Friday, July 15, 2011

HER2 Part 7: DNAarray HER2 PRO

Bottom line: CombiMatrix's DNAarray HER2 PRO test offers a more complete picture of HER2 amplification than FISH and can avoid some false negatives. It also shows other important chromosomal problems beyond HER2.

Understanding a breast tumor's HER2 status is critical for treatment planning. But what to do if a pathology report describes HER2 status as "equivocal" (FISH result between 1.8 and 2.2; IHC result of 2+) or if IHC and FISH results contradict one another and so are "discordant?" Inconclusive HER2 results happen about 10-15% of the time. So this is not a rare situation.

As a side note: HER2 testing guidelines for gastic cancer now require dual IHC and FISH testing, an acknowledgement of both the importance of, and concerns over current HER2 testing methods.

In the past few blogs we've written about newer tests based on technologies different than the ones used in IHC and FISH that can be used to make the determination. Today we'll discuss CombiMatrix's DNAarray HER2 PRO.

First, what does this test "look at?" The answer: the entire chromosome 17 in breast tumor cells in your biopsy sample. The HER2 gene is on chromosome 17. But FISH also looks at chromosome 17. So what's the difference?

It's pretty simple. FISH looks at a specific gene (HER2) by attaching ("hybridizing"... the "H" in FISH) fluorescent molecules to it ("fluorescence" is the "F" in FISH). The more HER2 DNA there is, due to gene amplification, the brighter the fluorescence that's emitted.

FISH determines whether the HER2 gene has been amplified by comparing the amount of fluorescence at the HER2 gene with the amount at a different part of the chromosome that FISH also targets. So the pathologist looks at two points on the chromosome using a fluorescence microscope.

If the amount of fluorescence at the HER2 gene is much greater than the amount at the centromere (pronounced sen'-tro-mere and more technically called CEP17), then the assumption is that the gene has been amplified. So the test is all about the ratio of fluorescence emitted at two different know points on chromosome 17. Pretty tricky.

Now DNAarray HER2 PRO. As previously mentioned, it looks at many more points on the chromosome using a technology you might have heard of in the news called a "DNA microarray" or "DNA chip." The generic term for the DNAarray test is array-based Comparative Genomic Hybridization, or aCGH. You don't have to know this. But I didn't want anyone to be confused if they happened to come across the term.

aCGH uses somewhat similar technology to FISH, but by using the DNA chip, it can simultaneously look at hundreds or thousands of points on the chromosome using fluorescence hybridization, not two. The chip is analyzed using an automated instrument. No one looks through a microscope, as with FISH.

Next question: Why does it matter to look at the whole chromosome? Mainly because one potential problem of FISH is that it can give a false negative result. This is a situation where the test says the tumor is HER2 negative even though there is amplification. This can occur if BOTH the HER2 gene and the centromere are amplified. Remember, FISH looks at the ratio between the two. If both are amplified, the amount of fluorescence signal could be about the same but the reason would be that they are BOTH amplified, NOT that neither is amplified! And centromere amplification is relatively common.

Second, and this goes beyond the issue of HER2, tumors that are more aggressive tend to have bigger problems than just HER2 gene amplification. They tend to have amplification elsewhere, changes in the numbers of chomosomes and other problems that can be summed up as "chromosomal chaos." Chromosomal chaos is easily visualized using aCGH. And if the DNAarray test shows big chromosomal problems on chromosome 17, then there's little doubt that the same thing has happened on other chromosomes. Knowing this, and thus that the tumor is aggressive, might alter treatment decisions.

DNAarray HER2 PRO costs $1,500. Reimbursement not certain, as it is with IHC and FISH. But for patients who either don't have a clear-cut HER2 status or who might be willing to pay for a high-tech method that might provide additional insights into the tumor's characteristics, then it's worth a look.

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