For decades, karyotyping has been the standard diagnostic method for prenatal testing. As a method that dates back to the late 1960s, chromosome analysis or karyotype analysis is a test that assesses the size, shape, and number of chromosomes. Extra or missing chromosomes, or abnormal positions of chromosomal fragments, may cause problems in growth, development, and body function. Chromosome analysis often helps to determine the contribution of genetics to a range of medical and/or developmental problems. In addition, stem cells in culture can accumulate changes, including chromosomal abnormalities. Genomic changes can lead to changes in gene expression and cell function, increasing the risk of stem cell tumors. Therefore, it is essential to monitor any chromosomal abnormalities in cultures, especially in stem cells for therapeutic purposes.
Traditional karyotype analysis utilizes G banding and applies Giemsa staining to the separated chromosomes to highlight the high adenine-thymine binding region. This produces different banding patterns (G-banding), which can reveal whether the entire chromosome or chromosome segment is missing, translocated, or other abnormalities, and from there help diagnose many diseases caused by these chromosomal abnormalities.
Unfortunately, the resolution of G-banding is limited, at the level of 5-10 megabases, which means it cannot detect abnormalities smaller than this limit. G-banding results are only readable at specific cell cycle stages and depend on complete chromosomes with good morphology, so many stained cells cannot be used. Partly to alleviate previous weaknesses, G-band involves culturing collected cells to produce enough material for analysis, which takes time and introduces small changes that may affect the results.
Chromosome microarrays avoid most of these pitfalls. From the Human Genome Project that emerged in the mid to late 2000s, microarrays can test thousands or millions of different variants in a single measurement. Cells studied with CMA do not need to be alive or in a specific phase of the cell cycle, nor do they need to be present in large numbers, so CMA can collect data from the original sample without the need for culture. CMA can even be used for formalin-fixed, paraffin-embedded (FFPE) samples for comparative studies, such as comparisons between success and failure of in vitro fertilization attempts.
By using small, well-defined probes instead of band patterns and microscopes, microarrays can detect differences as small as 500 kilobases, which are orders of magnitude smaller than the limits of traditional karyotyping, revealing that they may cause disease and are invisible The micro-deletion and micro-duplication of the G-band. Arrays with single nucleotide polymorphism (SNP) probes are called SNP arrays and can detect smaller variations. These advantages, combined with the ease of use of CMA, have led many organizations to recommend SNP arrays as the first round of testing options, and other tests as follow-up actions.
Although it seems that CMA has completely replaced traditional karyotype analysis, this is not the case. Although CMAs provide similar or improved performance to karyotyping for a variety of abnormalities, they cannot easily detect balanced chromosomal rearrangements, such as translocations without copy number changes. These changes are evident in karyotypes and by fluorescence in situ hybridization (FISH) and other visual inspection methods, but are basically invisible in arrays (including SNP arrays). Therefore, karyotyping, along with chromosome microarrays and other technologies, still has a place in the diagnostic toolkit, each of which can provide the insights needed to help new parents make informed decisions. When microarrays cannot produce usable information, other methods such as karyotyping are the ideal next step.
