The complete genome of an individual by massively parallel DNA sequencing

By D. Wheeler, Maithreyan Srinivasan, M. Egholm, Yufeng Shen, Lei Chen, A. McGuire, Wenshe He, Yi-Ju Chen, V. Makhijani, G. T. Roth and 17 more. Nature, 2008

1,909 citations recorded by the source corpus.

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 genome, 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 individual 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’.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/073aeea8c1e5c261d2fc9d6f91fd20bfa3d04013

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Citations in the corpus

Positional conservation and amino acids shape the correct diagnosis and population frequencies of benign and damaging personal amino acid mutations. (2009, background): “Already, complete genomes from many individual humans have been sequenced, and projects are underway to expand that number to over a thousand genomes in the near future (Levy et al. 2007; Bentley et al. 2008; Wang et al. 2008; Wheeler et al. 2008).”
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A review on machine learning principles for multi-view biological data integration (2016, background): “For example, whole genome (or exome) sequencing [6] detects single-nucleotide and structural variations (genetic level); ChIP-seq [7] identifies transcription factor binding sites (protein– DNA interactomic level) and histone modifications (epigenomic level) in the entire human genome; DNase-seq [8]”
A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries (2011, background): “As a result, it has recently become feasible to sequence nontrivial numbers of whole human genomes [3,5-10].”
The Effects of Vegetarian and Vegan Diets on Gut Microbiota (2019, background): “9% identical to each other in terms of their genome (3), but their gut microbiome can be up to 80–90% different (4).”
BreakDancer: An algorithm for high resolution mapping of genomic structural variation (2009, positive): “…the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms individual genomes have revealed larger numbers of structural variants than originally expected, especially in the smaller size range ( 1 kb) 11,12 .”
Natural genetic variation caused by small insertions and deletions in the human genome. (2011, background): “They ranged from 1 bp to 10,000 bp in length and follow a size distribution where the majority of INDELs were <100 bp in length (Supplemental Fig. 2; Wheeler et al. 2008).”
Systems medicine: the future of medical genomics and healthcare (2009, background): “With the next-generation DNA mega-sequencing technologies currently available, which enable the collection of billions of nucleotides in single instrument runs [36], it is now possible to sequence and assemble a human genome in a matter of weeks at a small fraction of the cost of the reference genom”
Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes (2009, background): “…became reality with the publication of the first three human genomes sequenced with NGS platforms (Bentley et al. 2008; Wang et al. 2008; Wheeler et al. 2008), the sequencing of more than 1000 individuals (http://www.1000genomes.org), computational methods for analyzing and managing the…”
Evaluation of next generation sequencing platforms for population targeted sequencing studies (2009, background): “sequencing to profile the mammalian transcriptome [7,8], as well as whole human genome sequencing [9-11].”