioInform | Informatics | GenomeWeb". Retrieved 28 March 2010.
External links [edit]
