PT  - JOURNAL ARTICLE
AU  - Christopher A. Miller
AU  - Jason R. Walker
AU  - Travis L. Jensen
AU  - William F. Hooper
AU  - Robert S. Fulton
AU  - Jeffrey S. Painter
AU  - Mikkael A. Sekeres
AU  - Timothy J. Ley
AU  - David H Spencer
AU  - Johannes B. Goll
AU  - Matthew J. Walter
TI  - Failure to detect mutations in <em>U2AF1</em> due to changes in the GRCh38 reference sequence
AID  - 10.1101/2021.05.07.442430
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.05.07.442430
4099  - http://biorxiv.org/content/early/2021/05/08/2021.05.07.442430.short
4100  - http://biorxiv.org/content/early/2021/05/08/2021.05.07.442430.full
AB  - 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 StatementThe authors have declared no competing interest.