Understanding what a test cannot do is just as important as understanding what it can do, so that results are interpreted correctly and no one is falsely reassured.

1. It cannot detect small spelling changes in genetic material, single letter changes or tiny insertions/deletions within a gene require sequencing, not this technique
2. It cannot detect balanced chromosomal rearrangements such as balanced translocations or inversions, where genetic material is rearranged but nothing is actually gained or lost in total amount.
3. It only examines the specific regions included in the probe kit, if a person’s genetic change lies outside the exons covered by that particular panel, it will not be picked up, since the test does not scan the entire gene freely.
4. It has reduced reliability for low-level mosaicism, if only a small percentage of a person’s cells carry the change (typically below roughly 20 to 30 percent), the test may not reliably detect it.
5. It cannot tell you the exact size or exact boundary of a deletion or duplication instead it tells you which probes/exons are affected, not the precise breakpoint.
6. Rare false positives can occur occasionally a normal variation at the exact spot where a probe attaches can make that region look falsely deleted; this is why unexpected or unclear results are usually confirmed with a second method before being acted upon clinically.

Because of these limitations, this test is almost always used alongside sequencing, not as a replacement for it, so that both types of genetic errors, spelling changes and copy number changes, are properly checked.