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BioinformaticsFMRP / TCGAbiolinks

TCGAbiolinks
http://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html
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BRAF V600E mutation why turn into V640E mutaion in TCGA COAD cohort? #624

Open LULUCHIU opened 6 months ago

LULUCHIU commented 6 months ago

From the publication worldwide shows that BRAF V600E is most common point mutation, but recently I worked on the TCGA dataset, all V600E were converted to V640E which is so different from the data in the past.

asmlgkj commented 5 months ago

it maybe the reason of the GDC data, I found gdc also were V640E @LULUCHIU

bryanjjones commented 2 months ago

I just came across this issue. It depends on which isoform or splice variant you use for numbering. If you use isoform 1 or 2 (NP_004324.2 or NP_001341538.1), that amino acid ends up being number 600. If you use isoform 3 or 4 for numbering (NP_001361173.1 or NP_001361187.1), the amino acid is in position 640.

mschubert commented 1 month ago

Related: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/516

The annotation at position 640 is now also the canonical transcript in Ensembl, so this should be the "correct" name