One now-standard approach to the problem of finding genes that are frequently mutated among multiple cases of a particular type of tumor is the MutSig system developed at the Broad Institute. The general idea is to determine whether a gene is found to be mutated more frequently in tumor samples than might be expected by chance, rather than setting an arbitrary threshold.
The problem is that mutation rates "expected by chance" can differ substantially among genes depending on their size, replication time during the cell cycle, and so on. The MutSig page has a useful introduction to how thinking about this issue has evolved over the past several years.
If you actually have (as your question might imply) 40 matched cell-line/primary tumor samples you might be able to answer your question by doing direct paired comparisons. If you have those paired data, you would lose a lot by grouping the results first into cell-line and primary, as your question suggests.
Whichever way you proceed, I'm a bit worried about how you determine that a gene is "mutated" in either the cell lines or the primary samples. Primary tumors typically contain normal cells with normal DNA, diluting the mutant alleles and thus making it harder to detect true mutations. Furthermore, tumors can contain subclones harboring different mutations. Extended passage in culture would be expected to select for the subclone that propagates the fastest under those culture conditions.
So if your primary tumor sample had a mutation detected at, say, only a 10% mutant-allele fraction, would you have counted that as "mutated" or not? Would you have been able to distinguish a 10% mutation fraction generated in error from a true heterozygous mutation in 20% of the cells? Those issues need to be addressed before you go much further down this path; detection of mutations within individual tumors (in comparison to normal-tissue controls) is handled for example by MuTect if you have the raw sequence data.
EDIT in response to further information in comment:
Without having paired comparisons of cell lines and primary tumors, one way to proceed would be to determine whether there are differences in the prevalence of specific mutations between the panel of cell lines and an appropriate panel of primary tumors. This could be done with standard contingency-table approaches (e.g., Fisher exact test), with correction for multiple hypothesis testing. This would remove the need to define "frequently mutated gene" first.
In the case of breast cancer, however, previous work on the subject matter indicates that prevalence of specific mutations can depend on subtypes of breast cancer defined by patterns of gene expression. So in this case a proper comparison would first involve separating the cell lines into these subtypes, and comparing each cell-line subtype against its corresponding primary-tumor subtype. With only 40 cell lines, there might not be much power for detecting any differences.
