$1,000 genome

Not to be confused with The 1000 Genomes Project.

The $1,000 genome refers to an era of predictive and personalized medicine during which the cost of full genome sequencing an individual or patient costs roughly USD $1,000.[1][2] It is also the title of a book by British science writer and founding editor of Nature Genetics, Kevin Davies.[3]

History

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 HGP, convened by the National Human Genome Research Institute at Airlie House in Virginia.[4] 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.[5][6] In 2003, Venter announced that his foundation would earmark $500,000 for a breakthrough leading to the $1,000 genome.[7] 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."[8]

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.”:[9]

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?”:[10]

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.[11] Watson's genome sequence was published in 2008.[12]

Commercial efforts

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.[13] 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.[14] Pacific Biosciences became the latest entrant in what the New York Times called "a heated race for the '$1,000 genome'", suggesting it would offer the 15-minute genome by 2013.[15][16]

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.[17] That same year, Complete Genomics debuted its proprietary whole-genome sequencing service for researchers, charging as little as $5,000/genome for bulk orders.[18]

In 2010, Illumina (company) 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.[19]

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.[20] 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.”[21]

As the cost of personal genome sequencing plummets, the bottleneck will increasingly become the cost of interpreting genomic data, or what Bruce Korf, past president of the American College of Medical Genetics, calls “the $1-million interpretation.”[22] Washington University’s Elaine Mardis prefers “the $100,000 analysis.”[23]

In September 2011, the consumer genomics company 23andMe announced it would begin offering the $999 exome to existing clients.[24]

Even before the realization of the $1,000 genome, at least one biotech company, Genia Technologies, proclaimed in 2011 it would achieve the $100 genome.[25]

In January 2014, Illumina (company) launched its HiSeq X Ten Sequencer which delivers the first $1,000 genome at 30x coverage,[26] including reagent costs ($797), instrument depreciation ($137 per genome), and sample preparation ($55–$65 per genome) amortised over 18,000 genomes sequenced per year over a four-year operational period .[27] The first three institutions in the world to purchase the X Ten machines and become capable of sequencing the $1,000 genome were the Garvan Institute of Medical Research in Sydney, Australia; The Broad Institute in Cambridge, Massachusetts, United States; Macrogen in Rockville, Maryland, United States.[28]

In September 2015, Veritas Genetics (co-founded by George Church) announced $1000 full-genome sequencing including interpretation for participants in the Personal Genome Project.[29][30][31]

Archon Genomics X PRIZE

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."[32]

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" [33]

References

  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 1779559Freely accessible. 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.
  3. ↑ Kevin Davies. The $1,000 Genome. (New York: Free Press, 2010). ISBN 1-4165-6959-6
  4. ↑ Beyond the Beginning: The Future of Genomics. Meeting webcast. http://www.genome.gov/10001294.
  5. ↑ Sylvia Pagan Westphal. "Race for the $1000 genome is on." New Scientist 12 October 2002.
  6. ↑ Mark D. Uehling. "Wanted: The $1000 Genome." Bio-IT World November 2002.
  7. ↑ "Venter raises stakes for $1,000 genome prize." Bio-IT World October 2005.
  8. ↑ NIH press release. "NHGRI seeks next generation of sequencing technologies." 14 October 2004.
  9. ↑ Church, G. M. (2006). "Genomes for all" (PDF). Scientific American. 294 (1): 46–54. doi:10.1038/scientificamerican0106-46. PMID 16468433.
  10. ↑ Question of the Year. Nature Genetics. http://www.nature.com/ng/qoty/index.html
  11. ↑ BCM press release. "Nobel laureate James Watson receives personal genome in ceremony at Baylor College of Medicine." 31 May 2007.
  12. ↑ 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. doi:10.1038/nature06884. PMID 18421352.
  13. ↑ Amy Harmon. "Gene map becomes a luxury item." New York Times, March 4, 2008.
  14. ↑ Bernadette Tansey. "Applied Biosystems cuts DNA sequencing cost." SF Gate, March 13, 2008.
  15. ↑ Andrew Pollack. "The race to read genomes on a shoestring, relatively speaking." New York Times, February 9, 2008.
  16. ↑ 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.
  17. ↑ 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. PMID 19668243.
  18. ↑ Emily Singer. Technology Review. 2008.
  19. ↑ 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 3174201Freely accessible. PMID 21935354.
  20. ↑ Defrancesco, L. (2012). "Life Technologies promises $1,000 genome". Nature Biotechnology. 30 (2): 126. doi:10.1038/nbt0212-126a. PMID 22318022.
  21. ↑ Sharon Begley. "Insight: New DNA Reader to Bring Promise." Reuters.com. 10 January 2012.
  22. ↑ Kevin Davies. "The $1,000,000 genome interpretation." Bio-IT World October 2010.
  23. ↑ Mardis, E. R. (2010). "The $1,000 genome, the $100,000 analysis?". Genome Medicine. 2 (11): 84. doi:10.1186/gm205. PMC 3016626Freely accessible. PMID 21114804.
  24. ↑ 23andMe website.
  25. ↑ Kevin Davies. "Genia's nanopore/microchip technology gains Life Technologies' support." Bio-IT World November 2011.
  26. ↑ HiSeq X Ten and HiSeq X Five Systems
  27. ↑ Is the $1,000 genome for real? : Nature News & Comment
  28. ↑ "Illumina Introduces the HiSeq X™ Ten Sequencing System" (Press release). Illumina. January 14, 2014. Retrieved 2015-07-14.
  29. ↑ "Veritas Genetics Breaks $1,000 Whole Genome Barrier" (Press release). PR Newswire. 2015-09-29.
  30. ↑ Alexandra Ossola (2015-10-01). "Your Full Genome Can Be Sequenced and Analyzed For Just $1,000". PopSci.
  31. ↑ Margaret Jackson (2015-09-25). "VERITAS GENETICS BREAKS $1,000 WHOLE GENOME BARRIER". CerconeBrown.
  32. ↑ 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.
  33. ↑ nbcnews

Further reading

Additional Resources

Webcast of James Watson personal genome presentation, 31 May 2007. http://www.bcm.edu/news/packages/watson_genome.cfm

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