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Correspondence: Recurrent GNAQ mutation encoding T96S in natural killer/T cell lymphoma
- Publication Year :
- 2020
- Publisher :
- Cold Spring Harbor Laboratory, 2020.
-
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.
Details
- Language :
- English
- Database :
- OpenAIRE
- Accession number :
- edsair.doi.dedup.....cfcbd84f466af08aa25b6f9415846b1c
- Full Text :
- https://doi.org/10.1101/2020.04.01.020198