What are the challenges of chromosomal microarrays?

These arrays cannot detect balanced chromosome translocations or inversions, which do not result in the duplication or deletion of genetic material, or low-level tissue mosaicism in the fetus. Since this is a prenatal diagnostic technique, the presence or absence of mosaicism in fetal cells analyzed may not represent the level of mosaicism in peripheral blood. Additionally, microarrays which are not based on the analysis of SNPs are unable to detect triploidy. These arrays are also unable to detect small changes in the sequence of single gene. Another challenge is that tiny duplications and deletions of DNA segments within a single gene are also unable to be detected.