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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 is not the most common mutatin in lollipopPlot?? i see the raw data and no V600E in HGVSp_Short #516

Closed dannyteng1971 closed 2 years ago

dannyteng1971 commented 2 years ago

To dear whol in concern: I am a clinical physican. I use TCGAbiolink and MAFtools to plot lollipopPlot. data is TCGA-COAD suddenly, i find : no V600E mutation on lollipopPlot. if i use the cbioportal, V600E is most common. is it a big bug??? the following is the code i used. could someone can help me thanks is the problem of TCGAbiolinks or Maftools?? my mail is hwteng1971@gmail.com

code as follow ing query.COAD.TCGA.CNV <- GDCquery( project = "TCGA-COAD", data.category = "Simple Nucleotide Variation", access = "open", legacy = FALSE, data.type = "Masked Somatic Mutation" , workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking" ) GDCdownload(query.COAD.TCGA.CNV) maf.cnv.coad <- GDCprepare(query.COAD.TCGA.CNV) xmaf<-read.maf(maf.cnv.coad) oncoplot(maf = xmaf, top = 30)

lollipopPlot( maf = xmaf, gene = 'BRAF',

AACol = NULL,

showMutationRate = TRUE, labelPos = "all" )

dannyteng1971 commented 2 years ago

i see the raw data and no V600E in HGVSp_Short no V600E as i see V600E is the top 1 mutation in BRAF gene in colorectal cancer TCGA-COAD This is a big error?!!

dannyteng1971 commented 2 years ago

IF I USE hG19 FILE THE PICTURE IS RIGHT ?? query.maf.hg19 <- GDCquery( project = "TCGA-COAD", data.category = "Simple nucleotide variation", data.type = "Simple somatic mutation", access = "open", legacy = TRUE )

GDCdownload(query.maf.hg19) maf19 <- GDCprepare(query.maf.hg19) maf19<-read.maf(maf19)

lollipopPlot(maf = maf19, gene = "BRAF", labelPos = 'all')

dannyteng1971 commented 2 years ago

I THINK Mutation data (hg38) IS DAMGOUS

dannyteng1971 commented 2 years ago

is anyone could help me? I thiink no BRAF V600E band is a big problem? the following resulted data might be error from the view point of clinical staff?? Thanks

dannyteng1971 commented 2 years ago

maf.cnv.coad <- GDCprepare(query.COAD.TCGA.CNV) There were 17 warnings (use warnings() to see them)
I think the GDCprepare has a parsing problem??

dannyteng1971 commented 2 years ago

but interesting if I used same data ajust replace BRAF by KRAS the figure is correct? so what happen to parsing "BRAF????" why a shift noted. ???? could anyone takecare this important issue??

lollipopPlot( maf = coad.maf2, gene = 'NRAS', showMutationRate = TRUE, labelPos = "all", AACol = 'HGVSp_Short' )

tiagochst commented 2 years ago

@dannyteng1971 Is this a data problem or a plot problem ? if it is a plot you need to contact maftools developer (https://github.com/PoisonAlien/maftools)

tiagochst commented 2 years ago

@dannyteng1971 There is no V600E in the data from GDC, it has p.V640E

tiagochst commented 2 years ago

You can also use GDC to check the data:

https://portal.gdc.cancer.gov/exploration?facetTab=mutations&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-COAD%22%5D%7D%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22genes.gene_id%22%2C%22value%22%3A%5B%22ENSG00000157764%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22genes.is_cancer_gene_census%22%2C%22value%22%3A%5B%22true%22%5D%7D%2C%22op%22%3A%22in%22%7D%5D%7D&genesTable_size=60&searchTableTab=mutations

dannyteng1971 commented 2 years ago

To dear Tiago: Thanks for your important information. I learn a lot from you and your software TCGAbiolink. I thinks you are right . I do it again and BRAF V640E is most common (NCI GDC). But in clinical V600 E is most common, not 640!!!(this is important) anyway thanks lot. I will write to GDC. Thanks if come to Taiwan , welcome to our hospital for a visit.

https://portal.gdc.cancer.gov/exploration?filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-COAD%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22genes.gene_id%22%2C%22value%22%3A%5B%22ENSG00000157764%22%5D%7D%7D%5D%7D&searchTableTab=mutations

Tiago Chedraoui Silva @.***> 於 2022年6月14日 週二 晚上10:46寫道：

You can also use GDC to check the data:

https://portal.gdc.cancer.gov/exploration?facetTab=mutations&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.program.name%22%2C%22value%22%3A%5B%22TCGA%22%5D%7D%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-COAD%22%5D%7D%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22genes.gene_id%22%2C%22value%22%3A%5B%22ENSG00000157764%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22genes.is_cancer_gene_census%22%2C%22value%22%3A%5B%22true%22%5D%7D%2C%22op%22%3A%22in%22%7D%5D%7D&genesTable_size=60&searchTableTab=mutations

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Best Regards Hao-Wei Teng

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LULUCHIU commented 5 months ago

Have any update for this issue? It's quite confusing. It should be V600E.

dannyteng1971 commented 5 months ago

good day, Tina It is an old but important problem since 2023/3. clinically we used V600E as a important word. however, due to the change of ref mRNA, it will groth of number. But still the same change . it is hard to reading if you area a clinical physician best from hao-wei teng

Tina @.***> 於 2024年3月24日 週日 上午4:19寫道：

Have any update for this issue? It's quite confusing. It should be V600E.

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/516#issuecomment-2016593083, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPVETFAG4MS4BTLFFCKX7LYZXPURAVCNFSM5XB2W3R2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMBRGY2TSMZQHAZQ . You are receiving this because you were mentioned.Message ID: @.***>

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Best Regards Hao-Wei Teng

http://crc.uptocare.com/ http://uptocare.com/

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LULUCHIU commented 5 months ago

So that's how it is. Thank you so much for your explanation!

dannyteng1971 commented 5 months ago

You're welcome!

Tina @.***> 於 2024年3月27日 週三 21:17 寫道：

So that's how it is. Thank you so much for your explanation!

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bryanjjones commented 1 month 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 same amino acid is in position 640. Both refer to the same mutation in the genome: chr7:g.140753336A>T.

dannyteng1971 commented 1 month ago

to Dear Bryan Thanks for your information and it is a important inofrmation . but for a clinicacal staff, V600 is well known and nobody see V640. so it confuse most of clinical guys. thansk for your help

Bryan

Bryan @.***> 於 2024年7月30日 週二 上午4:57寫道：

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 same amino acid is in position 640. Both refer to the same mutation in the genome: chr7:g.140753336A>T.

— Reply to this email directly, view it on GitHub https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/516#issuecomment-2256954282, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPVETFSF6KOQGQKRA5ZXMTZO2UEXAVCNFSM5XB2W3R2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TEMRVGY4TKNBSHAZA . You are receiving this because you were mentioned.Message ID: @.***>

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Best Regards Hao-Wei Teng

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