Genome Sequenced at High Speed

[sharon sanders]

James Watson's genome sequenced at high speed

New-generation technology takes just four months and costs a fraction of old method.
Meredith Wadman

<!-- --> The first full genome to be sequenced using next-generation rapid-sequencing technology is published today (see page 872)¹, marking another milestone in the extraordinarily fastmoving field of human genome sequencing.

It took just four months, a handful of scientists and less than US$1.5 million to sequence the 6 billion base pairs of DNA pioneer James Watson. The achievement is first proof of principle that these rapid-sequencing machines can decipher large, complex genomes (see page 819)². Made in this case by Connecticut-based 454 Life Sciences — a division of Roche Diagnostics — they allow many more sequencing reactions to proceed at the same time, on the same surface, than the previous generation of machines that produced the inaugural human genomes³^,⁴. That change has had big pay-offs in speed, efficiency and, ultimately, cost (see Table 1).

James Watson's is not the first full genome to be published; that distinction goes to genomics entrepreneur J. Craig Venter, whose genome was sequenced using previous-generation machines⁵ at a cost of $100 million. “Venter's genome was at the end of the last generation,” says 454 founder Jonathan Rothberg of the Rothberg Institute for Childhood Diseases in Guilford, Connecticut, who is the Watson paper's lead author. “We did this work in January 2007, with last January's technology,” he points out; the raw data were released in May 2007. “It just keeps on getting better and cheaper.” Rothberg calls Watson “the first of the rest of us”, but the low cost the team managed is still a far cry from the '$1,000 genome' challenge set by the X Prize Foundation.

Not everyone agrees the method is better. “It's a new standard of sequencing technology,” says Venter. “But I don't think it's a new standard of genome coverage and independent assembly.”

One concern is that rapid-sequencing methods cut DNA into much shorter snippets (in this case, 250 bases) for decoding than the old method used by the international Human Genome Project (HGP) and Venter's former company Celera for their 2001 sequences. These used 500–1,000-base snippets. Shorter snippets make reassembly more technically challenging and mean it is harder to probe areas of the genome that have large, repeating sequences.

Evan Eichler, a geneticist at the University of Washington in Seattle, notes that 5–10% of the genome consists of these complex areas, which contain disease-causing genes and vary widely among individuals. “My concern specifically is whether short-sequence technology will give us any information in those areas,” Eichler says. “How much do we understand about these particular regions in Jim Watson's genome?”

Others point out that the authors on the Watson paper relied heavily on the HGP reference sequence, which they used as a guide to help them reassemble the snippets. “This paper certainly seems to be proof that they can do a good job with the 454 sequencing when they have a reference genome,” says Jonathan Eisen, an evolutionary biologist at the University of California, Davis, who wants to use the machines to sequence other species. “Their next task will be to show that they can do a good job when they have no reference genome.” Despite all the sequencing advances, very little is known about how to read the book of life that is opening before us, says Michael Egholm, vicepresident of research and development at 454. Egholm was part of a counselling session advising Watson on the meaning of the 20 mutations in his sequence that are reported to be associated with increased disease risk. “It was so profound, how little we were actually able to say [to him] about that,” he says. “To me, it really proved that this is the beginning, not the end.”

• References
  1. <!-- . -->Wheeler, D. A. et al. Nature 452, 872-876 (2008). | Article |
  2. <!-- . -->Olson, M. V. Nature 452, 819-820 (2008). | Article |
  3. <!-- . --> The International Human Genome Mapping Consortium Nature 409, 934-941 (2001). | Article | PubMed | ISI | ChemPort |
  4. <!-- . -->Venter, J. C. et al. Science 291, 1304-1351 (2001). | Article | PubMed | ISI | ChemPort |
  5. <!-- . -->Levy, S. et al. PLoS Biol. 5, e254-e286 (2007). | Article | PubMed | ChemPort |

http://www.nature.com/news/2008/080416/full/452788b.html

 

[sharon sanders]

