Generations of Sequencing Technologies

Department of Gene Technology, Royal Institute of Technology (KTH), AlbaNova University Center, Roslagstullsbacken 21, SE-10691 Stockholm, Sweden.
Genomics (Impact Factor: 2.28). 12/2008; 93(2):105-11. DOI: 10.1016/j.ygeno.2008.10.003
Source: PubMed


Advancements in the field of DNA sequencing are changing the scientific horizon and promising an era of personalized medicine for elevated human health. Although platforms are improving at the rate of Moore's Law, thereby reducing the sequencing costs by a factor of two or three each year, we find ourselves at a point in history where individual genomes are starting to appear but where the cost is still too high for routine sequencing of whole genomes. These needs will be met by miniaturized and parallelized platforms that allow a lower sample and template consumption thereby increasing speed and reducing costs. Current massively parallel, state-of-the-art systems are providing significantly improved throughput over Sanger systems and future single-molecule approaches will continue the exponential improvements in the field.

Full-text preview

Available from:
  • Source
    • "The Ion-Torrent PGM represents a low-cost and rapid sequencing methodology generating around 80 million sequence reads in a single run of approximately 90 min. The Illumina approach has been one of the most widely used sequencing approaches in recent years and can generate a large volume of sequencing data (Metzker 2010), although the average read length is relatively low, in particular when compared to the newer PacBio SMRT platform. Current Illumina sequencing-by-synthesis (SBS) instruments are capable of generating over 1 terabase of data in a single run and are capable of sequencing bacterial genomes in a matter of hours. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Lactococcal and streptococcal starter strains are crucial ingredients to manufacture fermented dairy products. As commercial starter culture suppliers and dairy producers attempt to overcome issues of phage sensitivity and develop new product ranges, there is an ever increasing need to improve technologies for the rational selection of novel starter culture blends. Whole genome sequencing, spurred on by recent advances in next-generation sequencing platforms, is a promising approach to facilitate rapid identification and selection of such strains based on gene-trait matching. This review provides a comprehensive overview of the available methodologies to analyse the technological potential of candidate starter strains and highlights recent advances in the area of dairy starter genomics.
    Dairy Science & Technology 04/2015; 95(5). DOI:10.1007/s13594-015-0227-4 · 1.60 Impact Factor
  • Source
    • "been a sharp increase in the number of genetic association studies being carried out, especially in the form of genome-wide association studies (GWAS, statistics available at As whole genome sequencing (WGS) is prohibitively expensive for large genetic association studies [4] [5] [6], whole exome sequencing (WES) has emerged as the attractive alternative, where only the protein coding region of the genome (i.e., exome) is targeted and sequenced [7]. The decision to carry out WES over WGS is not solely influenced by the cost which currently stands at one-third in comparison [8], but also by the fact that most of the known Mendelian disorders (∼85%) are caused by mutations in the exome [9]; and reliably interpreting variation outside of the exome is still challenging as there is little consensus on interpreting their functional effects (even with ENCODE data [10] and noncoding variant effect prediction tools such as CADD [11], FATHMM-MKL [12], and GWAVA [13]). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent technological advances have created challenges for geneticists and a need to adapt to a wide range of new bioinformatics tools and an expanding wealth of publicly available data (e.g., mutation databases, and software). This wide range of methods and a diversity of file formats used in sequence analysis is a significant issue, with a considerable amount of time spent before anyone can even attempt to analyse the genetic basis of human disorders. Another point to consider that is although many possess " just enough " knowledge to analyse their data, they do not make full use of the tools and databases that are available and also do not fully understand how their data was created. The primary aim of this review is to document some of the key approaches and provide an analysis schema to make the analysis process more efficient and reliable in the context of discovering highly penetrant causal mutations/genes. This review will also compare the methods used to identify highly penetrant variants when data is obtained from consanguineous individuals as opposed to nonconsanguineous; and when Mendelian disorders are analysed as opposed to common-complex disorders.
    BioMed Research International 03/2015; DOI:10.1155/2015/923491 · 1.58 Impact Factor
  • Source
    • "The latter sequencing technologies are referred to as the next-generation sequencing (NGS) technologies . Currently, the available commercial NGS platforms include GA, MiSeq, and HiSeq from Illumina [1], SOLiD and Ion Torrent from Life Technologies [2], RS system from Pacific Bioscience, and Heliscope from Helicos Biosciences [3] [4] [5] [6] [7]. Next generation sequencing machines can sequence the whole human genome in a few days, and this capability has inspired a flood of new projects that are aimed at sequencing large kinds of animals and plants [8] [9]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Background: Next generation sequencing platforms can generate shorter reads, deeper coverage, and higher throughput than those of the Sanger sequencing. These short reads may be assembled de novo before some specific genome analyses. Up to now, the performances of assembling repeats of these current assemblers are very poor. Results: To improve this problem, we proposed a new genome assembly algorithm, named SWA, which has four properties: (1) assembling repeats and nonrepeats; (2) adopting a new overlapping extension strategy to extend each seed; (3) adopting sliding window to filter out the sequencing bias; and (4) proposing a compensational mechanism for low coverage datasets. SWA was evaluated and validated in both simulations and real sequencing datasets. The accuracy of assembling repeats and estimating the copy numbers is up to 99% and 100%, respectively. Finally, the extensive comparisons with other eight leading assemblers show that SWA outperformed others in terms of completeness and correctness of assembling repeats and nonrepeats. Conclusions: This paper proposed a new de novo genome assembly method for resolving complex repeats. SWA not only can detect where repeats or nonrepeats are but also can assemble them completely from NGS data, especially for assembling repeats. This is the advantage over other assemblers.
    BioMed Research International 11/2014; 2014:736473. DOI:10.1155/2014/736473 · 1.58 Impact Factor
Show more