CoChat
Sign Up
Cited by 182Genomics and Phylogenetic StudiesGenomic variations and chromosomal abnormalitiesGenomics and Rare Diseases

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area

Open access
Nakano, Kazuma, Shiroma, Akino, Shimoji, Makiko, Tamotsu, Hinako, Ashimine, Noriko, Ohki, Shun, Shinzato, Misuzu, Minami, Maiko +4 more·2017·Human Cell
DOI 10.1007/s13577-017-0168-8PMC PMC5486853
Open this paper in CoChat — free accountOpen PDF

Abstract

PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1007/s13577-017-0168-8

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Tools like PacBio's SMRT Analysis and Oxford Nanopore's MinION-based Minimap2 have been specifically designed for long reads and are adept at untangling complex genomic architectures and reducing gaps in assemblies.

    “Tools like PacBio's SMRT Analysis and Oxford Nanopore's MinION-based Minimap2 have been specifically designed for long reads and are adept at untangling complex genomic architectures and reducing gaps in assemblies [7].”

    From Whole-Genome Alignment: Methods, Challenges, and Future Directions (2024) · cites this paper as [7]

    The Introduction and Mechanism and performance sections say PacBio SMRT long reads help resolve difficult regions and structural variations. The Applications section describes HGAP for assembling PacBio long reads. Our copy does not identify SMRT Analysis or Minimap2, discuss Oxford Nanopore tools, or attribute reduced assembly gaps to those named tools. (LLM, conf=0.87)

