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TransVar: a multilevel variant annotator for precision genomics

Nature Methods volume 12, pages 1002–1003 (2015)Cite this article

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One DNA sequence can code for multiple different mRNAs, and therefore many different proteins. Conversely, a variant identified at the protein or mRNA level may have a non-unique genomic origin. For example, the protein variant EGFR:p.L747S, which mediates acquired resistance of non–small cell lung cancer to tyrosine kinase inhibitors1, can be translated from multiple genomic variants such as chr7:g.55249076_55249077delinsAG and chr7:g.55242470T>C on different isoforms defined on the human reference assembly GRCh37 (Fig. 1a). One-to-many, many-to-one and many-to-many relationships among sequence variants at the genomic level and those at transcript and protein levels introduce frequent inconsistencies in current practice when vital information about the annotation process (for example, transcript or isoform I.D.s) is omitted from variant identifiers.

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Figure 1: Overview of TransVar and comparison with other annotation tools.

References

  1. Yamaguchi, F. et al. Oncol. Lett. 7, 357–360 (2014).

    Article  Google Scholar 

  2. Wang, K., Li, M. & Hakonarson, H. Nucleic Acids Res. 38, e164 (2010).

    Article  Google Scholar 

  3. McLaren, W. et al. Bioinformatics 26, 2069–2070 (2010).

    Article  CAS  Google Scholar 

  4. Cingolani, P. et al. Fly (Austin) 6, 80–92 (2012).

    Article  CAS  Google Scholar 

  5. Ramos, A.H. et al. Hum. Mutat. 36, E2423–E2429 (2015).

    Article  Google Scholar 

  6. Hornbeck, P.V. et al. Nucleic Acids Res. 40, D261–D270 (2012).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank P. Ng and K. Shaw for critical feedback, as well as A. Johnson, A. Bailey, V. Holla, B. Litzenburger, J. Zhang and A. Chang for assistance. This work was supported in part by the US National Institutes of Health (grants CA172652, CA168394, CA083639, CA143883, UL1 TR000371, P50 CA083639, U54 CA112970 and P50 CA098258), the MD Anderson Cancer Center Sheikh Khalifa Ben Zayed Al Nahyan Institute of Personalized Cancer Therapy, the Bosarge Family Foundation, the Mary K. Chapman Foundation, the Michael & Susan Dell Foundation (honoring Lorraine Dell) and the National Cancer Institute Cancer Center (Support Grant P30 CA016672).

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Author notes

  1. Wanding Zhou and Tenghui Chen: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

    Wanding Zhou, Tenghui Chen, Zechen Chong, Mary A Rohrdanz, James M Melott, Chris Wakefield, John N Weinstein & Ken Chen

  2. Khalifa Bin Zayed Al Nahyan Institute of Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

    Jia Zeng, Funda Meric-Bernstam & Gordon B Mills

  3. Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

    John N Weinstein & Gordon B Mills

  4. Department of Investigational Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

    Funda Meric-Bernstam

  5. Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

    Funda Meric-Bernstam

Authors
  1. Wanding Zhou
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Correspondence to Ken Chen.

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Supplementary information

Supplementary Tables and Notes

Supplementary Tables 1–3 and Supplementary Notes 1 and 2 (PDF 286 kb)

Supplementary Software

TransVar code, examples and documentation. (ZIP 5667 kb)

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Zhou, W., Chen, T., Chong, Z. et al. TransVar: a multilevel variant annotator for precision genomics. Nat Methods 12, 1002–1003 (2015). https://doi.org/10.1038/nmeth.3622

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