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Question: Inferring zygosity information from MAF
1
gravatar for newDNASeqer
6.6 years ago by
newDNASeqer • 710
United States
newDNASeqer • 710 wrote:

I've heard that we can't infer heterozygosity or homozygosity for the mutations identified in MAF files, but I noticed that the MAF file's columns 11-13 may have information for inferring this info. For example

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

 

From a comparison of Ref and Tumor alleles, can we infer that all these mutations are heterozygous? because One tumor allele is the same as Ref allele. Is this understanding correct?

 

 

 
maf • 2.7k views
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modified 6.5 years ago by Cyriac Kandoth ♦ 5.5k • written 6.6 years ago by newDNASeqer • 710
1
gravatar for Cyriac Kandoth
6.5 years ago by
Cyriac Kandoth ♦ 5.5k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth ♦ 5.5k wrote:

In an ideal world, yes. These fields are meant to represent zygosity. But for TCGA MAFs, as explained in this comment: It's often assumed that somatic point mutations or small indels in cancer are infrequent enough, that they almost always result in a homozygous site becoming heterozygous. Combine that imperfect assumption with someone's good old fashioned indifference, and you get MAF columns 12 and 13.

A more reliable way to infer zygosity would be to look at REF/ALT allele counts or fractions. There is no standard column that stores these numbers in TCGA MAFs, but these are some of the various column headers I have seen used: t_alt_count, t_ref_count, NVarCov, NTotCov, tumors_var_reads, tumor_ref_reads.
ADD COMMENT • link modified 15 months ago by _r_am ♦ 32k • written 6.5 years ago by Cyriac Kandoth ♦ 5.5k

I am still veray confused .so what's the actual meaning of Tumor-Seq-Allele1 and Tumor-Seq-Aelle2

ADD REPLY • link modified 13 months ago • written 13 months ago by 1378917721 • 0

The two alleles observed in the tumor sequencing data which MAF format assumes is diploid.

ADD REPLY • link written 12 months ago by Cyriac Kandoth ♦ 5.5k
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