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Tracking genetic variants in the biomedical literature using LitVar 2.0

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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.

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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 

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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.

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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
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  2. Chih-Hsuan Wei
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  3. Lon Phan
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  4. Timothy Hefferon
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  5. Melissa Landrum
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  6. Heidi L. Rehm
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  7. Zhiyong Lu
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Corresponding author

Correspondence to Zhiyong Lu.

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The authors declare no competing interests.

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

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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

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