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

Research output: Contribution to journalArticlepeer-review

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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 myelodysplastic syndrome, acute myeloid leukemia, and other cancers. A change introduced in the GRCh38 version of the human reference build prevents detection of mutations in this gene, and others, by variant calling pipelines. This study describes the problem in detail and shows that a modified GRCh38 reference build with unchanged coordinates can be used to ameliorate the issue.

Original languageEnglish
Pages (from-to)219-223
Number of pages5
JournalJournal of Molecular Diagnostics
Volume24
Issue number3
DOIs
StatePublished - Mar 2022

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