Which column between Tumor_Seq_Allele1 vs. Tumor_Seq_Allele2 to select in TCGA MAF files from cBioPortal for the "alteration column allele" for re-annotation purposes?

[Vlachavas, Efstathios-Iason]

Dear cBioPortal community,

 

I would like to ask you for a rather general but quite challenging question regarding the utilization of mutational MAF cancer files from distinct cancer types, for re-annotation and downstream analysis using cBioPortal; In detail, based on a current project analysis, of testing one variant scoring pipeline, I was trying to fetch some MAF files from distinct resources (here the “extended” MAF file from CPTAC CRC dataset):

 

# after loading the maf file and keeping specific columns:

 

head(xx2)

   Hugo_Symbol Chromosome Start_Position End_Position Strand Variant_Type Reference_Allele

1:      PTPN22          1      114380884    114380884                         +           SNP                A

2:        CD1D          1      158151458    158151458                           +          SNP                G

3:       ZMYM1          1       35580705     35580705                           +          SNP                C

4:       ITIH5         10        7679197      7679197                                 +          SNP                C

5:      LRRTM3         10       68687135     68687135                          +          SNP                G

6:       CDH23         10       73553339     73553339                            +          SNP                C

   Tumor_Seq_Allele1 Tumor_Seq_Allele2

1:                 A                 T

2:                 G                 A

3:                 C                 T

4:                 C                 T

5:                 G                 A

6:                 C                 A

 

My crucial question is that as I would like to re-annotate the available mutations for specific patients, I would need to fetch specific columns, two of these are the reference (normal) and tumor (alteration)

Allele; from the above information, there are two available tumor allele columns: Tumor_Seq_Allele1 and Tumor_Seq_Allele2; however, which one should I use as the “ alteration allele” ? based also on the

Reference_Allele column?

 

I also found some relative posts: https://www.biostars.org/p/424846/

https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#mutation-data

https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/

 

but I did not find a clear answer how to proceed with this; Is there a direct approach? For example as Tumor_Seq_Allele1 is the same with the Reference_Allele column, I should choose the Tumor_Seq_Allele2?

 

Cheers,

 

Efstathios

 

Efstathios-Iason Vlachavas

Post-doc/Guest Scientist

 

German Cancer Research Center (DKFZ)

Foundation under Public Law

Im Neuenheimer Feld 280

69120 Heidelberg

Germany

phone: +49 6221 42-5123

fax:      +49 6221 42-5109

 

Efstathios-Ia...@dkfz-heidelberg.de  

www.dkfz.de

 

 

Management Board: Prof. Dr. med. Michael Baumann, Ursula Weyrich

VAT-ID No.: DE143293537

 

[Ritika Kundra]

Hi Efstathios,

Apologies for the delay.

For annotation, please consider Reference Allele and Tumor Seq Allele_2 as reference and variant alleles. As you noticed, tumor_seq_allele_1 is the same as Ref_allele.

Thanks,

Ritika

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