My understanding is that its not the gene that is patented, but the processes surrounding the isolation of it, or the actual isolated product.

There would be no patent infringement if you sequence an entire genome (including BRCA1 and BRCA2), as you are not dealing with the actual chemical processes or products covered by the patent.

They have a monopoly on their specific test, as it uses the chemical products covered by their patents (although the test aspect of the patent appears to have been thrown out).

Creating a different test based around, say Illumina or SOLiD sequencing is not going to infringe on this patent.