The complete genome of an individual by massively parallel DNA sequencing
Open accessAbstract
Next-generation sequencing technologies are revolutionizing human genomics, promising to yield draft genomes cheaply and quickly. One such technology has now been used to analyse much of the genetic code of a single individual — who happens to be James D. Watson. The procedure, which involves no cloning of the genomic DNA, makes use of the latest 454 parallel sequencing instrument. The sequence cost less than US$1 million (and a mere two months) to produce, compared to the approximately US$100 million reported for sequencing Craig Venter's genome by traditional methods. Still a major undertaking, but another step towards the goal of 'personalized genomes' and 'personalized medicine'. 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 is reported. 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’.
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Microarray-based detection of structural variation and exome- and genome-wide sequencing have been pivotal for rare disease gene discovery, supported by in silico analysis and variant prioritization.
“Microarray-based detection of structural variation10 and exome-and genome-wide sequencing11,12 have been pivotal, bolstered by in silico analysis and prioritization of the discovered genetic variants.”
From A brief history of human disease genetics (2020) · cites this paper as [12]
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- Authors
- 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.
- Affiliations
- Baylor College of Medicine (US)
- Rothberg Institute For Childhood Diseases (US)
- Texas Medical Center (US)
- Corresponding author
- Gibbs, Richard A.
- Rothberg, Jonathan M.
- ORCID
- Venue
- Nature
- Published
- 2008-04
- Volume
- 452
- Issue
- 7189
- Pages
- 872-876
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2113649367
- Cited by
- 1,838
- References
- 23
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- FWCI
- 108.62
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- journal article
- Language
- en
- Open access
- hybrid
- doi.org
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- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DigitalGeorgetown (Georgetown University Library) (submittedVersion)
- Funders
- Cold Spring Harbor Laboratory
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- human genome sequencing, James D. Watson, 454 pyrosequencing, next-generation sequencing, single nucleotide polymorphisms, copy number variation, insertion/deletion polymorphism, novel genes, personalized medicine, sequencing cost reduction, diploid genome, reference genome comparison, genomic medicine
- MeSH terms
- Alleles, Genotype, Humans, Individuality, Male, Sensitivity and Specificity, Software, Genetic Variation, Reproducibility of Results, Genome, Human, Sequence Alignment, Sequence Analysis, DNA, Computational Biology, Genetic Predisposition to Disease, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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