Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Comment
  • Published:

Tracking genetic variants in the biomedical literature using LitVar 2.0

Nature Genetics volume 55, pages 901–903 (2023)Cite this article

Subjects

Keeping up with the latest variant-related research is vital for genomic medicine. Here we present LitVar 2.0, a significantly improved web-based system to accurately search for genetic variants in the unstructured literature. LitVar 2.0 provides a unified search of full text and supplementary data, and improved variant recognition accuracy.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: The overall workflow of the LitVar system and its search results page.

References

  1. Landrum, M. J. et al. Nucleic Acids Res. 46, D1062–D1067 (2018).

    Article  CAS  PubMed  Google Scholar 

  2. Stenson, P. D. et al. Genome Med. 1, 1–6 (2009).

    Article  Google Scholar 

  3. Fokkema, I. F. A. C. et al. Hum Mutat. 32, 557–563 (2011).

    Article  CAS  PubMed  Google Scholar 

  4. Allot, A. et al. Nucleic Acids Res. 46, W530–W536 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Setlere, S., Jurcenko, M., Gailite, L., Rots, D. & Kenina, V. Neurol. Genet. 8, e200019 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Sadler, K. V. et al. Hum. Mutat. 43, 643–654 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Liu, M. et al. Front Genet. 13, 985500 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  8. Baux, D. et al. Eur. J. Hum. Genet. 29, 356–360 (2021).

    Article  CAS  PubMed  Google Scholar 

  9. Papageorgiou, L. et al. Int. J. Mol. Med. 49, 8 (2022).

    Article  CAS  PubMed  Google Scholar 

  10. Sherry, S. T., Ward, M. & Sirotkin, K. Genome Res. 9, 677–679 (1999).

    Article  CAS  PubMed  Google Scholar 

  11. Cariaso, M. & Lennon, G. Nucleic Acids Res. 40, D1308–D1312 (2012).

    Article  CAS  PubMed  Google Scholar 

  12. Jimeno Yepes, A. & Verspoor, K. Database 2014, bau003 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Naderi, N., Mottaz, A., Teodoro, D. & Ruch, P. Stud. Health Technol. Inform. 294, 876–877 (2022).

    PubMed  Google Scholar 

  14. Wei, C.-H., Allot, A., Riehle, K., Milosavljevic, A. & Lu, Z. Bioinformatics 38, 4449–4451 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wei, C.-H., Allot, A., Leaman, R. & Lu, Z. Nucleic Acids Res. 47, W587–593 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This research is supported by the NIH Intramural Research Program, National Library of Medicine. H.L.R. was supported by NIH/NHGRI grant U24HG006834. We thank Q. Chen for his help on the early draft of this manuscript.

Author information

Author notes

  1. These authors contributed equally: Alexis Allot, Chih-Hsuan Wei.

Authors and Affiliations

  1. National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA

    Alexis Allot, Chih-Hsuan Wei, Lon Phan, Timothy Hefferon, Melissa Landrum & Zhiyong Lu

  2. Program in Medical and Population Genetics, Broad institute of MIT and Harvard, Cambridge, MA, USA

    Heidi L. Rehm

  3. Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA

    Heidi L. Rehm

Authors
  1. Alexis Allot
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Chih-Hsuan Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Lon Phan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Timothy Hefferon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Melissa Landrum
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Heidi L. Rehm
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zhiyong Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zhiyong Lu.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Genetics thanks Bing Zhang, Shyamasree Saha, and the other, anonymous, reviewers for their contribution to the peer review of this work.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Allot, A., Wei, CH., Phan, L. et al. Tracking genetic variants in the biomedical literature using LitVar 2.0. Nat Genet 55, 901–903 (2023). https://doi.org/10.1038/s41588-023-01414-x

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41588-023-01414-x

Search

Advanced search

Quick links

Nature Briefing AI and Robotics

Sign up for the Nature Briefing: AI and Robotics newsletter — what matters in AI and robotics research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: AI and Robotics