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$1,000 genome

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Not to be confused with The 1000 Genomes Project.
Evolution of the cost of sequencing a human genome from 2001 to 2021

The $1,000 genome refers to an era of predictive and personalized medicine during which the cost of fully sequencing an individual's genome (WGS) is roughly one thousand USD.[1][2] It is also the title of a book by British science writer and founding editor of Nature Genetics, Kevin Davies.[3] By late 2015, the cost to generate a high-quality "draft" whole human genome sequence was just below $1,500.[4]

History

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The "$1,000 genome" catchphrase was first publicly recorded in December 2001 at a scientific retreat to discuss the future of biomedical research following publication of the first draft of the Human Genome Project (HGP), convened by the National Human Genome Research Institute at Airlie House in Virginia.[5] The phrase neatly highlighted the chasm between the actual cost of the Human Genome Project, estimated at $2.7 billion over a decade, and the benchmark for routine, affordable personal genome sequencing.

On 2 October 2002, Craig Venter introduced the opening session of GSAC (The Genome Sequencing and Analysis Conference) at the Hynes Convention Center in Boston: "The Future of Sequencing: Advancing Towards the $1,000 Genome." Speakers included George M. Church and executives from 454 Life Sciences, Solexa, U.S. Genomics, VisiGen and Amersham plc.[6][7] In 2003, Venter announced that his foundation would earmark $500,000 for a breakthrough leading to the $1,000 genome.[8] That sum was subsequently rolled into the Archon X Prize.

In October 2004, NHGRI introduced the first in a series of '$1,000 Genome' grants designed to advance "the development of breakthrough technologies that will enable a human-sized genome to be sequenced for $1,000 or less."[9]

In a January 2006 article in Scientific American making the case for the Personal Genome Project, George M. Church wrote

The "$1,000 genome" has become shorthand for the promise of DNA-sequencing capability made so affordable that individuals might think the once-in-a-lifetime expenditure to have a full personal genome sequence read to a disk for doctors to reference is worthwhile.[10]

In 2007, the journal Nature Genetics invited dozens of scientists to respond to its 'Question of the Year':

The sequencing of the equivalent of an entire human genome for $1,000 has been announced as a goal for the genetics community... What would you do if [the $1,000 genome was] available immediately?[11]

In May 2007, during a ceremony held at Baylor College of Medicine, 454 Life Sciences founder Jonathan Rothberg presented James D. Watson with a digital copy of his personal genome sequence on a portable hard drive. Rothberg estimated the cost of the sequence—the first personal genome produced using a next-generation sequencing platform—at $1 million.[12] Watson's genome sequence was published in 2008.[13]

A number of scientists have highlighted the cost of additional analysis after performing sequencing. Bruce Korf, past president of the American College of Medical Genetics, described "the $1-million interpretation."[14][failed verification] Washington University's Elaine Mardis prefers "the $100,000 analysis."[15]

Commercial efforts

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At the end of 2007, the biotech company Knome debuted the first direct-to-consumer genome sequencing service at an initial price of $350,000 (including analysis). One of the first clients was Dan Stoicescu, a Swiss-based biotech entrepreneur.[16] As the costs of sequencing continued to plummet, in 2008, Illumina announced that it had sequenced an individual genome for $100,000 in reagent costs. Applied Biosystems countered by saying the cost on its platform was $60,000.[17] Pacific Biosciences became the latest entrant in what The New York Times called "a heated race for the '$1,000 genome'".[18][19] In 2009, Stanford University professor Stephen Quake published a paper sequencing his own genome on an instrument built by Helicos Biosciences (a company he co-founded) for a reported cost in consumables of $48,000.[20] That same year, Complete Genomics debuted its proprietary whole-genome sequencing service for researchers, charging as little as $5,000/genome for bulk orders.[21]

In 2010, Illumina introduced its individual genome sequencing service for consumers, who were required to present a doctor's note. The initial price was $50,000/person. One of the first clients was former Solexa CEO John West, who had his entire family of four sequenced.[22] In January 2012, Life Technologies unveiled a new sequencing instrument, the Ion Proton Sequencer, which it said would achieve the $1,000 genome in a day within 12 months.[23] Sharon Begley wrote: "After years of predictions that the '$1,000 genome' – a read-out of a person's complete genetic information for about the cost of a dental crown—was just around the corner, a U.S. company is announcing... that it has achieved that milestone."[24]

In January 2014, Illumina launched its HiSeq X Ten Sequencer, claiming to have produced the first $1,000 genome at 30× coverage. Some researchers hailed the HiSeq X Ten's release as a milestone – Michael Schatz of Cold Spring Harbor Laboratory said that "it is a major human accomplishment on par with the development of the telescope or the microprocessor". However, critics pointed out that the $10 million upfront investment required to purchase the system would deter customers. Furthermore, the $1,000 genome cost calculation left out overheads, such as the cost of powering the machine.[25] In September 2015, Veritas Genetics (co-founded by George Church) announced $1,000 full-genome sequencing including interpretation for participants in the Personal Genome Project.[26]

