Question: How to get SNP genotypes in somatic mutation files with MAF(Mutation Annotation Format) ?
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gravatar for cying
4.2 years ago by
cying10
China
cying10 wrote:

 Hi! Guys, I want to do some association researches between SNP genotypes and phenotypes in cancer patients, just like this article for investigating association between SNPs in UGT2B and breast cancer.

I know SNP information is located in somatic mutation, while I have downloaded somatic mutation MAF files, there are 5 subset files. I leave them as here.

  1. BCGSC__IlluminaHiSeq_DNASeq_automated

  2. BCM__IlluminaGA_DNASeq_automated

  3. BCM__Mixed_DNASeq_curated

  4. BI__IlluminaGA_DNASeq_automated

  5. UCSC__IlluminaGA_DNASeq_automated

Actually these files are all somatic mutation files, but sequenced by different institutions and platforms. There are also some differences between these files, for example, here is a part of BCGSC__IlluminaHiSeq_DNASeq_automated file(11,12 13column), the genotypes of SNPs in Tumor_Seq_Allele are all zygosity.

Reference_Allele    Tumor_Seq_Allele1    Tumor_Seq_Allele2
G    A    A
G    A    A
A    G    G
A    T    T
C    A    A
C    T    T
A    G    G
....

But in BI__IlluminaGA_DNASeq_automated file, the mutations are all heterozygous.

Reference_Allele    Tumor_Seq_Allele1    Tumor_Seq_Allele2
G    G    A
G    G    A
A    A    T
C    C    T
A    A    G
A    A    G
G    G    A
....

Although having read the TutorialC: Working With Maf Files (Mutation Annotation Format) From The Tcga (The Cancer Ge, I still have no idea which file to choose.

To conclude, I have two major problems troubled me.
Firstly,can Tumor_Seq_Allele 1 and Tumor_Seq_Allele 2 really represent the SNP's genotype?  Because in the next step , I will select TagSNPs based on MAF(Minor Allele Frequency, filter criterion >0.05),but if I acquire genotyps like that, all the SNPs' frequency are below 0.05, which means no TagSNPs! I'm not sure whether it is right, Inferring zygosity information from MAF also metioned the Tumor_Seq_Allele, but I don't understand REF/ALT allele and how to get a more reliable SNP genotype.
Secondly, the great disparities between BCGSC and BI files make me confused which file to choose for my next step.

I hope you guys can give me some suggestions. Many thanks!

snp genotype tcga maf files • 2.4k views
ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by cying10
1

Please see this comment about zygosity and the answer to it - C: Working With Maf Files (Mutation Annotation Format) From The Tcga (The Cancer Ge

ADD REPLYlink written 4.2 years ago by Cyriac Kandoth5.3k
0
gravatar for cying
4.2 years ago by
cying10
China
cying10 wrote:

I have made supplement about my questions, thank you!

ADD COMMENTlink written 4.2 years ago by cying10
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