    Experimental — accuracy not yet measured

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 46

  1. [1]Naidoo N Pawitan Y Soong R Cooper DN Ku C-S Human genetics and genomics a decade after the release of the draft sequence of the human genome Hum Genomics 2011 5 577 622 10.1186/1479-7364-5-6-577 22155605 PMC3525251 · DOI
  2. [2]Goodwin S McPherson JD McCombie WR Coming of age: ten years of next-generation sequencing technologies Nat Rev Genet 2016 17 333 351 10.1038/nrg.2016.49 27184599 PMC10373632 · DOI · Paper page
  3. [3]Schadt EE Turner S Kasarskis A A window into third-generation sequencing Hum Mol Genet 2010 19 R227 R240 10.1093/hmg/ddq416 20858600 · DOI
  4. [4]Koren S Harhay GP Smith TP Bono JL Harhay DM Mcvey SD Reducing assembly complexity of microbial genomes with single-molecule sequencing Genome Biol 2013 14 R101 10.1186/gb-2013-14-9-r101 24034426 PMC4053942 · DOI
  5. [5]Rhoads A Au KF PacBio sequencing and its applications Genomics Proteomics Bioinform 2015 13 278 289 10.1016/j.gpb.2015.08.002 PMC4678779 26542840 · DOI
  6. [6]Levene MJ Korlach J Turner SW Foquet M Craighead HG Webb WW Zero-mode waveguides for single-molecule analysis at high concentrations Science 2003 299 682 686 10.1126/science.1079700 12560545 · DOI
  7. [7]Eid J Fehr A Gray J Luong K Lyle J Otto G Real-time DNA sequencing from single polymerase molecules Science 2009 323 133 138 10.1126/science.1162986 19023044 · DOI · Paper page
  8. [8]Shin SC Ahn DH Kim SJ Lee H Oh T-J Lee JE Advantages of single-molecule real-time sequencing in high-GC content genomes PLoS One 2013 8 7 e68824 10.1371/journal.pone.0068824 23894349 PMC3720884 · DOI
  9. [9]Gordon D Huddleston J Chaisson MJP Hill CM Kronenberg ZN Munson KM Long-read sequence assembly of the gorilla genome Science. 2016 352 aae0344 10.1126/science.aae0344 27034376 PMC4920363 · DOI · Paper page
  10. [10]Pendleton M Sebra R Pang AWC Ummat A Franzen O Rausch T Assembly and diploid architecture of an individual human genome via single-molecule technologies Nat Methods 2015 12 780 786 10.1038/nmeth.3454 26121404 PMC4646949 · DOI
  11. [11]Chin C-S Alexander DH Marks P Klammer AA Drake J Heiner C Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data Nat Methods 2013 10 563 569 10.1038/nmeth.2474 23644548 · DOI
  12. [12]Larsen PA Heilman AM Yoder AD The utility of PacBio circular consensus sequencing for characterizing complex gene families in non-model organisms BMC Genomics 2014 15 720 10.1186/1471-2164-15-720 25159659 PMC4152597 · DOI
  13. [13]Frank JA Pan Y Tooming-Klunderud A Eijsink VGH McHardy AC Nederbragt AJ Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data Sci Rep 2016 6 25373 10.1038/srep25373 27156482 PMC4860591 · DOI
  14. [14]Kelleher P Murphy J Mahony J van Sinderen D Next-generation sequencing as an approach to dairy starter selection Dairy Sci Technol 2015 95 545 568 10.1007/s13594-015-0227-4 26798445 PMC4712225 · DOI · Paper page
  15. [15]Okumura K Kato M Kirikae T Kayano M Miyoshi-Akiyama T Construction of a virtual Mycobacterium tuberculosis consensus genome and its application to data from a next generation sequencer BMC Genomics 2015 16 218 10.1186/s12864-015-1368-9 25879806 PMC4425900 · DOI
  16. [16]Kato-Miyazawa M Miyoshi-Akiyama T Kanno Y Takasaki J Kirikae T Kobayashi N Genetic diversity of Mycobacterium tuberculosis isolates from foreign-born and Japan-born residents in Tokyo Clin Microbiol Infect 2015 21 248.e1 248.e8 10.1016/j.cmi.2014.09.013 25595707 · DOI
  17. [17]Miyoshi-Akiyama T Satou K Kato M Shiroma A Matsumura K Tamotsu H Complete annotated genome sequence of Mycobacterium tuberculosis (Zopf) Lehmann and Neumann (ATCC35812) (Kurono) Tuberculosis 2015 95 37 39 10.1016/j.tube.2014.10.007 25458614 · DOI
  18. [18]Shrestha S Tada T Miyoshi-Akiyama T Ohara H Shimada K Satou K Molecular epidemiology of multidrug-resistant Acinetobacter baumannii isolates in a university hospital in Nepal reveals the emergence of a novel epidemic clonal lineage Int J Antimicrob Agents 2015 46 5 526 531 10.1016/j.ijantimicag.2015.07.012 26362951 · DOI
  19. [19]Tada T Miyoshi-Akiyama T Shimada K Shiroma A Nakano K Teruya K A carbapenem-resistant Pseudomonas aeruginosa isolate harboring two copies of bla IMP-34 encoding a metallo-β-lactamase PLoS One 2016 11 e0149385 10.1371/journal.pone.0149385 27055243 PMC4824433 · DOI
  20. [20]Satou K Shimoji M Tamotsu H Juan A Ashimine N Shinzato M Complete genome sequences of low-passage virulent and high-passage avirulent variants of pathogenic Leptospira interrogans serovar Manilae strain UP-MMC-NIID, originally isolated from a patient with severe leptospirosis, determined using PacBio single-molecule real-time technology Genome Announc 2015 3 e00882-15 10.1128/genomeA.00882-15 26272567 PMC4536678 · DOI
  21. [21]Satou K Shiroma A Teruya K Shimoji M Nakano K Juan A Complete genome sequences of eight Helicobacter pylori strains with different virulence factor genotypes and methylation profiles, isolated from patients with diverse gastrointestinal diseases on Okinawa Island, Japan, determined using PacBio single-molecule real-time technology Genome Announc 2014 2 2 e00286-14 10.1128/genomeA.00286-14 24744331 PMC3990747 · DOI
  22. [22]Vemula SV Zhao J Liu J Wang X Biswas S Hewlett I Current approaches for diagnosis of influenza virus infections in humans Viruses 2016 8 96 10.3390/v8040096 27077877 PMC4848591 · DOI
  23. [23]Wong S-S Webby RJ Traditional and new influenza vaccines Clin Microbiol Rev 2013 26 476 492 10.1128/CMR.00097-12 23824369 PMC3719499 · DOI
  24. [24]Höper D Hoffmann B Beer M A comprehensive deep sequencing strategy for full-length genomes of influenza A PLoS One 2011 6 4 e19075 10.1371/journal.pone.0019075 21559493 PMC3084732 · DOI