Re: Genome Sequenced at High Speed

The complete genome of an individual by massively parallel DNA sequencing

David A. Wheeler^1,⁷, Maithreyan Srinivasan^2,⁷, Michael Egholm^2,⁷, Yufeng Shen^1,⁷, Lei Chen¹, Amy McGuire³, Wen He², Yi-Ju Chen², Vinod Makhijani², G. Thomas Roth², Xavier Gomes², Karrie Tartaro^2,⁸, Faheem Niazi², Cynthia L. Turcotte², Gerard P. Irzyk², James R. Lupski^4,^5,⁶, Craig Chinault⁴, Xing-zhi Song¹, Yue Liu¹, Ye Yuan¹, Lynne Nazareth¹, Xiang Qin¹, Donna M. Muzny¹, Marcel Margulies², George M. Weinstock^1,⁴, Richard A. Gibbs^1,⁴ & Jonathan M. Rothberg^2,⁸

1. Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
2. 454 Life Sciences, Roche Diagnostics, 20 Commercial Street, Bradford, Connecticut 06405, USA
3. Center for Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston Texas 77030, USA
4. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston Texas 77030, USA
5. Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston Texas 77030, USA
6. Texas Children's Hospital, Texas Medical Center, Houston, Texas 77030, USA
7. These authors contributed equally to this work.
8. Present addresses: Molecular Imaging Systems, Carestream Health, Inc., 4 Science Park, New Haven, Connecticut 06511, USA (K.T.); Rothberg Institute for Childhood Diseases, 530 Whitfield Street, Guilford, Connecticut 06437, USA (J.M.R.).

Correspondence to: Richard A. Gibbs^1,⁴Jonathan M. Rothberg^2,⁸ Correspondence and requests for materials should be addressed to J.M.R. (Email: jonathan.rothberg@gmail.com) or R.A.G. (Email: agibbs@bcm.tmc.edu).

Top of pageAbstract

The association of genetic variation with disease and drug response, and improvements in nucleic acid technologies, have given great optimism for the impact of 'genomic medicine'. However, the formidable size of the diploid human genome¹, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete individual human genomes. To realize the full potential of genomics for human health, this limitation must be overcome. Here we report the DNA sequence of a diploid genome of a single individual, James D. Watson, sequenced to 7.4-fold redundancy in two months using massively parallel sequencing in picolitre-size reaction vessels. This sequence was completed in two months at approximately one-hundredth of the cost of traditional capillary electrophoresis methods. Comparison of the sequence to the reference genome led to the identification of 3.3 million single nucleotide polymorphisms, of which 10,654 cause amino-acid substitution within the coding sequence. In addition, we accurately identified small-scale (2?40,000 base pair (bp)) insertion and deletion polymorphism as well as copy number variation resulting in the large-scale gain and loss of chromosomal segments ranging from 26,000 to 1.5 million base pairs. Overall, these results agree well with recent results of sequencing of a single individual² by traditional methods. However, in addition to being faster and significantly less expensive, this sequencing technology avoids the arbitrary loss of genomic sequences inherent in random shotgun sequencing by bacterial cloning because it amplifies DNA in a cell-free system. As a result, we further demonstrate the acquisition of novel human sequence, including novel genes not previously identified by traditional genomic sequencing. This is the first genome sequenced by next-generation technologies. Therefore it is a pilot for the future challenges of 'personalized genome sequencing'.

1. Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
2. 454 Life Sciences, Roche Diagnostics, 20 Commercial Street, Bradford, Connecticut 06405, USA
3. Center for Ethics and Health Policy, Baylor College of Medicine, One Baylor Plaza, Houston Texas 77030, USA
4. Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston Texas 77030, USA
5. Department of Pediatrics, Baylor College of Medicine, One Baylor Plaza, Houston Texas 77030, USA
6. Texas Children's Hospital, Texas Medical Center, Houston, Texas 77030, USA
7. These authors contributed equally to this work.
8. Present addresses: Molecular Imaging Systems, Carestream Health, Inc., 4 Science Park, New Haven, Connecticut 06511, USA (K.T.); Rothberg Institute for Childhood Diseases, 530 Whitfield Street, Guilford, Connecticut 06437, USA (J.M.R.).

http://www.nature.com/nature/journal/v452/n7189/full/nature06884.html;jsessionid=6F3BC267054B4C41950BD58342D2C96B

 

[gsgs]

Re: Genome Sequenced at High Speed

what does that mean for influenza ?