Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence

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 mutat...

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Detalles Bibliográficos
Autores principales: Miller, Christopher A., Walker, Jason R., Jensen, Travis L., Hooper, William F., Fulton, Robert S., Painter, Jeffrey S., Sekeres, Mikkael A., Ley, Timothy J., Spencer, David H., Goll, Johannes B., Walter, Matthew J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Investigative Pathology 2022
Materias:
Regular Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8950341/
https://www.ncbi.nlm.nih.gov/pubmed/35041928
http://dx.doi.org/10.1016/j.jmoldx.2021.10.013
Descripción
Sumario: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.

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