Hi,
we are conducting some study of cancer genomes or their parts. We are studying clonality in single samples. We do a NGS and when we obtain a mutation, we typically observe it in 1%-100% of reads.
We are explaining our observation by the fact that cell populations in our samples are different and therefore we can have mutation present in say 10% of cells.
However the question is how to call that 10%. When performing analysis, this number is reported as Allelic Balance. But colleagues of mine tend to report it as Variant allele frequency. I feel that VAF is a term that is used frequently with regard to populations of many individuals and therefore I am unsure how to call the proportion of the cells (or alleles) in the sample that carry particular variant.
Thank you, Vojtech.
we are conducting some study of cancer genomes or their parts. We are studying clonality in single samples. We do a NGS and when we obtain a mutation, we typically observe it in 1%-100% of reads.
We are explaining our observation by the fact that cell populations in our samples are different and therefore we can have mutation present in say 10% of cells.
However the question is how to call that 10%. When performing analysis, this number is reported as Allelic Balance. But colleagues of mine tend to report it as Variant allele frequency. I feel that VAF is a term that is used frequently with regard to populations of many individuals and therefore I am unsure how to call the proportion of the cells (or alleles) in the sample that carry particular variant.
Thank you, Vojtech.
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