Apr 2, 2020

Correspondence: Recurrent GNAQ mutation encoding T96S in natural killer/T cell lymphoma

BioRxiv : the Preprint Server for Biology
J. Q. LimChoon Kiat Ong

Abstract

Recurrent GNAQ mutation encoding p.T96S in natural-killer/T cell lymphoma (NKTCL) was recently reported in 8.7% (11/127) of NKTCL patients. At the time of publication, this phenomenon was not observed in preceding genomic studies of NKTCL. We suspected that p.T96S was a false-positive somatic call due to misaligned sequencing reads that originated from the highly similar GNAQ-pseudogene (GNAQP) chr2q21.1 locus. Linkage disequilibrium analysis also revealed that GNAQP has high frequencies of co-occurring polymorphic mismatches which led to the preferential misalignment of sequencing reads to the GNAQ chr9q21.2 locus instead. This correspondence implicates our interpretation of true-positive somatic variants and many other studies which could be affected by similar suboptimal interpretation of somatic mutations.

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