  25. [25]Iha Y Higa F Sunagawa S Naka M Cash HL Miyagi K Effect of climatic conditions on epidemic patterns of influenza in Okinawa, Japan, during the pandemic of 2009: surveillance of rapid antigen test results Jpn J Infect Dis 2012 65 295 300 10.7883/yoken.65.295 22814150 · DOI
  26. [26]Fujita J Sunagawa S Higa F Tateyama M Uno T Comparison of critically ill patients between different outbreaks caused by pandemic H1N1 2009 influenza virus in Okinawa, Japan Influenza Other Respir Viruses 2011 5 e477 e478 10.1111/j.1750-2659.2011.00275.x 21752232 PMC5780664 · DOI
  27. [28]Deka H Chakraborty S Insights into the usage of nucleobase triplets and codon context pattern in five influenza A virus subtypes J Microbiol Biotechnol 2016 26 11 1972 1982 10.4014/jmb.1605.05016 27470283 · DOI
  28. [29]He J Sundararajan A Devitt NP Schilkey FD Ramaraj T Melançon CE Complete genome sequence of Streptomyces venezuelae ATCC 15439, producer of the methymycin/pikromycin family of macrolide antibiotics using PacBio technology Genome Announc 2016 4 e00337-16 10.1128/genomeA.00337-16 27151802 PMC4859184 · DOI
  29. [30]Hashimoto T Hashimoto J Teruya K Hirano T Shin-ya K Ikeda H Biosynthesis of versipelostatin: identification of an enzyme-catalyzed [4+2]-cycloaddition required for macrocyclization of spirotetronate-containing polyketides J Am Chem Soc 2015 137 572 575 10.1021/ja510711x 25551461 PMC4308742 · DOI
  30. [31]Miyanaga A Hayakawa Y Numakura M Hashimoto J Teruya K Hirano T Identification of the fluvirucin B2 (Sch 38518) biosynthetic gene cluster from Actinomadura fulva subsp. indica ATCC 53714: substrate specificity of the β-amino acid selective adenylating enzyme FlvN Biosci Biotechnol Biochem 2016 80 935 941 10.1080/09168451.2015.1132155 26818633 · DOI
  31. [32]Nakano K Shiroma A Tamotsu H Ohki S Shimoji M Ashimine N First complete genome sequence of the skin-improving Lactobacillus curvatus strain FBA2, isolated from fermented vegetables, determined by PacBio single-molecule real-time technology Genome Announc 2016 4 e00884-16 10.1128/genomeA.00884-16 27587811 PMC5009968 · DOI
  32. [33]Yohda M Yagi O Takechi A Kitajima M Matsuda H Miyamura N Genome sequence determination and metagenomic characterization of a Dehalococcoides mixed culture grown on cis-1,2-dichloroethene J Biosci Bioeng 2015 120 69 77 10.1016/j.jbiosc.2014.12.001 25579666 · DOI
  33. [34]Ikuta T Takaki Y Nagai Y Shimamura S Tsuda M Kawagucci S Heterogeneous composition of key metabolic gene clusters in a vent mussel symbiont population ISME J 2015 10 4 990 1001 10.1038/ismej.2015.176 26418631 PMC4796938 · DOI
  34. [36]Shinzato N Aoyama H Saitoh S Nikoh N Nakano K Shimoji M Complete genome sequence of the intracellular bacterial symbiont TC1 in the anaerobic ciliate Trimyema compressum Genome Announc 2016 4 e01032-16 10.1128/genomeA.01032-16 27660797 PMC5034148 · DOI
  35. [37]Sakai H Naito K Ogiso-Tanaka E Takahashi Y Iseki K Muto C The power of single molecule real-time sequencing technology in the de novo assembly of a eukaryotic genome Sci Rep 2015 5 16780 10.1038/srep16780 26616024 PMC4663752 · DOI
  36. [38]Zook JM Chapman B Wang J Mittelman D Hofmann O Hide W Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls Nat Biotechnol 2014 32 246 251 10.1038/nbt.2835 24531798 · DOI
  37. [39]Collins FS Hamburg MA First FDA authorization for next-generation sequencer N Engl J Med 2013 369 2369 2371 10.1056/NEJMp1314561 24251383 PMC5101955 · DOI
  38. [40]Olson ND Zook JM Samarov DV Jackson SA Salit ML PEPR: pipelines for evaluating prokaryotic references Anal Bioanal Chem 2016 408 2975 2983 10.1007/s00216-015-9299-5 26935931 PMC4819933 · DOI
  39. [41]Terabayashi Y Juan A Tamotsu H Ashimine N Nakano K Shimoji M First complete genome sequence of Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 13311 (NCTC 74), a reference strain of multidrug resistance, as achieved by use of PacBio single-molecule real-time technology Genome Announc. 2014 2 e00986-14 10.1128/genomeA.00986-14 25278532 PMC4183876 · DOI
  40. [42]Shiroma A Terabayashi Y Nakano K Shimoji M Tamotsu H Ashimine N First complete genome sequences of Staphylococcus aureus subsp. aureus Rosenbach 1884 (DSM 20231T), determined by PacBio single-molecule real-time technology Genome Announc 2015 3 e00800-15 10.1128/genomeA.00800-15 26184947 PMC4505135 · DOI
  41. [43]Nakano K Terabayashi Y Shiroma A Shimoji M Tamotsu H Ashimine N First complete genome sequence of Pseudomonas aeruginosa (Schroeter 1872) Migula 1900 (DSM 50071T), determined using PacBio single-molecule real-time technology Genome Announc 2015 3 e00932-15 10.1128/genomeA.00932-15 26294631 PMC4543509 · DOI
  42. [44]Nakano K Terabayashi Y Shiroma A Shimoji M Tamotsu H Ashimine N First complete genome sequence of Clostridium sporogenes DSM 795T, a nontoxigenic surrogate for Clostridium botulinum, determined using PacBio single-molecule real-time technology Genome Announc 2015 3 e00832-15 10.1128/genomeA.00832-15 26227598 PMC4520896 · DOI
  43. [45]Ueta M Sawai H Sotozono C Hitomi Y Kaniwa N Kim MK IKZF1, a new susceptibility gene for cold medicine-related Stevens–Johnson syndrome/toxic epidermal necrolysis with severe mucosal involvement J Allergy Clin Immunol 2015 135 1538–1545 e17 25672763
  44. [46]Mullighan CG Goorha S Radtke I Miller CB Coustan-Smith E Dalton JD Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia Nature 2007 446 758 764 10.1038/nature05690 17344859 · DOI
  45. [47]Georgopoulos K Moore DD Derfler B Ikaros, an early lymphoid-specific transcription factor and a putative mediator for T cell commitment Science 1992 258 808 812 10.1126/science.1439790 1439790 · DOI · Paper page
  46. [48]Treangen TJ Salzberg SL Repetitive DNA and next-generation sequencing: computational challenges and solutions Nat Rev Genet 2011 13 36 46 22124482 PMC3324860

