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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence

View ORCID ProfileChristopher A. Miller, Jason R. Walker, Travis L. Jensen, William F. Hooper, Robert S. Fulton, Jeffrey S. Painter, Mikkael A. Sekeres, Timothy J. Ley, David H Spencer, Johannes B. Goll, Matthew J. Walter
doi: https://doi.org/10.1101/2021.05.07.442430
Christopher A. Miller
1Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
2Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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  • ORCID record for Christopher A. Miller
  • For correspondence: c.a.miller@wustl.edu
Jason R. Walker
3McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Travis L. Jensen
4The Emmes Company, 401 North Washington Street, Suite 700, Rockville, MD 20850, USA
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William F. Hooper
4The Emmes Company, 401 North Washington Street, Suite 700, Rockville, MD 20850, USA
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Robert S. Fulton
3McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Jeffrey S. Painter
5Moffitt Cancer Center, Tampa, FL, USA
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Mikkael A. Sekeres
6Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami School of Medicine, Miami, FL, USA
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Timothy J. Ley
1Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
2Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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David H Spencer
1Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
2Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
7Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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Johannes B. Goll
4The Emmes Company, 401 North Washington Street, Suite 700, Rockville, MD 20850, USA
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Matthew J. Walter
1Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
2Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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Abstract

The U2AF1 gene is a core part of mRNA splicing machinery and frequently contains somatic mutations that contribute to oncogenesis in MDS, AML, and other cancers. A change introduced in the GRCh38 version of the human reference build prevents mutations in this gene from being detected by many variant calling pipelines. We describe the problem in detail and show that a modified GRCh38 reference build with unchanged coordinates can be used to ameliorate the issue. This reference is available at https://zenodo.org/record/4684553 (doi:10.5281/zenodo.4684553)

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 08, 2021.
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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence
Christopher A. Miller, Jason R. Walker, Travis L. Jensen, William F. Hooper, Robert S. Fulton, Jeffrey S. Painter, Mikkael A. Sekeres, Timothy J. Ley, David H Spencer, Johannes B. Goll, Matthew J. Walter
bioRxiv 2021.05.07.442430; doi: https://doi.org/10.1101/2021.05.07.442430
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Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence
Christopher A. Miller, Jason R. Walker, Travis L. Jensen, William F. Hooper, Robert S. Fulton, Jeffrey S. Painter, Mikkael A. Sekeres, Timothy J. Ley, David H Spencer, Johannes B. Goll, Matthew J. Walter
bioRxiv 2021.05.07.442430; doi: https://doi.org/10.1101/2021.05.07.442430

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