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

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.

SUBMITTER: Miller CA 

PROVIDER: S-EPMC8950341 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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

Miller Christopher A CA   Walker Jason R JR   Jensen Travis L TL   Hooper William F WF   Fulton Robert S RS   Painter Jeffrey S JS   Sekeres Mikkael A MA   Ley Timothy J TJ   Spencer David H DH   Goll Johannes B JB   Walter Matthew J MJ  

The Journal of molecular diagnostics : JMD 20220115 3

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 ameli  ...[more]

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