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What does BAF mean?
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17 months ago
Walnut Creek, USA

I recently encountered the term "BAF" in a post on Biostars. I've looked up the definition, which is "B-Allele Frequency" (the extended definition is no more enlightening; one allele is A and the other is B). To me, that has no meaning other than being "Allele Frequency" with perhaps implicit assumptions about ploidy that are not generalizable, or maybe assumptions about the major/minor allele counts (from sequencing depth), or perhaps population frequencies, or maybe the reference allele. Can anyone explain where BAF is a useful term, or when one should use "BAF" instead of "AF"?

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It looks like there is contention about what B-Allele frequency means. If you know the origin of the term, please post here!

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14 months ago
Freiburg, Germany

I've mostly seen BAF used in the context of SNP arrays, when there are two probes (an A probe and a B probe) covering a specific position. I think the A probe is generally the reference sequence (or was at the time the array was designed), so BAF and AF end up being the same, with the exception that SNP arrays are obviously limited in what they can detect.

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Actually, the definition of what is allele A and B is a bit more complex tha assigning calling allele A to the reference allele. What is allele A and allele B is sequence dependent and it's not related to the population allele frequency (which would be the case if the reference allele was allele A). This has the benefit of making the B allele frequencies balanced between 0 and 1 and the global BAF plots almost symmetric around 0.5, which helps with the analysis.

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To clarify - are you saying that the term "B-Allele Frequency" was developed to describe this naming system developed by Illumina to describe one of their products, and was not used prior to Illumina's TOP/BOT nomenclature?

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I don't know if this is the case. I can say that B-allele frequency (BAF) is different than variant allele frequency (VAF) and that I've always seen it referred to the portion of signal coming from one of the alleles in SNP-array data. I do not know if the terminology was coined for that, but I've never seen it referring to anything else. Anyone else with additional info?

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Ah, that makes sense. Thanks!

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http://cnvkit.readthedocs.io/en/stable/baf.html

I just noticed the description of BAF in CNVkit, which may be helpful for understanding.

Post as below:

In this context, the “B” allele is the non-reference allele observed in a germline heterozygous SNP, i.e. in the normal/control sample. Since the tumor cells’ DNA originally derived from normal cells’ DNA, most of these SNPs will also be present in the tumor sample. But due to allele-specific copy number alterations, loss of heterozygosity or allelic imbalance, the allelic frequency of these SNPs may be different in the tumor, and that’s evidence that one (or both) of the germline copies was gained or lost during tumor evolution. The shift in b-allele frequency is calculated relative to the expected heterozygous frequency 0.5, and minor allele frequencies are “mirrored” above and below 0.5 so that it does not matter which allele is considered the reference – the relative shift from 0.5 will be the same either way. (Multiple alternate alleles are not considered here.)

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