The complete genome of an individual by massively parallel DNA sequencing Export

@article{citeulike:2678793, abstract = {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'.}, author = {Wheeler, David A. and Srinivasan, Maithreyan and Egholm, Michael and Shen, Yufeng and Chen, Lei and McGuire, Amy and He, Wen and Chen, Yi-Ju and Makhijani, Vinod and Roth, G. Thomas and Gomes, Xavier and Tartaro, Karrie and Niazi, Faheem and Turcotte, Cynthia L. and Irzyk, Gerard P. and Lupski, James R. and Chinault, Craig and Song, Xing-zhi and Liu, Yue and Yuan, Ye and Nazareth, Lynne and Qin, Xiang and Muzny, Donna M. and Margulies, Marcel and Weinstock, George M. and Gibbs, Richard A. and Rothberg, Jonathan M.}, citeulike-article-id = {2678793}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature06884}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature06884}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/18421352}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=18421352}, day = {17}, doi = {10.1038/nature06884}, issn = {0028-0836}, journal = {Nature}, keywords = {454, dna, genomics, human, isis, next-gen, sequencing}, month = {April}, number = {7189}, pages = {872--876}, posted-at = {2009-04-15 22:44:29}, priority = {2}, publisher = {Nature Publishing Group}, title = {The complete genome of an individual by massively parallel DNA sequencing}, url = {http://dx.doi.org/10.1038/nature06884}, volume = {452}, year = {2008} }

TY - JOUR ID - citeulike:2678793 L3 - citeulike-article-id:2678793 N2 - 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'. IS - 7189 JF - Nature SN - 0028-0836 EP - 876 TI - The complete genome of an individual by massively parallel DNA sequencing PB - Nature Publishing Group VL - 452 SP - 872 KW - 454 KW - dna KW - genomics KW - human KW - isis KW - next-gen KW - sequencing AU - Wheeler, David AU - Srinivasan, Maithreyan AU - Egholm, Michael AU - Shen, Yufeng AU - Chen, Lei AU - McGuire, Amy AU - He, Wen AU - Chen, Yi-Ju AU - Makhijani, Vinod AU - Roth, Thomas AU - Gomes, Xavier AU - Tartaro, Karrie AU - Niazi, Faheem AU - Turcotte, Cynthia AU - Irzyk, Gerard AU - Lupski, James AU - Chinault, Craig AU - Song, Xing-zhi AU - Liu, Yue AU - Yuan, Ye AU - Nazareth, Lynne AU - Qin, Xiang AU - Muzny, Donna AU - Margulies, Marcel AU - Weinstock, George AU - Gibbs, Richard AU - Rothberg, Jonathan PY - 2008/04/17/ UR - http://dx.doi.org/10.1038/nature06884 ER -