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Old 07-18-2013, 04:27 PM   #2
DavidShih
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Location: Toronto

Join Date: Jun 2013
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Instead of "allele frequency", did you mean "clonal frequency" or "cellular multiplicity"?

You can get allele frequency just by dividing the count of the alternate nucleotide by the counts of the alternate and reference nucleotide.

After correcting these allele frequencies for copy-number, ploidy, and purity, you can determine the number of copies of the alleles per tumour cell (clonal frequency or cellular multiplicity).

In most cases, this step requires allele-specific copy-number estimates, which cannot be derived from aCGH data as far as know.

But the ABSOLUTE program does allow the use of total copy-number estimates to calculate both the absolute copy-number and the cellular multiplicity of the SNVs. The results won't be as good as when allele-specific copy-number is available.

See http://www.broadinstitute.org/cancer/cga/absolute
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