Complete Genomics

Complete Genomics is a life sciences company that has developed and commercialized a DNA sequencing platform for human genome sequencing and analysis. This solution combines the company’s proprietary human genome sequencing technology with its informatics and data management software to provide finished variant reports and assemblies at Complete Genomics’ own commercial genome center in Mountain View, California. In March 2013 Complete Genomics was acquired by BGI-Shenzhen, a genomics services company in Shenzhen, Guangdong, China.[1] After the acquisition Complete Genomics moved to San Jose, and in June 2018 become part of MGI, the instruments manufacturing business of BGI.[2]

History

Complete Genomics was founded in March 2006 by Clifford Reid, Radoje (Rade) Drmanac, and John Curson. Clifford Reid was the chairman, president and chief executive officer of Complete Genomics before leaving in 2015 to setup Genos, a spinoff of Complete Genomics' consumer division.[3]

In February 2009, Complete Genomics announced that it had sequenced its first human genome and submitted the resulting variant data to the National Center for Biotechnology Information database. Then, in November 2009, Complete Genomics published sequence data for three human genomes in the journal Science.[4] By the end of 2009, Complete Genomics had sequenced 50 human genomes. To date, the company has sequenced more than 20,000 genomes.

The resulting data has supported research in diverse areas such as screening of embryos,[5] detection of genetic relationships,[6][7] neurology,[8] aging,[9] a novel Mendelian disease with neuromuscular and cardiac involvement,[10] eating disorders,[11] Prader-Willi syndrome and autism,[12] ophthalmology,[13] and oncology.[14][15][16][17][18] In 2014, a collaboration among Radboud University (The Netherlands), Maastricht University Medical Centre (The Netherlands), Central South University (China) and Complete Genomics identified major causes of intellectual disability using whole genome sequencing.[19]

In 2016, Complete Genomics contributed over 184 phased human genomes to George Church's Personal Genome Project.[20] In 2019, they published on their new single-tube long fragment read (stLFR) technology, enabling construction of long DNA molecules from short reads using a combinatorial process of DNA barcoding. This enables phasing, SV detection, scaffolding, and cost-effective diploid de novo genome assembly, from second generation sequencing technology.[21]

Technology platform

Complete Genomics’ proprietary human genome sequencing technology is optimized for the exclusive study of human DNA, providing assembled sequences and variation files. The technology relies on DNA nanoball sequencing, which assembles short sequences of DNA into a full genome. It is designed to use lower volumes and concentrations of reagents than existing systems, and have large numbers of base reads per image.[4]