In April 2017, the newly formed European company Dante Labs started offering the WGS for $900.[27][28] In 2017, Beijing Genomics Institute began offering WGS for $600.[29] In July 2018, on Amazon Prime Day, Dante Labs offered it for $349.[30] In November 2018, around the time of Black Friday, Dante Labs offered WGS for the first time less than $200,[31] and Veritas Genetics for two days for the same price of $199 offered WGS limited to a thousand customers.[32] In March of the same year, geneticist Matthew Hurles of Wellcome Sanger Institute noted that the private companies, including Illumina,[33] are currently competing to reach a new target for WGS of only $100.[34] On 18 February 2020, Nebula Genomics announced that has partnered up with BGI Group to start offering 30x WGS for $299.[35]

Archon Genomics X PRIZE

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It was originally announced that the revamped Archon Genomics X PRIZE presented by Medco would hold a $10-million grand prize competition in January 2013 for the team that reaches (or comes closest to reaching) the $1,000 genome. The grand prize would go to "the team(s) able to sequence 100 human genomes within 30 days to an accuracy of 1 error per 1,000,000 bases, with 98% completeness, identification of insertions, deletions and rearrangements, and a complete haplotype, at an audited total cost of $1,000 per genome."[36] In August 2013, the Archon Genomics X PRIZE was cancelled, as the founders felt it had been "Outpaced by Innovation," and "was not incentivizing the technological changes".[37]

