What can CMAs not detect?

CMAs cannot detect small changes in the sequence of single genes. They also cannot detect chromosomal alterations that do not result in net gains or losses of genomic material, such as balanced translocations and inversions. In addition, they cannot detect indels and genomic imbalances in regions that are not represented on the array. Small duplications and deletions of DNA segments within a single gene also cannot be detected. Most CMAs are unable to detect mosaicism below 20-25%. Some of these arrays also do not detect triploidy or excessive homozygosity.