Cited by

Sorted by citations

Authors
Nakano, K., Shiroma, A., Shimoji, M., Tamotsu, H., Ashimine, N., Ohki, S., Shinzato, M., Minami, M., Nakanishi, T., Teruya, K., Satou, K., & Hirano, T.
Corresponding author
Nakano, Kazuma
ORCID
Venue
Human Cell
Publisher
Springer Science and Business Media LLC
Published
2017-03-31
Volume
30
Issue
3
Pages
149-161
ISSN
  • 0914-7470 (ISSN-L)
  • 1749-0774
DOI
10.1007/s13577-017-0168-8
PMC
PMC5486853
OpenAlex
W2601346929
Cited by
182
References
1
Citations by year
2026: 4 · 2025: 11 · 2024: 14 · 2023: 14 · 2022: 21 · 2021: 25 · 2020: 30 · 2019: 33 · 2018: 25 · 2017: 5
FWCI
2.41
Type
journal article
Language
en
Open access
Licence
Locations
  • Human Cell (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
National Institute of Standards and Technology
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Keywords
single-molecule real-time sequencing, long-read sequencing, whole genome sequencing, viral genome sequencing, bacterial genome assembly, plant genome assembly, clinical genomics
MeSH terms
Animals, Communicable Diseases, Humans, Genome, Genome, Viral, Genome, Bacterial, Sequence Analysis, DNA, Genome, Plant, DNA Methylation

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 ›

Are you an author, or do you see a problem with this page? Request a review