References

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  1. ^ Mardis, E. R. (2006). "Anticipating the 1,000 dollar genome". Genome Biology. 7 (7): 112. doi:10.1186/gb-2006-7-7-112. PMC 1779559. PMID 17224040.
  2. ^ Service, R. F. (2006). "GENE SEQUENCING: The Race for the $1000 Genome". Science. 311 (5767): 1544–1546. doi:10.1126/science.311.5767.1544. PMID 16543431. S2CID 23411598.
  3. ^ Kevin Davies. The $1,000 Genome. (New York: Free Press, 2010). ISBN 1-4165-6959-6
  4. ^ "The Cost of Sequencing a Human Genome". Retrieved 15 April 2018.
  5. ^ Beyond the Beginning: The Future of Genomics. Meeting webcast. http://www.genome.gov/10001294.
  6. ^ Sylvia Pagan Westphal. "Race for the $1000 genome is on." New Scientist 12 October 2002.
  7. ^ Mark D. Uehling. "Wanted: The $1000 Genome." Bio-IT World November 2002 Archived 4 January 2012 at the Wayback Machine.
  8. ^ "Venter raises stakes for $1,000 genome prize." Bio-IT World October 2005 Archived 13 December 2011 at the Wayback Machine.
  9. ^ NIH press release. "NHGRI seeks next generation of sequencing technologies." 14 October 2004.
  10. ^ Church, G. M. (2006). "Genomes for all" (PDF). Scientific American. 294 (1): 46–54. Bibcode:2006SciAm.294a..46C. doi:10.1038/scientificamerican0106-46. PMID 16468433. S2CID 28769137.
  11. ^ Question of the Year. Nature Genetics. http://www.nature.com/ng/qoty/index.html
  12. ^ BCM press release. "Nobel laureate James Watson receives personal genome in ceremony at Baylor College of Medicine." 31 May 2007 Archived 6 February 2012 at the Wayback Machine.
  13. ^ Wheeler, D. A.; Srinivasan, M.; Egholm, M.; Shen, Y.; Chen, L.; McGuire, A.; He, W.; Chen, Y. J.; Makhijani, V.; Roth, G. T.; Gomes, X.; Tartaro, K.; Niazi, F.; Turcotte, C. L.; Irzyk, G. P.; Lupski, J. R.; Chinault, C.; Song, X.-Z.; Liu, Y.; Yuan, Y.; Nazareth, L.; Qin, X.; Muzny, D. M.; Margulies, M.; Weinstock, G. M.; Gibbs, R. A.; Rothberg, J. M. (2008). "The complete genome of an individual by massively parallel DNA sequencing". Nature. 452 (7189): 872–876. Bibcode:2008Natur.452..872W. doi:10.1038/nature06884. PMID 18421352.
  14. ^ Kevin Davies. "The $1,000,000 genome interpretation." Bio-IT World October 2010.
  15. ^ Mardis, E. R. (2010). "The $1,000 genome, the $100,000 analysis?". Genome Medicine. 2 (11): 84. doi:10.1186/gm205. PMC 3016626. PMID 21114804.
  16. ^ Amy Harmon. "Gene map becomes a luxury item." The New York Times, March 4, 2008.
  17. ^ Bernadette Tansey. "Applied Biosystems cuts DNA sequencing cost." SF Gate, March 13, 2008.
  18. ^ Andrew Pollack. "The race to read genomes on a shoestring, relatively speaking." New York Times, February 9, 2008.
  19. ^ Wade, N. (2006). "The quest for the $1,000 human genome: DNA sequencing in the doctor's office? At birth? It may be coming closer". The New York Times: F1, F3. PMID 16874933.
  20. ^ Pushkarev, D.; Neff, N. F.; Quake, S. R. (2009). "Single-molecule sequencing of an individual human genome". Nature Biotechnology. 27 (9): 847–850. doi:10.1038/nbt.1561. PMC 4117198. PMID 19668243.
  21. ^ Emily Singer. Technology Review. 2008.
  22. ^ Dewey, F. E.; Chen, R.; Cordero, S. P.; Ormond, K. E.; Caleshu, C.; Karczewski, K. J.; Whirl-Carrillo, M.; Wheeler, M. T.; Dudley, J. T.; Byrnes, J. K.; Cornejo, O. E.; Knowles, J. W.; Woon, M.; Sangkuhl, K.; Gong, L.; Thorn, C. F.; Hebert, J. M.; Capriotti, E.; David, S. P.; Pavlovic, A.; West, A.; Thakuria, J. V.; Ball, M. P.; Zaranek, A. W.; Rehm, H. L.; Church, G. M.; West, J. S.; Bustamante, C. D.; Snyder, M.; Altman, R. B.; Klein, T. E.; Butte, A. J.; Ashley, E. A. (2011). "Phased Whole-Genome Genetic Risk in a Family Quartet Using a Major Allele Reference Sequence". PLOS Genetics. 7 (9): e1002280. doi:10.1371/journal.pgen.1002280. PMC 3174201. PMID 21935354.
  23. ^ Defrancesco, L. (2012). "Life Technologies promises $1,000 genome". Nature Biotechnology. 30 (2): 126. doi:10.1038/nbt0212-126a. PMID 22318022. S2CID 11851834.
  24. ^ Sharon Begley. "Insight: New DNA Reader to Bring Promise." Reuters.com. 10 January 2012.
  25. ^ Check Hayden, Erika (2014). "Is the $1,000 genome for real?". Nature. doi:10.1038/nature.2014.14530. S2CID 211730238.
  26. ^ Alexandra Ossola (1 October 2015). "Your Full Genome Can Be Sequenced and Analyzed For Just $1,000". PopSci.
  27. ^ "Dante Labs Offers EUR 850 Whole Genome Sequencing and Interpretation for the First Time in the World". PR Newswire. 24 April 2017. Retrieved 2 December 2018.
  28. ^ Julia Karow (23 May 2017). "Dante Labs Offers Direct-to-Consumer Hereditary Disease Risk, Genome, Exome Tests in Europe". GenomeWeb. Retrieved 2 December 2018.
  29. ^ Megan Molteni (18 May 2017). "A Chinese Genome Giant Sets Its Sights on the Ultimate Sequencer". Wired. Retrieved 2 December 2018.
  30. ^ "Dante Labs Offers $349 Whole Genome Sequencing on Amazon Prime Day". PR Newswire. 16 July 2018. Retrieved 2 December 2018.
  31. ^ Anthony Cuthbertson (23 November 2018). "Black Friday weirdest deals: iPad potties, twerking robots and DNA sequencing". The Independent. Archived from the original on 1 May 2022. Retrieved 2 December 2018.
  32. ^ Megan Molteni (19 November 2018). "Now You Can Sequence Your Whole Genome for Just $200". Wired. Retrieved 2 December 2018.
  33. ^ Matthew Herper (9 January 2017). "Illumina Promises To Sequence Human Genome For $100 -- But Not Quite Yet". Forbes. Retrieved 2 December 2018.
  34. ^ Sarah Neville (5 March 2018). "Cheaper DNA sequencing unlocks secrets of rare diseases". Financial Times. Retrieved 2 December 2018.
  35. ^ "Nebula Genomics, Partnering with BGI, Sets Industry Standard by Offering 30x Whole-Genome Sequencing for $299". BioSpace. 18 February 2020. Archived from the original on 18 January 2022. Retrieved 18 February 2022.
  36. ^ Kedes, L.; Campany, G. (2011). "The new date, new format, new goals and new sponsor of the Archon Genomics X PRIZE Competition". Nature Genetics. 43 (11): 1055–1058. doi:10.1038/ng.988. PMID 22030612.
  37. ^ "$10 million Genomics X Prize canceled: 'Outpaced by innovation'". NBC News. 24 August 2013.

Further reading

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Additional resources

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