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Question: Inferring zygosity information from MAF
1
gravatar for newDNASeqer
5.2 years ago by
newDNASeqer • 650
United States
newDNASeqer • 650 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 • 2.1k views
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modified 5.1 years ago by Cyriac Kandoth ♦ 5.3k • written 5.2 years ago by newDNASeqer • 650
1
gravatar for Cyriac Kandoth
5.1 years ago by
Cyriac Kandoth ♦ 5.3k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth ♦ 5.3k wrote:

In an ideal world, yes. These fields are meant to represent zygosity. But for TCGA MAFs, as explained in Working With Maf Files (Mutation Annotation Format) From The Tcga (The Cancer Genome Atlas): 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 5.1 years ago • written 5.1 years ago by Cyriac Kandoth ♦ 5.3k
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