References
  1. Specter, Michael (6 January 2014) The Gene Factory The New Yorker, Retrieved 28 October 2014
  2. brandonvd. "About Us". Complete Genomics. Retrieved 2019-06-15.
  3. "Consumer Genomics Startup Genos Research Plans to Let Customers Explore, Share Their Data". GenomeWeb. Retrieved 2019-06-15.
  4. Drmanac R; Sparks, A. B.; Callow, M. J.; Halpern, A. L.; Burns, N. L.; Kermani, B. G.; Carnevali, P.; Nazarenko, I.; Nilsen, G. B.; Yeung, G.; Dahl, F.; Fernandez, A.; Staker, B.; Pant, K. P.; Baccash, J.; Borcherding, A. P.; Brownley, A.; Cedeno, R.; Chen, L.; Chernikoff, D.; Cheung, A.; Chirita, R.; Curson, B.; Ebert, J. C.; Hacker, C. R.; Hartlage, R.; Hauser, B.; Huang, S.; Jiang, Y.; et al. (November 2009). "Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays". Science. 327 (5961): 78–81. Bibcode:2010Sci...327...78D. doi:10.1126/science.1181498. PMID 19892942.
  5. Winard R; et al. (2014). "In vitro screening of embryos by whole-genome sequencing: now, in the future or never?". Hum Reprod. 29 (4): 842–851. doi:10.1093/humrep/deu005. PMID 24491297.
  6. Li H; et al. (2014). "Relationship estimation from whole-genome sequence data". PLoS Genet. 10 (1): e1004144. doi:10.1371/journal.pgen.1004144. PMC 3907355. PMID 24497848.
  7. Su S-Y; et al. (2012). "Detection of identity by descent using next-generation whole genome sequencing data". BMC Bioinformatics. 13: 121. doi:10.1186/1471-2105-13-121. PMC 3403908. PMID 22672699.
  8. Bundo M (2014). "Increased L1 retrotransposition in the neuronal genome in schizophrenia". Neuron. 81 (2): 306–313. doi:10.1016/j.neuron.2013.10.053. PMID 24389010.
  9. Kai Y; et al. (2013). "Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs". Twin Research and Human Genetics. 16 (6): 1026–1032. doi:10.1017/thg.2013.73. PMID 24182360.
  10. Wang K; et al. (2013). "Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement". Genome Medicine. 5 (7): 67. doi:10.1186/gm471. PMC 3971341. PMID 23889995.
  11. Cui H; et al. (2013). "Eating disorder predisposition is associated with ESRRA and HDAC4 mutations". J Clin Invest. 123 (11): 4706–4713. doi:10.1172/jci71400. PMC 3809805. PMID 24216484.
  12. Schaaf CP; et al. (2013). "Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism". Nature Genetics. 45 (11): 1405–1408. doi:10.1038/ng.2776. PMC 3819162. PMID 24076603.
  13. Nishiguchi KM; et al. (2012). "Genes associated with retinitis pigmentosa and allied diseases are frequently mutated in the general population". PLoS ONE. 7 (7): e41902. Bibcode:2012PLoSO...741902N. doi:10.1371/journal.pone.0041902. PMC 3407128. PMID 22848652.
  14. Ma Y; et al. (2012). "Developmental timing of mutations revealed by whole-genome sequencing of twins with acute lymphoblastic leukemia". Proc Natl Acad Sci USA. 110 (18): 7429–7433. Bibcode:2013PNAS..110.7429M. doi:10.1073/pnas.1221099110. PMC 3645544. PMID 23569245.
  15. Kiel MJ; et al. (2012). "Whole-genome sequencing identifies recurrent somatic NOTCH2 mutations in splenic marginal zone lymphoma". The Journal of Experimental Medicine. 209 (9): 1553–1565. doi:10.1084/jem.20120910. PMC 3428949. PMID 22891276.
  16. Molenaar JJ; et al. (2012). "Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes". Nature. 483 (7391): 589–593. Bibcode:2012Natur.483..589M. doi:10.1038/nature10910. PMID 22367537.
  17. Turajlic S; et al. (2011). "Whole genome sequencing of matched primary and metastatic acral melanomas". Genome Res. 22 (2): 196–207. doi:10.1101/gr.125591.111. PMC 3266028. PMID 22183965.
  18. Yokoyama S; et al. (2011). "GA novel recurrent mutation in MITF predisposes to familial and sporadic melanoma". Nature. 480 (7375): 99–103. Bibcode:2011Natur.480...99Y. doi:10.1038/nature10630. PMC 3266855. PMID 22080950.
  19. Gilissen C; et al. (2014). "Genome sequencing identifies major causes of severe intellectual disability". Nature. 511 (7509): 344–347. Bibcode:2014Natur.511..344G. doi:10.1038/nature13394. PMID 24896178.
  20. Peters, Brock A.; Drmanac, Radoje; Church, George M.; Estep, Preston W.; Zaranek, Alexander Wait; Vandewege, Ward; Connelly, Abram; Clegg, Tom; Agarwal, Misha R. (2016-12-01). "The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes". GigaScience. 5 (1): 42. doi:10.1186/s13742-016-0148-z. PMC 5057367. PMID 27724973.
  21. Peters, Brock A.; Drmanac, Radoje; Xu, Xun; Kristiansen, Karsten; Wang, Jian; Yang, Huanming; Alexeev, Andrei; Zhang, Wenwei; Dong, Yuliang (2019-05-01). "Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly". Genome Research. 29 (5): 798–808. doi:10.1101/gr.245126.118. ISSN 1088-9051. PMC 6499310. PMID 30940689.
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